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<front>
<journal-meta>
<journal-id journal-id-type="publisher-id">Front. Plant Sci.</journal-id>
<journal-title>Frontiers in Plant Science</journal-title>
<abbrev-journal-title abbrev-type="pubmed">Front. Plant Sci.</abbrev-journal-title>
<issn pub-type="epub">1664-462X</issn>
<publisher>
<publisher-name>Frontiers Media S.A.</publisher-name>
</publisher>
</journal-meta>
<article-meta>
<article-id pub-id-type="doi">10.3389/fpls.2022.1115513</article-id>
<article-categories>
<subj-group subj-group-type="heading">
<subject>Plant Science</subject>
<subj-group>
<subject>Original Research</subject>
</subj-group>
</subj-group>
</article-categories>
<title-group>
<article-title>Systematic analysis of MADS-box gene family in the U&#x2019;s triangle species and targeted mutagenesis of <italic>BnaAG</italic> homologs to explore its role in floral organ identity in <italic>Brassica napus</italic>
</article-title>
</title-group>
<contrib-group>
<contrib contrib-type="author">
<name>
<surname>Song</surname>
<given-names>Min</given-names>
</name>
<xref ref-type="aff" rid="aff1">
<sup>1</sup>
</xref>
<xref ref-type="author-notes" rid="fn003">
<sup>&#x2020;</sup>
</xref>
<uri xlink:href="https://loop.frontiersin.org/people/2124433"/>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Zhang</surname>
<given-names>Yanfeng</given-names>
</name>
<xref ref-type="aff" rid="aff2">
<sup>2</sup>
</xref>
<xref ref-type="author-notes" rid="fn003">
<sup>&#x2020;</sup>
</xref>
<uri xlink:href="https://loop.frontiersin.org/people/1724881"/>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Jia</surname>
<given-names>Qingli</given-names>
</name>
<xref ref-type="aff" rid="aff2">
<sup>2</sup>
</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Huang</surname>
<given-names>Shuhua</given-names>
</name>
<xref ref-type="aff" rid="aff2">
<sup>2</sup>
</xref>
<uri xlink:href="https://loop.frontiersin.org/people/442663"/>
</contrib>
<contrib contrib-type="author">
<name>
<surname>An</surname>
<given-names>Ran</given-names>
</name>
<xref ref-type="aff" rid="aff2">
<sup>2</sup>
</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Chen</surname>
<given-names>Nana</given-names>
</name>
<xref ref-type="aff" rid="aff2">
<sup>2</sup>
</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Zhu</surname>
<given-names>Yantao</given-names>
</name>
<xref ref-type="aff" rid="aff2">
<sup>2</sup>
</xref>
<uri xlink:href="https://loop.frontiersin.org/people/1462048"/>
</contrib>
<contrib contrib-type="author" corresp="yes">
<name>
<surname>Mu</surname>
<given-names>Jianxin</given-names>
</name>
<xref ref-type="aff" rid="aff2">
<sup>2</sup>
</xref>
<xref ref-type="author-notes" rid="fn001">
<sup>*</sup>
</xref>
<uri xlink:href="https://loop.frontiersin.org/people/1462052"/>
</contrib>
<contrib contrib-type="author" corresp="yes">
<name>
<surname>Hu</surname>
<given-names>Shengwu</given-names>
</name>
<xref ref-type="aff" rid="aff1">
<sup>1</sup>
</xref>
<xref ref-type="author-notes" rid="fn001">
<sup>*</sup>
</xref>
</contrib>
</contrib-group>
<aff id="aff1">
<sup>1</sup>
<institution>State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest Agriculture and Forestry University</institution>, <addr-line>Yangling, Shaanxi</addr-line>, <country>China</country>
</aff>
<aff id="aff2">
<sup>2</sup>
<institution>Hybrid Rapeseed Research Center of Shaanxi Province</institution>, <addr-line>Yangling, Shaanxi</addr-line>, <country>China</country>
</aff>
<author-notes>
<fn fn-type="edited-by">
<p>Edited by: Helin Tan, Nanjing Agricultural University, China</p>
</fn>
<fn fn-type="edited-by">
<p>Reviewed by: Cunmin Qu, Southwest University, China; Jian Wu, Yangzhou University, China</p>
</fn>
<fn fn-type="corresp" id="fn001">
<p>*Correspondence: Shengwu Hu, <email xlink:href="mailto:swhu83251@nwsuaf.edu.cn">swhu83251@nwsuaf.edu.cn</email>; Jianxin Mu, <email xlink:href="mailto:jxmsxyc@163.com">jxmsxyc@163.com</email>
</p>
</fn>
<fn fn-type="equal" id="fn003">
<p>&#x2020;These authors contributed equally to this work</p>
</fn>
<fn fn-type="other" id="fn002">
<p>This article was submitted to Plant Metabolism and Chemodiversity, a section of the journal Frontiers in Plant Science</p>
</fn>
</author-notes>
<pub-date pub-type="epub">
<day>12</day>
<month>01</month>
<year>2023</year>
</pub-date>
<pub-date pub-type="collection">
<year>2022</year>
</pub-date>
<volume>13</volume>
<elocation-id>1115513</elocation-id>
<history>
<date date-type="received">
<day>04</day>
<month>12</month>
<year>2022</year>
</date>
<date date-type="accepted">
<day>23</day>
<month>12</month>
<year>2022</year>
</date>
</history>
<permissions>
<copyright-statement>Copyright &#xa9; 2023 Song, Zhang, Jia, Huang, An, Chen, Zhu, Mu and Hu</copyright-statement>
<copyright-year>2023</copyright-year>
<copyright-holder>Song, Zhang, Jia, Huang, An, Chen, Zhu, Mu and Hu</copyright-holder>
<license xlink:href="http://creativecommons.org/licenses/by/4.0/">
<p>This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.</p>
</license>
</permissions>
<abstract>
<p>MADS-box transcription factors play an important role in regulating floral organ development and participate in environmental responses. To date, the MADS-box gene family has been widely identified in <italic>Brassica rapa</italic> (<italic>B. rapa</italic>), <italic>Brassica oleracea</italic> (<italic>B. oleracea</italic>), and <italic>Brassica napus</italic> (<italic>B. napus</italic>); however, there are no analogous reports in <italic>Brassica nigra</italic> (<italic>B. nigra</italic>), <italic>Brassica juncea</italic> (<italic>B. juncea</italic>), and <italic>Brassica carinata</italic> (<italic>B. carinata</italic>). In this study, a whole-genome survey of the MADS-box gene family was performed for the first time in the triangle of U species, and a total of 1430 MADS-box genes were identified. Based on the phylogenetic relationship and classification of MADS-box genes in <italic>Arabidopsis thaliana</italic> (<italic>A. thaliana</italic>), 1430 MADS-box genes were categorized as M-type subfamily (627 genes), further divided into M&#x3b1;, M&#x3b2;, M&#x3b3;, and M&#x3b4; subclades, and MIKC-type subfamily (803 genes), further classified into 35 subclades. Gene structure and conserved protein motifs of MIKC-type MADS-box exhibit diversity and specificity among different subclades. Comparative analysis of gene duplication events and syngenic gene pairs among different species indicated that polyploidy is beneficial for MIKC-type gene expansion. Analysis of transcriptome data within diverse tissues and stresses in <italic>B. napus</italic> showed tissue-specific expression of MIKC-type genes and a broad response to various abiotic stresses, particularly dehydration stress. In addition, four representative floral organ mutants (<italic>wtl</italic>, <italic>feml</italic>, <italic>aglf-2</italic>, and <italic>aglf-1</italic>) in the T0 generation were generated by editing four AGAMOUS (<italic>BnaAG</italic>) homoeologs in <italic>B. napus</italic> that enriched the floral organ variant phenotype. In brief, this study provides useful information for investigating the function of MADS-box genes and contributes to revealing the regulatory mechanisms of floral organ development in the genetic improvement of new varieties.</p>
</abstract>
<kwd-group>
<kwd>Brassica</kwd>
<kwd>U&#x2019;s triangle</kwd>
<kwd>MADS-box genes</kwd>
<kwd>floral organ development</kwd>
<kwd>AGAMOUS</kwd>
</kwd-group>
<contract-sponsor id="cn001">Shaanxi Creative Talents Promotion Plan-Technological Innovation Team<named-content content-type="fundref-id">10.13039/501100017602</named-content>
</contract-sponsor>
<contract-sponsor id="cn002">Scientific Research and Sharing Platform Construction Project of Shaanxi Province<named-content content-type="fundref-id">10.13039/501100013150</named-content>
</contract-sponsor>
<contract-sponsor id="cn003">National Key Research and Development Program of China<named-content content-type="fundref-id">10.13039/501100012166</named-content>
</contract-sponsor>
<counts>
<fig-count count="8"/>
<table-count count="0"/>
<equation-count count="0"/>
<ref-count count="87"/>
<page-count count="16"/>
<word-count count="6576"/>
</counts>
</article-meta>
</front>
<body>
<sec id="s1" sec-type="intro">
<title>Introduction</title>
<p>
<italic>Brassica</italic>, a genus of Cruciferae, includes many oils, feed, and vegetable crops. <italic>Brassica</italic> species are the most economically valuable species providing edible oil, industrial oil, vegetables, condiments, and feed necessary for production and life (<xref ref-type="bibr" rid="B11">Cheng et&#xa0;al., 2013</xref>). Among them, the significant crops are three diploid plants: <italic>Brassica rapa</italic> (<italic>B. rapa</italic>, AA, 2n=20), <italic>Brassica oleracea</italic> (<italic>B. oleracea</italic>, CC, 2n=18), and <italic>Brassica nigra</italic> (<italic>B. nigra</italic>, BB, 2n=16), and three allotetraploid species: <italic>Brassica napus</italic> (<italic>B. napus</italic>, AACC, 2n=38), <italic>Brassica juncea</italic> (<italic>B. juncea</italic>, AABB, 2n=36), and <italic>Brassica carinata</italic> (<italic>B. carinata</italic>, BBCC, 2n=34), forming the triangle of U model. U&#x2019;s triangle model, proposed by Nagaharu in 1935, is a typical theory for studying the complexity of evolutionary relationships and polyploidization among brassicas (<xref ref-type="bibr" rid="B45">Nagaharu and Nagaharu, 1935</xref>). With the completion and sharing of high-quality and large-scale genomic, resequencing, and comprehensive transcriptome data, a bioinformatics platform was established to explore the gene function of species in U&#x2019;s triangle. <italic>B. rapa</italic> was the first U&#x2019;s triangle species to have its reference genome (<xref ref-type="bibr" rid="B44">Mun et&#xa0;al., 2010</xref>; <xref ref-type="bibr" rid="B69">Wang et&#xa0;al., 2011</xref>; <xref ref-type="bibr" rid="B6">Cai et&#xa0;al., 2017</xref>; <xref ref-type="bibr" rid="B80">Zhang et&#xa0;al., 2018</xref>; <xref ref-type="bibr" rid="B82">Zhang et&#xa0;al., 2022</xref>), followed by <italic>B. oleracea</italic> (<xref ref-type="bibr" rid="B33">Kim et&#xa0;al., 2014</xref>; <xref ref-type="bibr" rid="B41">Liu et&#xa0;al., 2014</xref>; <xref ref-type="bibr" rid="B50">Parkin et&#xa0;al., 2014</xref>; <xref ref-type="bibr" rid="B7">Cai et&#xa0;al., 2020</xref>). As an important oil crop in the world, <italic>B. napus</italic> was sequenced in 2014 (<xref ref-type="bibr" rid="B9">Chalhoub et&#xa0;al., 2014</xref>), and many genome versions have been published (<xref ref-type="bibr" rid="B63">Sun et&#xa0;al., 2017</xref>; <xref ref-type="bibr" rid="B61">Song et&#xa0;al., 2020</xref>; <xref ref-type="bibr" rid="B12">Chen et&#xa0;al., 2021</xref>), including the winter-type oilseed rape Darmor-bzh, semi-winter oilseed rape Zhongshuang11 (ZS11), and spring-type oilseed rape Westar and so on. Subsequently, the reference genomes of <italic>B. juncea</italic> (<xref ref-type="bibr" rid="B75">Yang et&#xa0;al., 2016</xref>; <xref ref-type="bibr" rid="B49">Paritosh et&#xa0;al., 2021</xref>) and <italic>B. nigra</italic> were published successively (<xref ref-type="bibr" rid="B48">Paritosh et&#xa0;al., 2020</xref>; <xref ref-type="bibr" rid="B52">Perumal et&#xa0;al., 2020</xref>), and the reference genome of <italic>B. carinata</italic> was the latest to be reported (<xref ref-type="bibr" rid="B62">Song et&#xa0;al., 2021</xref>; <xref ref-type="bibr" rid="B77">Yim et&#xa0;al., 2022</xref>). To date, each of the six U&#x2019;s triangle species has its reference genomes.</p>
<p>MADS-box genes are critical transcription factors (TFs). The term &#x2018;MADS&#x2019; originated from four members of MADS family in fungi, plants, and animals: MCM1 in yeast, AGAMOUS in <italic>Arabidopsis thaliana</italic> (<italic>A. thaliana</italic>), DEFICIENS in snapdragon, and SERUM RESPONSE FACTOR in human (<xref ref-type="bibr" rid="B30">Jack, 2001</xref>). MADS-box genes are characterized by the presence of a conserved DNA-binding domain of approximately 60 amino acids in the N-terminal region of the MADS-box protein, also known as the MADS (M) domain (<xref ref-type="bibr" rid="B76">Yanofsky et&#xa0;al., 1990</xref>). MADS-box genes can be classified into Type I (M-type) and Type II (MIKC-type) subclasses according to their evolutionary relationships. Type I generally contains two exons and can further be divided into M&#x3b1;, M&#x3b2;, M&#x3b3;, and M&#x3b4; subgroups based on the similarities and differences in their exon-intron features (<xref ref-type="bibr" rid="B47">Parenicova et&#xa0;al., 2003</xref>), whereas Type II typically consists of 6-8 exons and is divided into two clades, named MIKC<sup>C</sup> and MIKC*. Except for the highly conserved M domain, MIKC-type TFs also comprise intervening (I), moderately conserved keratin-like (K), and variable C-terminal (C) domains (<xref ref-type="bibr" rid="B18">Egea-Cortines et&#xa0;al., 1999</xref>; <xref ref-type="bibr" rid="B26">Henschel et&#xa0;al., 2002</xref>). The M domain enables the DNA to bind CArG boxes (<xref ref-type="bibr" rid="B55">Riechmann and Meyerowitz, 1997</xref>; <xref ref-type="bibr" rid="B29">Immink et&#xa0;al., 2002</xref>); the I and K domains promote the formation of two or more MADS-domain proteins (<xref ref-type="bibr" rid="B19">Fan et&#xa0;al., 1997</xref>; <xref ref-type="bibr" rid="B26">Henschel et&#xa0;al., 2002</xref>; <xref ref-type="bibr" rid="B74">Yang and Jack, 2004</xref>), and the C domain regulates transcriptional activation of the MADS protein (<xref ref-type="bibr" rid="B27">Honma and Goto, 2001</xref>). To date, the functions of most MIKC*- and M-type MADS-box genes remain unclear; however, most MIKC<sup>C</sup>-type genes, playing vital roles in plant growth, development, and response to biotic and abiotic stress, have been elucidated (<xref ref-type="bibr" rid="B34">Kofuji et&#xa0;al., 2003</xref>).</p>
<p>Most TFs in the ABCDE model modulate floral organ development and belong to the MIKC-type MADS-box genes (<xref ref-type="bibr" rid="B13">Coen and Meyerowitz, 1991</xref>; <xref ref-type="bibr" rid="B53">Pinyopich et&#xa0;al., 2003</xref>; <xref ref-type="bibr" rid="B79">Zahn et&#xa0;al., 2006</xref>; <xref ref-type="bibr" rid="B60">Silva et&#xa0;al., 2015</xref>); examples include <italic>FLOWERING LOCUS C</italic> (<italic>FLC</italic>) (<xref ref-type="bibr" rid="B57">Searle et&#xa0;al., 2006</xref>), <italic>SUPPRESSOR OF OVEREXPRESSION OF CONSTANS</italic> (<italic>SOC1</italic>) (<xref ref-type="bibr" rid="B36">Lee and Lee, 2010</xref>), and <italic>SHORT VEGETATIVE PHASE</italic> (<italic>SVP</italic>) (<xref ref-type="bibr" rid="B25">Hartmann et&#xa0;al., 2000</xref>). In addition, MIKC-type genes are also involved in root (<italic>AGL14</italic> and <italic>AGL21</italic>) (<xref ref-type="bibr" rid="B21">Garay-Arroyo et&#xa0;al., 2013</xref>; <xref ref-type="bibr" rid="B78">Yu et&#xa0;al., 2014</xref>) and seed development (<italic>SHP1/2</italic>, <italic>FUL</italic>) (<xref ref-type="bibr" rid="B20">Ferrandiz et&#xa0;al., 2000</xref>; <xref ref-type="bibr" rid="B40">Liljegren et&#xa0;al., 2000</xref>). To date, the MADS-box TFs have been systematically investigated in dicotyledon plants, such as tomato (<italic>Solanum lycopersicum</italic> L.) (<xref ref-type="bibr" rid="B70">Wang et&#xa0;al., 2019</xref>), potato (<italic>Solanum tuberosum</italic> L.) (<xref ref-type="bibr" rid="B58">Shao et&#xa0;al., 2021</xref>), <italic>B. rapa</italic> (<xref ref-type="bibr" rid="B17">Duan et&#xa0;al., 2015</xref>), <italic>B. oleracea</italic> (<xref ref-type="bibr" rid="B59">Sheng et&#xa0;al., 2019</xref>), and <italic>B. napus</italic> (<xref ref-type="bibr" rid="B72">Wu et&#xa0;al., 2018</xref>; <xref ref-type="bibr" rid="B87">Zhou et&#xa0;al., 2022</xref>), and monocotyledon plants, such as maize (<italic>Zea mays L.</italic>) (<xref ref-type="bibr" rid="B84">Zhao et&#xa0;al., 2021a</xref>), wheat (<italic>Triticum aestivum</italic> L.) (<xref ref-type="bibr" rid="B43">Ma et&#xa0;al., 2017</xref>; <xref ref-type="bibr" rid="B56">Schilling et&#xa0;al., 2020</xref>), Foxtail Millet (<italic>Setaria italica</italic>) (<xref ref-type="bibr" rid="B86">Zhao et&#xa0;al., 2021b</xref>), and rice (<italic>Oryza sativa</italic>) (<xref ref-type="bibr" rid="B2">Arora et&#xa0;al., 2007</xref>). However, there have been no reports on the identification of MADS-box genes in three species of U&#x2019;s triangle: <italic>B. nigra</italic>, <italic>B. juncea</italic>, and <italic>B. carinata</italic>.</p>
<p>In recent years, new results have enriched the functions of genes related to the ABCDE model, including <italic>FhAG2</italic>, a key male-specific sex determination candidate gene identified using whole-genome sequencing and assembly of two Ficus species, <italic>F. microcarpa</italic> (monoecious) and <italic>F. hispida</italic> (functionally dioecious) (<xref ref-type="bibr" rid="B83">Zhang et&#xa0;al., 2020</xref>). Owing to polyploidization and gene expansion, the copies of MIKC-type MADS-box genes increased in <italic>B. napus</italic> compared with that in <italic>A. thaliana</italic>, limiting the exploration of the function of those genes involved in floral organ development. In this study, the MADS-box gene family in the genome of U&#x2019;s triangle species was identified for the first time, and gene structure characteristics, conserved domains, gene duplication, synteny events, and expression patterns of MIKC-type MADS-box genes were comprehensively analyzed. A series of <italic>bnaag</italic> mutants with different phenotypes were obtained using CRISPR/Cas9 technology to edit four <italic>BnaAGAMOUS</italic> (<italic>BnaAG</italic>) homologous genes in rapeseed, which offers important insights into the function of different copies of <italic>BnaAG</italic>.</p>
</sec>
<sec id="s2" sec-type="materials|methods">
<title>Materials and methods</title>
<sec id="s2_1">
<title>Sequence search and identification of MADS-box genes in species of U&#x2019;s triangle</title>
<p>The genomic sequence, annotated file, and protein sequences of the six <italic>Brassica</italic> species in U&#x2019;s triangle were downloaded (<xref ref-type="supplementary-material" rid="SM1">
<bold>Supplementary Table S1</bold>
</xref>), and the longest transcript was used for subsequent analysis. In summary, 105 AtMADS protein sequences downloaded from the TAIR database (<uri xlink:href="https://www.arabidopsis.org/">https://www.arabidopsis.org/</uri>) (<xref ref-type="bibr" rid="B47">Parenicova et&#xa0;al., 2003</xref>) were used to perform a BLASTP search of the local protein database of the six U&#x2019;s triangle species with an E-value &lt; e<sup>-10</sup> and identity &#x2265; 50% (<xref ref-type="bibr" rid="B8">Camacho et&#xa0;al., 2009</xref>). The hidden Markov model (HMM) profiles of SRF-TF (PF00319) and K-box (PF01486) were retrieved from the Pfam database (<uri xlink:href="http://pfam-legacy.xfam.org/">http://pfam-legacy.xfam.org/</uri>), and HMMER software (version 3.0) was used to search for homeodomains with an E-value &lt; 1e<sup>-5</sup>. Subsequently, all MADS-box protein sequences were submitted to the National Center for Biotechnology Information Conserved Domain Database (NCBI-CDD) (<uri xlink:href="https://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi">https://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi</uri>) (<xref ref-type="bibr" rid="B42">Lu et&#xa0;al., 2020</xref>) and SMART database (<uri xlink:href="http://smart.embl-heidelberg.de/smart/batch.pl">http://smart.embl-heidelberg.de/smart/batch.pl</uri>) to examine the integrity of the MADS-box or K-box domains (<xref ref-type="bibr" rid="B38">Letunic and Bork, 2018</xref>). The theoretical isoelectric point (pI) and molecular weight (MW) of all candidate MADS-box proteins were predicted using ExPASy (<uri xlink:href="https://www.expasy.org/">https://www.expasy.org/</uri>) (<xref ref-type="bibr" rid="B22">Gasteiger et&#xa0;al., 2003</xref>).</p>
</sec>
<sec id="s2_2">
<title>Phylogenetic tree, gene structure, and conserved motif analysis</title>
<p>Multiple sequence alignment of MADS-box protein sequences was performed using MAFFT software with the FFT-NS-I method (<xref ref-type="bibr" rid="B31">Katoh et&#xa0;al., 2019</xref>). Unrooted and rooted Maximum Likelihood (ML) trees were constructed using FastTree software (<xref ref-type="bibr" rid="B54">Price et&#xa0;al., 2009</xref>) and visualized using EvolView (<uri xlink:href="http://www.evolgenius.info/evolview">http://www.evolgenius.info/evolview</uri>) (<xref ref-type="bibr" rid="B81">Zhang et&#xa0;al., 2012</xref>) and iTOL (<uri xlink:href="http://itol.embl.de/">http://itol.embl.de/</uri>) (<xref ref-type="bibr" rid="B37">Letunic and Bork, 2007</xref>). The gene structure files of all the MIKC-type genes were extracted using a genome annotation file. The conserved motifs were predicted using the MEME software, with the number of motif sets at 10 (<uri xlink:href="http://meme-suite.org/tools/meme">http://meme-suite.org/tools/meme</uri>) (<xref ref-type="bibr" rid="B3">Bailey et&#xa0;al., 2009</xref>). TBtools was used to draw the exon-intron structure and conserved motif features (<xref ref-type="bibr" rid="B10">Chen et&#xa0;al., 2020</xref>).</p>
</sec>
<sec id="s2_3">
<title>Gene duplication and genomic synteny analysis</title>
<p>The MIKC-type protein sequences of the U&#x2019;s triangle species were aligned using BLASTP with an E-value &lt; 1e<sup>-10</sup> (<xref ref-type="bibr" rid="B8">Camacho et&#xa0;al., 2009</xref>). The tandem and segmental duplication events in each species were analyzed using the MCScanX program (<xref ref-type="bibr" rid="B68">Wang et&#xa0;al., 2012</xref>) and visualized using Circos (<xref ref-type="bibr" rid="B35">Krzywinski et&#xa0;al., 2009</xref>). Genomic synteny was analyzed using JCVI software and the detailed workflow reference Python version MCscan (<uri xlink:href="https://github.com/tanghaibao/jcvi/wiki/">https://github.com/tanghaibao/jcvi/wiki/</uri>).</p>
</sec>
<sec id="s2_4">
<title>Expression profiles of MIKC-type MADS-box genes in <italic>B. napus</italic>
</title>
<p>RNA-seq data for six tissues (roots, stems, leaves, flowers, seeds, and siliques) and four abiotic stressors (dehydration, salt, ABA, and cold) in <italic>B. napus</italic> were downloaded from the National Genomics Data Center (NGDC) (project ID: CRA001775) (<uri xlink:href="https://ngdc.cncb.ac.cn/?lang=en">https://ngdc.cncb.ac.cn/?lang=en</uri>). The transcriptome data of embryos and seed coats at different developmental stages and two different white powder-resistant rapeseed lines after inoculation with powdery mildew were downloaded from the NCBI database (project ID: PRJNA641876 and PRJNA778657). All transcriptome data were mapped to the Darmor-bzh genome using HISAT2 (<xref ref-type="bibr" rid="B32">Kim et&#xa0;al., 2015</xref>). The Transcripts Per Million (TPM) values were calculated using the FeatureCounts R package, and a heatmap of expression level was plotted using TBtools software (<xref ref-type="bibr" rid="B39">Liao et&#xa0;al., 2014</xref>; <xref ref-type="bibr" rid="B10">Chen et&#xa0;al., 2020</xref>).</p>
</sec>
<sec id="s2_5">
<title>The sgRNA design, vector construction, and hypocotyl genetic transformation in <italic>B. napus</italic>
</title>
<p>First, four <italic>BnaAG</italic> genes with the highest homology to <italic>A. thaliana</italic> (<italic>AT4G18960</italic>) were selected for designing single guide RNA (sgRNA). The sgRNA1 was designed to target the MADS-box and sgRNA2 to target the K-box, and then a multiplex genome editing tool CRISPR/Cas9 with two sgRNAs was used to mutate <italic>BnaAG</italic> genes (<xref ref-type="bibr" rid="B73">Xing et&#xa0;al., 2014</xref>). Finally, the successfully constructed recombinant plasmid (<italic>pHSE401-BnaAG</italic>) was transformed into <italic>Agrobacterium tumefaciens</italic> strain GV3101, followed by genetic transformation of 19YB437 (recipient material) using a detailed transgenic operation method described by Bhalla and Singh (<xref ref-type="bibr" rid="B5">Bhalla and Singh, 2008</xref>). Primers used to construct the vectors are listed in <xref ref-type="supplementary-material" rid="SM1">
<bold>Supplementary Table S12</bold>
</xref>.</p>
</sec>
<sec id="s2_6">
<title>Identification of positive mutants and characterization of floral organ phenotype</title>
<p>All positive tissue culture plantlets were transplanted into humus soil and grown under a 16&#xa0;h light/8&#xa0;h dark photoperiod at 22&#xb0;C until they reached the five-leaf stage. After four weeks of vernalization, the seedlings were transplanted into a normal environment for growth. The variant phenotypes of floral organs were observed and recorded; DNA was extracted from leaf tissues of each type of flower organ mutant, and the fragments near the two target sequences were amplified using PCR with specific primers (<xref ref-type="supplementary-material" rid="SM1">
<bold>Supplementary Table S12</bold>
</xref>). The PCR products and positive colonies were sequenced, and the editing events of each mutant were analyzed according to the results of Sanger sequencing.</p>
</sec>
</sec>
<sec id="s3" sec-type="results">
<title>Results</title>
<sec id="s3_1">
<title>MADS-box genes in the six U&#x2019;s triangle species</title>
<p>In total, 1430 MADS-box genes were identified in the genome of the six U&#x2019;s triangle species. To uncover the kinship relationships of MADS-box genes among <italic>A. thaliana</italic> and U&#x2019;s triangle species, the ML method was used to construct the phylogenetic tree based on the alignment of 105 MADSs in <italic>A. thaliana</italic> and 1430 MADS-box proteins in U&#x2019;s triangle species (<xref ref-type="fig" rid="f1">
<bold>Figure&#xa0;1A</bold>
</xref>; <xref ref-type="supplementary-material" rid="SM1">
<bold>Supplementary Table S2</bold>
</xref>). The 1,535 MADS-box genes were divided into M-type and MIKC-type subfamilies; among them, the MIKC subfamily had the highest number of members (842), followed by the M&#x3b1; (287), M&#x3b2; (143), M&#x3b3; (164), and M&#x3b4; (99) subfamilies (<xref ref-type="fig" rid="f1">
<bold>Figure&#xa0;1B</bold>
</xref>; <xref ref-type="supplementary-material" rid="SM1">
<bold>Supplementary Table S3</bold>
</xref>). The three diploid <italic>Brassica</italic> species <italic>B. rapa</italic> (AA), <italic>B. nigra</italic> (BB), and <italic>B. oleracea</italic> (CC) in the U&#x2019;s triangle have undergone a whole genome triplication event (WGT) (<xref ref-type="bibr" rid="B69">Wang et&#xa0;al., 2011</xref>; <xref ref-type="bibr" rid="B71">Woodhouse et&#xa0;al., 2014</xref>) resulting in the expansion of MADS-box genes compared with <italic>A. thaliana</italic>; however, the gene numbers were significantly different. For example, 159, 184, and 180 MADS-box genes were identified in <italic>B. rapa</italic>, <italic>B. nigra</italic>, and <italic>B. oleracea</italic> genomes, respectively. In addition, although allopolyploidy facilitated the expansion of MADS-box genes, the total number of MADS-box genes identified in allotetraploid species differed from the total number of genes in its two progenitor species. For example, 240 MADS-box genes were identified in the genome of <italic>B. juncea</italic>, which was significantly less than the sum of genes in its progenitor species <italic>B. rapa</italic> (159) and <italic>B. nigra</italic> (184), and the number of MADS-box genes in <italic>B. carinata</italic> genome (335) was slightly lower than the sum of genes in its progenitor species <italic>B. nigra</italic> (184) and <italic>B. oleracea</italic> (180). The 1430 MADS-box genes were renamed based on the gene information about their distribution on chromosomes, and the protein length, molecular weight (MW), and isoelectric points (pI) of each MADS protein were analyzed synthetically to understand the basic information more comprehensively (<xref ref-type="supplementary-material" rid="SM1">
<bold>Supplementary Table S3</bold>
</xref>).</p>
<fig id="f1" position="float">
<label>Figure&#xa0;1</label>
<caption>
<p>Evolutionary tree of MADS-box proteins in the six U&#x2019;s triangle species and <italic>A thaliana</italic> and the number of subfamily members. <bold>(A)</bold> The phylogenetic tree of 1535 MADS proteins was constructed using the maximum likelihood method, and different colors represent different subfamilies. <bold>(B)</bold> The red star represents that the genome has undergone a genome-wide triplication event (WGT).</p>
</caption>
<graphic mimetype="image" mime-subtype="tiff" xlink:href="fpls-13-1115513-g001.tif"/>
</fig>
</sec>
<sec id="s3_2">
<title>Phylogenetic tree of MIKC-type MADS-box genes</title>
<p>MIKC-type MADS-box genes are numerous, and their classification in plants is complicated. The ML phylogenetic tree was constructed for 39 MIKC-type genes in <italic>A. thaliana</italic> and 803 in the U&#x2019;s triangle species (<xref ref-type="fig" rid="f2">
<bold>Figure&#xa0;2</bold>
</xref>). Subsequently, 842 MIKC-type genes were divided into 35 subclades according to classification criteria and nomenclature in <italic>A. thaliana</italic>. Among them, 32 subclades contained MIKC-type genes from each species, and these subclades were renamed referring to the corresponding name in <italic>A. thaliana</italic>. The other three subclades (AGL72-like, AGL18-like, and FLC-like) did not contain corresponding homologous genes in <italic>A. thaliana</italic>; therefore, their renaming was based on the name of the branch closest to their evolutionary relationships (<xref ref-type="fig" rid="f2">
<bold>Figure&#xa0;2</bold>
</xref>). AGL72-like subclades had the highest number of genes, which may be another sister group of AGL72 subclades. In addition, most subclades had a clear evolutionary classification, whereas the SEP subclade had the highest number of genes and a complicated branch topology, implying that SEP subclades may have undergone multiple duplication events in the U&#x2019;s triangle species.</p>
<fig id="f2" position="float">
<label>Figure&#xa0;2</label>
<caption>
<p>Neighbor-joining (NJ) tree of MIKC-type MADS-box genes identified in the six U&#x2019;s triangle species; the genes were divided into 35 subgroups. Different colors represent different subclusters.</p>
</caption>
<graphic mimetype="image" mime-subtype="tiff" xlink:href="fpls-13-1115513-g002.tif"/>
</fig>
</sec>
<sec id="s3_3">
<title>Gene structure and conserved motifs of MIKC-type MADS-box genes</title>
<p>The exon-intron structural characteristics of MIKC-type genes varied remarkably in different subclades; however, the number and arrangement of exon-introns were similar in the same subclade (<xref ref-type="supplementary-material" rid="SF1">
<bold>Figure S1</bold>
</xref>). Most of the genes in the AG and AP3 subclades comprised seven exons and six introns (<xref ref-type="fig" rid="f3">
<bold>Figures&#xa0;3A, D</bold>
</xref>), AP1 and CAL subclades possessed the closest evolutionary relationship, and the majority of MIKC-type genes in AP1 and CAL subgroups generally contained eight exons and seven introns (<xref ref-type="fig" rid="f3">
<bold>Figure&#xa0;3B</bold>
</xref>); the PI subclade (<xref ref-type="fig" rid="f3">
<bold>Figure&#xa0;3E</bold>
</xref>) had six exons, and the SEP subclade had eight exons (<xref ref-type="fig" rid="f3">
<bold>Figure&#xa0;3C</bold>
</xref>).</p>
<fig id="f3" position="float">
<label>Figure&#xa0;3</label>
<caption>
<p>Gene structure and conserved motifs of six MIKC-type subclades [AG (<bold>A</bold>), AP1 and CAL (<bold>B</bold>), SEP (<bold>C</bold>), AP3 (<bold>D</bold>), and PI (<bold>E</bold>)]. The green boxes, yellow boxes, and block lines represent the exons, UTR, and introns, respectively. Ten different colored boxes represent ten distinct motifs.</p>
</caption>
<graphic mimetype="image" mime-subtype="tiff" xlink:href="fpls-13-1115513-g003.tif"/>
</fig>
<p>Ten conserved motifs were observed in 803 MIKC-type protein sequences (<xref ref-type="supplementary-material" rid="SM1">
<bold>Supplementary Table S4</bold>
</xref>). Motif 1 and motif 3 existed in most of the MADS-box domains, and motif 2, comparatively conserved in the K-box domain, may be responsible for the conservation of MIKC-type proteins among different subclades. However, other motifs were specifically distributed in different subclades and determined the specificity of the MIKC-type subclades (<xref ref-type="fig" rid="f3">
<bold>Figure&#xa0;3</bold>
</xref>; <xref ref-type="supplementary-material" rid="SF1">
<bold>Figure S1</bold>
</xref>). For example, comparing the conserved motifs of the AG, AP1, and CAL subclades (<xref ref-type="fig" rid="f3">
<bold>Figures&#xa0;3A, B</bold>
</xref>), motif 8 was only found in the AP1 and CAL subclades, whereas motifs 6 and 7 were only found in the AG subclade. Furthermore, motif 4 and motif 10 were distinctively distributed in the AP3 and PI subclades (<xref ref-type="fig" rid="f3">
<bold>Figures&#xa0;3D, E</bold>
</xref>), respectively, determining the specificity of these two subclades. The gene structure and conserved motifs of the other subclades are shown in <xref ref-type="supplementary-material" rid="SF1">
<bold>Figure S1</bold>
</xref>.</p>
</sec>
<sec id="s3_4">
<title>Gene duplication and synteny of MIKC-type MADS-box genes</title>
<p>BLAST and MCScanX software were used to analyze the gene duplication events of MIKC-type genes in the U&#x2019;s triangle species. A mass of tandem and segmental duplication events were detected in the genomes of <italic>B. rapa</italic> (3/69) (<xref ref-type="fig" rid="f4">
<bold>Figure&#xa0;4A</bold>
</xref>), <italic>B. nigra</italic> (4/75) (<xref ref-type="fig" rid="f4">
<bold>Figure&#xa0;4B</bold>
</xref>), <italic>B. oleracea</italic> (8/66) (<xref ref-type="fig" rid="f4">
<bold>Figure&#xa0;4C</bold>
</xref>), <italic>B. juncea</italic> (2/137) (<xref ref-type="fig" rid="f4">
<bold>Figure&#xa0;4D</bold>
</xref>), <italic>B. napus</italic> (4/194) (<xref ref-type="fig" rid="f4">
<bold>Figure&#xa0;4E</bold>
</xref>), and <italic>B. carinata</italic> (8/281) (<xref ref-type="fig" rid="f4">
<bold>Figure&#xa0;4F</bold>
</xref>). The duplication event numbers of MIKC-type genes in three diploid basic species were nearly the same. However, there was a significant difference among the three allotetraploids, particularly in segmental duplication events (<xref ref-type="supplementary-material" rid="SM1">
<bold>Supplementary Tables S5</bold>
</xref>, <xref ref-type="supplementary-material" rid="SM1">
<bold>6</bold>
</xref>), suggesting that MIKC-type genes have different evolutionary processes in the three allotetraploid species. Furthermore, the subgenome distribution of segmental duplication events in the genomes of three tetraploid <italic>Brassica</italic> species was analyzed. In <italic>B. juncea</italic>, 88 segmental duplication events occurred across the AA and BB subgenomes, 22 across the AA subgenome, and 27 across the BB subgenome (<xref ref-type="fig" rid="f4">
<bold>Figure&#xa0;4D</bold>
</xref>). In <italic>B. napus</italic>, 125 segmental duplication events occurred across the AA/CC subgenome, 41 across the AA subgenome, and 28 across the CC subgenome (<xref ref-type="fig" rid="f4">
<bold>Figure&#xa0;4E</bold>
</xref>). In <italic>B. carinata</italic>, 159 segmental duplication events occurred across the BB/CC subgenome, 85 across the BB subgenome, and 37 across the CC subgenome (<xref ref-type="fig" rid="f4">
<bold>Figure&#xa0;4F</bold>
</xref>). These results indicate that segmental duplication events among the three tetraploid <italic>Brassica</italic> species mainly occurred across the different subgenomes.</p>
<fig id="f4" position="float">
<label>Figure&#xa0;4</label>
<caption>
<p>Duplication events and synteny of MIKC-type MADS-box genes. <bold>(A-F)</bold> Chromosome location information and segmental duplication of MIKC-type MADS-box genes. <bold>(A&#x2013;F)</bold> indicate the segmental duplication events occurring within the genomes of <italic>B. rapa</italic>, <italic>B. nigra</italic>, <italic>B. oleracea</italic>, <italic>B. juncea</italic>, <italic>B. napus</italic>, and <italic>B. carinata</italic>, respectively. Colored lines represent replication events identified within different subgenomes, and black lines represent duplication gene pairs that occur on the same chromosome. <bold>(G-I)</bold> Genomic synteny between progenitor <italic>Brassica</italic> species <italic>B. rapa</italic>, <italic>B. nigra</italic>, and <italic>B. oleracea</italic>) and the allotetraploid species (<italic>B. carinata</italic>, <italic>B. juncea</italic>, and <italic>B. napus</italic>).</p>
</caption>
<graphic mimetype="image" mime-subtype="tiff" xlink:href="fpls-13-1115513-g004.tif"/>
</fig>
<p>To elucidate the evolutionary process of MIKC-type genes, synteny between three allotetraploid species (<italic>B. carinata</italic>, <italic>B. juncea</italic>, and <italic>B. napus</italic>) and its progenitor <italic>Brassica</italic> species (<italic>B. rapa</italic>, <italic>B. nigra</italic>, and <italic>B. oleracea</italic>) was performed (<xref ref-type="supplementary-material" rid="SM1">
<bold>Supplementary Table S7</bold>
</xref>). A total of 15 gene pairs were identified between <italic>B. rapa</italic> and the A subgenome of <italic>B. napus</italic> and <italic>B. juncea</italic> (<xref ref-type="fig" rid="f4">
<bold>Figure&#xa0;4G</bold>
</xref>). Among them, <italic>BnaMADS148</italic> (<italic>BnaAnng06990D</italic>) may be located on chrA02 of <italic>B. napus</italic> because its syntenic gene pairs were all located on chrA02. In addition, 32 gene pairs were detected across the <italic>B. nigra</italic> genome and B subgenomes of <italic>B. juncea</italic> and <italic>B. carinata</italic> (<xref ref-type="fig" rid="f4">
<bold>Figure&#xa0;4H</bold>
</xref>), of which 28 gene pairs were shared on the same chromosome among the B genome of progenitor species and B subgenome of its hybridized allotetraploid species, whereas the other four were shared on different chromosomes. Additionally, 37 MIKC-type gene pairs were identified across the <italic>B. oleracea</italic> genome and C subgenomes of <italic>B. napus</italic> and <italic>B. carinata</italic> (<xref ref-type="fig" rid="f4">
<bold>Figure&#xa0;4I</bold>
</xref>). Overall, the number of syntenic gene pairs in subgenome A was significantly lower than that in subgenome B or C.</p>
</sec>
<sec id="s3_5">
<title>Expression profile analysis of MIKC-type BnMADS-box genes in various tissues of <italic>B. napus</italic>
</title>
<p>
<italic>B. napus</italic> is an important oil crop in the U&#x2019;s triangle, and its abundant and reliable transcriptome data provide a basis for exploring the expression patterns of MIKC-type genes. Therefore, transcriptome data of various tissues, embryos, and seed coats at different developmental stages were downloaded from the public RNA-seq database to analyze the expression characteristics of MIKC-type genes. A total of 63 MIKC-type BnaMADS-box genes were screened from the expression matrix of different tissues (<xref ref-type="supplementary-material" rid="SM1">
<bold>Supplementary Table S8</bold>
</xref>), which were classified into five subgroups according to their expression patterns (<xref ref-type="fig" rid="f5">
<bold>Figure&#xa0;5A</bold>
</xref>). Subgroup I genes were highly expressed in stems and leaves, and some genes were also highly expressed in siliques and other tissues; however, all genes were expressed at low levels in the seed. Subgroup II genes were mainly expressed in flowers, seeds, and siliques, but their expression was low in roots. The subgroup III genes were root-specific. Nine genes, including especially <italic>BnaMADS37</italic>, <italic>BnaMADS111</italic>, <italic>BnaMADS155</italic>, and <italic>BnaMADS189</italic>, in subgroup IV were highly expressed in seeds. The genes in subgroup V, including <italic>BnaMADS12</italic>, <italic>BnaMADS30</italic>, <italic>BnaMADS300</italic>, and <italic>BnaMADS313</italic>, were only highly expressed in the flowers. Overall, the expression patterns of the 63 BnMADS-box genes were tissue-specific, suggesting that these genes may have vital biological functions in tissues during specific developmental processes.</p>
<fig id="f5" position="float">
<label>Figure&#xa0;5</label>
<caption>
<p>Expression patterns of MIKC-type MADS-box genes in different tissues and developmental stages. <bold>(A)</bold> Heatmap of TPM values in six different tissues (root, stem, leaf, flower, seed, and silique). <bold>(B)</bold> The gene expression trends during different unfertilized ovule, embryo, and seed coat stages.</p>
</caption>
<graphic mimetype="image" mime-subtype="tiff" xlink:href="fpls-13-1115513-g005.tif"/>
</fig>
<p>To explore the expression patterns of MIKC-type BnaMADS-box genes at different developmental stages of the embryo and seed coat, the expression patterns of 48 BnaMADS-box genes were divided into two major subgroups (<xref ref-type="fig" rid="f5">
<bold>Figure&#xa0;5B</bold>
</xref>; <xref ref-type="supplementary-material" rid="SM1">
<bold>Supplementary Table S9</bold>
</xref>). Subgroup I genes were mainly expressed during the unfertilized ovule stage and first three periods of embryonic development (zygote, octant, and globular stages), whereas subgroup II genes were generally expressed during the embryo and seed coat development stages, especially in the middle and late stages of embryo development, such as <italic>BnaMADS27</italic> was highly expressed in torpedo and bent stage embryos, <italic>BnaMADS141</italic> and <italic>BnaMADS32</italic>3 were highly expressed in octant, globular, and heart stage embryos. In addition, <italic>BnaMADS98</italic> was highly expressed in globular stage embryo, whereas it was less expressed during seed coat development. Therefore, analyzing the expression pattern of MIKC-type genes in <italic>B. napus</italic> provided a guide for exploring the biological functions of MIKC-type genes in various tissues during the entire developmental process.</p>
</sec>
<sec id="s3_6">
<title>Expression profiles of MIKC-type BnMADS-box genes under biotic and abiotic stressors in <italic>B. napus</italic>
</title>
<p>To determine the mechanism of MIKC-type genes responding to biotic and abiotic stress, transcriptome data for dehydration, salt, ABA, and cold stress were downloaded from the public RNA-seq database (<xref ref-type="supplementary-material" rid="SM1">
<bold>Supplementary Table S10</bold>
</xref>). Based on gene expression trends under abiotic stress, the 38 MIKC-type genes were divided into three categories: subgroups I, II, and III (<xref ref-type="fig" rid="f6">
<bold>Figure&#xa0;6A</bold>
</xref>). Subgroup I genes were expressed under various types of abiotic stresses. <italic>BnaMADS227</italic>, <italic>BnaMADS286</italic>, and <italic>BnaMADS297</italic> were significantly upregulated after dehydration, salt, ABA, and cold treatment, whereas <italic>BnaMADS104</italic> and <italic>BnaMADS311</italic> were more susceptible to dehydration, salt, and ABA stress. <italic>BnaMADS222</italic> was downregulated at 1&#xa0;h and 8&#xa0;h of dehydration stress, indicating that <italic>BnaMADS222</italic> was more sensitive to dehydration stress. A small subset of the genes in subgroup II was sensitive to abiotic stress. <italic>BnaMADS2</italic> and <italic>BnaMADS164</italic> were induced by dehydration and cold treatment; <italic>BnaMADS38</italic> and <italic>BnaMADS302</italic> were upregulated under dehydration and salt stress, and <italic>BnaMADS56</italic> was significantly downregulated after dehydration stress. Subgroup III genes had low expression under abiotic treatments; however, individual genes were upregulated after stress treatment. For example, <italic>BnaMADS123</italic> and <italic>BnaMADS63</italic> were significantly highly expressed after 24&#xa0;h of cold treatment, and <italic>BnaMADS35</italic> was upregulated after 24&#xa0;h of ABA treatment. The rapeseed leaf transcriptome data of resistant and susceptible lines after inoculation with powdery mildew were downloaded for further analysis (<xref ref-type="fig" rid="f6">
<bold>Figure&#xa0;6B</bold>
</xref>; <xref ref-type="supplementary-material" rid="SM1">
<bold>Supplementary Table S11</bold>
</xref>). A total of 21 MIKC-type genes responded to powdery mildew stress, of which 16 genes, including <italic>BnaMADS113</italic>, <italic>BnaMADS118</italic>, and <italic>BnaMADS321</italic>, showed significantly higher expression in resistant strains than in sensitive strains. Furthermore, <italic>BnaMADS2</italic>, <italic>BnaMADS11</italic>, <italic>BnaMADS164</italic>, <italic>BnaMADS190</italic>, and <italic>BnaMADS215</italic> showed higher expression in susceptible strains than in resistant strains.</p>
<fig id="f6" position="float">
<label>Figure&#xa0;6</label>
<caption>
<p>Expression of MIKC-type MADS-box genes in response to biotic and abiotic stresses. <bold>(A)</bold> Expression profiles of genes in rapeseed leaves under four different abiotic stressors (dehydration, salt, ABA, and cold). <bold>(B)</bold> The leaves expression patterns of two different white powder-resistant rapeseed lines after inoculation with powdery mildew.</p>
</caption>
<graphic mimetype="image" mime-subtype="tiff" xlink:href="fpls-13-1115513-g006.tif"/>
</fig>
</sec>
<sec id="s3_7">
<title>Sequence analysis of <italic>BnaAG</italic> and vector construction</title>
<p>To further verify the contribution of <italic>BnaAG</italic> genes to floral organ development, four highly homologous <italic>BnaAG</italic>s, <italic>BnaA01g09760D</italic>, <italic>BnaA03g43820D</italic>, <italic>BnaC01g11460D</italic>, <italic>BnaC03g62970D</italic> (also named <italic>BnaAG.A01</italic>, <italic>BnaAG.A03</italic>, <italic>BnaAG.C01</italic>, and <italic>BnaAG.C03</italic>, respectively), located on chromosomes A01, A03, C01, and C03, respectively, were isolated by Blastp with <italic>AtAG</italic>. Phylogenetic tree analysis showed that <italic>BnaAG.A01</italic> and <italic>BnaAG.C01</italic> had the closest relationships with <italic>AtAG</italic> (<xref ref-type="fig" rid="f7">
<bold>Figure&#xa0;7A</bold>
</xref>). The observation of gene structure features showed that most of the <italic>BnaAG</italic> genes contained seven exons, whereas <italic>BnaAG.C01</italic> was composed of nine exons but had no effect on its conserved domain at the gene structure level (<xref ref-type="fig" rid="f7">
<bold>Figures&#xa0;7B</bold>
</xref>). Based on multiple alignments of <italic>BnaAG</italic> homologous genes, CRISPR/Cas9 vectors were constructed to target the conserved regions of four <italic>BnaAG</italic> homoeologs. In brief, the consensus sequence on the first exon of <italic>BnaAG.A01</italic>, <italic>BnaAG.A03</italic>, <italic>BnaAG.C03</italic>, and the third exon of <italic>BnaAG.C01</italic> were targeted by sgRNA1. SgRNA2 targeted the consensus sequence on the third exon of <italic>BnaAG.A01</italic>, <italic>BnaAG.A03</italic>, <italic>BnaAG.C03</italic>, and the fifth exon of <italic>BnaAG.C01</italic> (<xref ref-type="fig" rid="f7">
<bold>Figures&#xa0;7C</bold>
</xref>). Based on these results, sgRNA1 was located on the MADS-box domain and sgRNA2 on the K-box domain.</p>
<fig id="f7" position="float">
<label>Figure&#xa0;7</label>
<caption>
<p>Construction of vectors for targeting <italic>BnaAG</italic> homologous genes. <bold>(A)</bold> NJ tree of <italic>BnaAG</italic> homologous genes in <italic>B napus</italic> and <italic>A thaliana</italic>. The red stars represent the <italic>BnaAG</italic> homologs of <italic>B napus</italic> closely related to the <italic>AG</italic> gene in <italic>A thaliana</italic>. <bold>(B)</bold> Gene structure, conserved domain, and distribution of sgRNA1 and sgRNA2 targeting four homologous genes of <italic>BnaAG</italic>. The black line represents introns, and the black boxes represent the exon. The red arrows indicate the location of sgRNA targets on the exon, and the orange and blue boxes represent MADS-box and K-box domains, respectively. <bold>(C)</bold> Sequence information of two sgRNA, PAM is indicated in red.</p>
</caption>
<graphic mimetype="image" mime-subtype="tiff" xlink:href="fpls-13-1115513-g007.tif"/>
</fig>
</sec>
<sec id="s3_8">
<title>CRISPR/Cas9 mediated mutation in <italic>BnaAG</italic> homoeologs and enriched floral organ mutant phenotypes</title>
<p>After the genetic transformation of the rapeseed hypocotyl mediated by <italic>Agrobacterium tumefaciens</italic>, more than 40 T0 generation hygromycin B-positive plants were obtained, of which 20 lines consisted of four concentric wheels and showed no difference from the wild-type (WT), whereas the other lines showed a disorganized floral structure. Therefore, T0 generation lines can be classified into four types based on their floral organ mutation phenotypes. To verify the mutation type, plants of all phenotypes were screened using Sanger sequencing, and the editing efficiency of sgRNA1 was found to be significantly lower than that of sgRNA2 (<xref ref-type="supplementary-material" rid="SF2">
<bold>Figures S2</bold>
</xref>, <xref ref-type="supplementary-material" rid="SF3">
<bold>3</bold>
</xref>). Specifically, compared to wild type (WT) (<xref ref-type="fig" rid="f8">
<bold>Figures&#xa0;8A&#x2013;C</bold>
</xref>), there were no phenotypic differences found in <italic>wt-like</italic> (<italic>wtl</italic>) (<xref ref-type="fig" rid="f8">
<bold>Figures&#xa0;8D&#x2013;F</bold>
</xref>). Sequencing results showed that no editing events existed in target 1, and all <italic>BnaAG</italic> homologs had a single base inserted except <italic>BnaAG.A01</italic> in target 2 (<xref ref-type="fig" rid="f8">
<bold>Figure&#xa0;8S</bold>
</xref>). The <italic>female flower-like</italic> (<italic>feml</italic>) mutant (<xref ref-type="fig" rid="f8">
<bold>Figures&#xa0;8G&#x2013;I</bold>
</xref>), which led to the conversion of stamens into petals and expansion of carpels, generated low seed-setting and distorted siliques after cross-pollination (<xref ref-type="fig" rid="f8">
<bold>Figure&#xa0;8P</bold>
</xref>). The sequencing results showed that no editing events happened except for single base insertion in <italic>BnaAG.C01</italic> of target 1. <italic>BnaAG.C01</italic>, <italic>BnaAG.C03</italic>, and <italic>BnaAG.A03</italic> had a single base insertion in target 2, whereas <italic>BnaAG.A01</italic> had a deletion of three bases (CGA) in target 2 that did not cause frameshift mutation (<xref ref-type="supplementary-material" rid="SM1">
<bold>Figure S4</bold>
</xref>). The next mutant, like <italic>ag-2</italic> mutant in <italic>A. thaliana</italic>, gave rise to the following phenotype: six stamens replaced by six petals, and the carpel replaced by a new flower with an elongated pedicel, in which stamens and carpels were replaced by petals (also called <italic>agamous-like flower-2</italic> (<italic>aglf-2</italic>) (<xref ref-type="bibr" rid="B76">Yanofsky et&#xa0;al., 1990</xref>; <xref ref-type="bibr" rid="B65">Tsutsui and Higashiyama, 2017</xref>) (<xref ref-type="fig" rid="f8">
<bold>Figures&#xa0;8J&#x2013;L, Q, R</bold>
</xref>). Target 1 of the <italic>BnAG</italic> homologous gene was not edited; however, insertion or deletion occurred in all <italic>BnAG</italic> homologous genes in target 2, resulting in a frameshift mutation. The phenotype of the last mutant was similar to the <italic>ag-1</italic> mutant in <italic>A. thaliana</italic> (<xref ref-type="bibr" rid="B76">Yanofsky et&#xa0;al., 1990</xref>); its outermost whorl had four normal sepals, while its third whorl stamens and fourth whorl carpel were all replaced by a multitude of petals. The resulting flower mutant, <italic>agamous-like flower-1</italic> (<italic>aglf-1</italic>), contained more than 85 petals (<xref ref-type="fig" rid="f8">
<bold>Figures&#xa0;8M&#x2013;O</bold>
</xref>), in which <italic>BnaAG.A01, BnaAG.C01, and BnaAG.A03</italic> with base insertion or deletion in target 2 caused a frameshift mutation, whereas <italic>BnaAG.C03</italic> had a single base insertion in both the target squences, resulting in a frameshift mutation.</p>
<fig id="f8" position="float">
<label>Figure&#xa0;8</label>
<caption>
<p>Phenotype and target sequence validation of the T0 generation of the gene-edited <italic>BnaAG</italic> genes. mInflorescences of WT <bold>(A)</bold>, <italic>wtl</italic> <bold>(D)</bold>, <italic>feml</italic> <bold>(G)</bold>, <italic>aglf-2</italic> <bold>(J)</bold>, and <italic>aglf-1</italic> <bold>(M)</bold>. Scale bars, 3&#xa0;cm. The flowers of WT <bold>(B)</bold>, <italic>wtl</italic> <bold>(E)</bold>, <italic>feml</italic> <bold>(H)</bold><italic>, aglf-2</italic> <bold>(K)</bold>, and <italic>aglf-1</italic> <bold>(N)</bold> plants. Scale bars, 0.5&#xa0;cm. Components from the anatomizing flowers of WT <bold>(C)</bold>, <italic>wtl</italic> <bold>(F)</bold>, <italic>feml</italic> <bold>(I)</bold>, <italic>aglf-2</italic> <bold>(L)</bold>, and <italic>aglf-1</italic> <bold>(O)</bold>. Scale bars, 0.5&#xa0;cm. <bold>(P)</bold> Mature siliques and seeds of <italic>feml</italic> lines after cross-pollination. Scale bars, 1&#xa0;cm. <bold>(Q, R)</bold> Flower <bold>(Q)</bold> and components from the anatomizing flower <bold>(R)</bold> of <italic>aglf-2</italic> during the flowering stage. <bold>(S)</bold> Validation of target sequences for various mutant phenotypes. Yellow and blue fonts represent the PAM of target sequences 1 and 2, respectively. Red &#x2018;-&#x2019; means deletions, and red font represents single base insertions. Yes or no indicates that the <italic>BnaAG</italic> gene underwent a frameshift mutation.</p>
</caption>
<graphic mimetype="image" mime-subtype="tiff" xlink:href="fpls-13-1115513-g008.tif"/>
</fig>
</sec>
</sec>
<sec id="s4" sec-type="discussion">
<title>Discussion</title>
<p>The U&#x2019;s triangle model represents the six globally important <italic>Brassica</italic> species and explains the genetic relationships among them. The <italic>B. carinata</italic> reference genome was published in 2021, marking the start of functional genomics. It also promoted the exploration of genetic evolution and molecular design breeding in the U&#x2019;s triangle species (<xref ref-type="bibr" rid="B62">Song et&#xa0;al., 2021</xref>; <xref ref-type="bibr" rid="B77">Yim et&#xa0;al., 2022</xref>). The MADS-box gene family is an important transcription factor that functions in floral homeostasis, morphogenesis, angiosperm reproductive development, and vegetative development (<xref ref-type="bibr" rid="B46">Okada and Shimura, 1994</xref>; <xref ref-type="bibr" rid="B4">Becker et&#xa0;al., 2000</xref>; <xref ref-type="bibr" rid="B1">Alvarez-Buylla et&#xa0;al., 2019</xref>).</p>
<sec id="s4_1">
<title>The MIKC-type MADS-box genes were significantly expanded in the genome of six U&#x2019;s triangle species</title>
<p>Previous studies showed that a total of 160, 91, and 307 MADS-box genes have been identified in <italic>B. rapa</italic>, <italic>B. oleracea</italic>, and <italic>B. napus</italic> genomes, respectively. However, there was no related research regarding MADS-box genes in <italic>B. nigra</italic>, <italic>B. juncea</italic>, and <italic>B. carinata</italic> genomes (<xref ref-type="bibr" rid="B17">Duan et&#xa0;al., 2015</xref>; <xref ref-type="bibr" rid="B72">Wu et&#xa0;al., 2018</xref>; <xref ref-type="bibr" rid="B59">Sheng et&#xa0;al., 2019</xref>). With the disclosure of the genome information of the remaining three <italic>Brassica</italic> species (<italic>B. nigra</italic>, <italic>B. juncea</italic>, and <italic>B. carinata</italic>), this study was the first to perform the systematic identification and classification of MADS-box genes in U&#x2019;s triangle species. A total of 159 MADS-box genes were identified in the <italic>B. rapa</italic> genome, which is consistent with previous results (<xref ref-type="bibr" rid="B17">Duan et&#xa0;al., 2015</xref>). However, 180 MADS-box genes were investigated in the <italic>B. oleracea</italic> genome, which was approximately twice the number previously reported (<xref ref-type="bibr" rid="B59">Sheng et&#xa0;al., 2019</xref>), and 332 MADS-box genes were identified in the <italic>B. napus</italic> genome, which was 25 more than originally reported (<xref ref-type="bibr" rid="B72">Wu et&#xa0;al., 2018</xref>) (<xref ref-type="fig" rid="f1">
<bold>Figure&#xa0;1B</bold>
</xref>). The differences in the number of members may be confined to the reference genome quality of previously assembled <italic>Brassica</italic> species. The MADS-box genes can be divided into M-type and MIKC-type according to their phylogenetic relationships. The gene number ratio of the two types was 1.69 (66:39) in <italic>A. thaliana</italic>, 0.8 (71:88) in <italic>B rapa</italic>, 1.0 (92:92) in <italic>B. nigra</italic>, 0.87 (84:96) in <italic>B. oleracea</italic>, 0.87 (112:128) in <italic>B. juncea</italic>, 0.75 (143:189) in <italic>B. napus</italic>, and 0.59 (125:210) in <italic>B. carinata</italic>, indicating that the ratio of M-type and MIKC-type genes decreased gradually compared with that of <italic>A. thaliana</italic>. Moreover, the genome of the three diploid U&#x2019;s triangle species has undergone genome-wide triploid events during the evolutionary process (<xref ref-type="bibr" rid="B69">Wang et&#xa0;al., 2011</xref>; <xref ref-type="bibr" rid="B71">Woodhouse et&#xa0;al., 2014</xref>), leading to a significantly higher ratio of MIKC-type genes in <italic>A. thaliana</italic> and three diploid species (<italic>A. thaliana</italic>:<italic>B. rapa</italic>:<italic>B. nigra</italic>:<italic>B. oleracea</italic> = 39:88:92:96) than that of M-type genes (<italic>A. thaliana</italic>:<italic>B. rapa</italic>:<italic>B. nigra</italic>:<italic>B. oleracea</italic> = 66:71:92:84). The function of M-type genes in plants is poorly understood, whereas MIKC-type genes are implicated in plant growth and development and environmental adaptation (<xref ref-type="bibr" rid="B34">Kofuji et&#xa0;al., 2003</xref>; <xref ref-type="bibr" rid="B75">Yang et&#xa0;al., 2016</xref>; <xref ref-type="bibr" rid="B24">Guo et&#xa0;al., 2021</xref>). Therefore, the significant expansion of MIKC-type genes in the U&#x2019;s triangle species may be an adaptive evolution.</p>
</sec>
<sec id="s4_2">
<title>The tissue-specific expression patterns of MIKC-type BnaMADS-box genes</title>
<p>Public transcriptome data helps effectively identify valuable genes. In this study, a large number of tissue-specific MIKC-type BnaMADS-box genes were discovered in various tissues and during embryo development processes in <italic>B napus</italic>, of which <italic>BnaMADS1</italic> and <italic>BnaMADS297</italic> were highly expressed in roots (<xref ref-type="fig" rid="f5">
<bold>Figure&#xa0;5A</bold>
</xref>). <italic>AtAGL14</italic> (<italic>XAL2</italic>, <italic>AT4G11880</italic>), a homologous gene of <italic>BnaMADS297</italic> in <italic>A. thaliana</italic>, which binds to the CArG box (a cis-regulatory element of <italic>PIN1</italic> and <italic>PIN4)</italic>, regulates root elongation by upregulating the abundance of PIN protein (<xref ref-type="bibr" rid="B21">Garay-Arroyo et&#xa0;al., 2013</xref>). <italic>AGL21</italic> (<italic>AT4G37940</italic>), a homolog of <italic>BnaMADS1</italic>, mainly regulates lateral root development, especially during lateral root growth under low-nitrogen conditions (<xref ref-type="bibr" rid="B78">Yu et&#xa0;al., 2014</xref>). <italic>BnaMADS111</italic> is specifically expressed in seeds and highly expressed during the early stage of seed coat development (zygote, octant, and globular stage) (<xref ref-type="fig" rid="f5">
<bold>Figure&#xa0;5B</bold>
</xref>); its homolog <italic>AGL32</italic> (<italic>TT16</italic>, <italic>AT5G23260</italic>) modulates the development of the sub-epidermal integument cell layer in <italic>A. thaliana</italic> seeds (<xref ref-type="bibr" rid="B14">Coen et&#xa0;al., 2017</xref>). <italic>BnMADS12</italic> and <italic>BnMADS313</italic> were specifically highly expressed only in flowers, and their homologous gene <italic>PI</italic> in <italic>A. thaliana</italic> acts as a floral homeotic gene mainly involved in the regulation of petal and stamen development (<xref ref-type="bibr" rid="B23">Goto and Meyerowitz, 1994</xref>). <italic>BnaMADS28</italic> is highly expressed during the later stages of embryo and seed coat development, and its homologous gene <italic>AGL15</italic> (<italic>AT5G13790</italic>) facilitates somatic embryogenesis in <italic>A. thalian</italic>a (<xref ref-type="bibr" rid="B51">Paul et&#xa0;al., 2022</xref>). <italic>BnaMADS161</italic> is highly expressed during the early stage of embryo development and throughout the seed coat development process, and its homologous gene <italic>AGL11</italic> (<italic>STK</italic>, <italic>AT4G09960</italic>) in <italic>Arabidopsis</italic> is involved in seed and silique development (<xref ref-type="bibr" rid="B15">Di Marzo et&#xa0;al., 2022</xref>).</p>
</sec>
<sec id="s4_3">
<title>MIKC-type BnaMADS-box genes are widely involved in drought stress in <italic>B. napus</italic>
</title>
<p>Plant responses to biotic and abiotic stresses reflect resilience to external challenges. Plants usually respond to drought stress by flowering early to complete their life cycle, a phenomenon called drought escape (<xref ref-type="bibr" rid="B66">Waadt et&#xa0;al., 2022</xref>). Transcriptome data analysis showed that some BnaMADS-box genes involved in flowering time are also highly expressed under drought stress, possibly regulating drought escape. For example, <italic>AGL20</italic> (<italic>SOC1</italic>, <italic>AT2G45660</italic>), a homologous gene of <italic>BnaMADS227</italic> in <italic>A. thaliana</italic>, is upregulated by <italic>ABF3</italic> and <italic>ABF4</italic> under drought stress, thus promoting flowering (<xref ref-type="bibr" rid="B28">Hwang et&#xa0;al., 2019</xref>). <italic>BnaMADS227</italic> is not only upregulated under drought stress but also induced by salt, ABA, and cold stress, indicating that <italic>BnaMADS227</italic> participates in drought response and other abiotic stresses. In addition, <italic>BnaMADS2</italic> and <italic>BnaMADS164</italic> also respond to various abiotic stresses, such as dehydration and cold stress, and homologous <italic>AGL16</italic> (<italic>AT3G57230</italic>) negatively regulates drought stress through stomatal density and movement in <italic>A. thaliana</italic> (<xref ref-type="bibr" rid="B85">Zhao et&#xa0;al., 2020</xref>). Thus, we speculated that these two genes may be involved in drought or cold stress. The expression of some genes, such as <italic>BnaMADS118</italic>, <italic>BnaMADS113</italic>, and <italic>BnaMADS321</italic>, was high in resistant strains and low in susceptible strains; however, the homologs of these genes in <italic>Arabidopsis</italic> are not reportedly involved in biotic stress. Exploring the mechanism of these genes in powdery disease can enrich the function of MIKC-type BnaMADS-box genes.</p>
</sec>
<sec id="s4_4">
<title>The <italic>BnaAG</italic> homolog genes may be functionally redundant</title>
<p>Polyploid plants enriched the floral organ phenotype due to the complex gene copy number but interfered with the systematic study of floral organ development. <italic>AG</italic> is responsible for stamen identity, carpel identity, and floral meristem determination (<xref ref-type="bibr" rid="B64">Theissen et&#xa0;al., 2000</xref>; <xref ref-type="bibr" rid="B16">Dreni and Kater, 2014</xref>). In this study, CRISPR/Cas9 technology was used to knock-out four <italic>BnaAG</italic> genes, and four lines with significant phenotypic differences in the T0 generation were obtained: <italic>wtl</italic>, <italic>feml</italic>, <italic>aglf-2</italic>, and <italic>aglf-1</italic> (<xref ref-type="fig" rid="f8">
<bold>Figure&#xa0;8</bold>
</xref>; <xref ref-type="supplementary-material" rid="SF3">
<bold>Figure S3</bold>
</xref>). The <italic>BnaAG.A01</italic> was not edited in <italic>wtl</italic>, suggesting that the presence of only one copy of <italic>BnaAG</italic> can maintain the normal development of floral organs. However, the amino acid mutation of <italic>BnaAG.A01</italic> did not cause a termination mutation, and the frameshift mutation occurred on the other three homologous genes, resulting in the <italic>feml</italic> phenotype. In addition, termination mutations of four <italic>BnaAG</italic> homologs in <italic>aglf-2</italic> and <italic>aglf-1</italic> resulted in phenotypes similar to those in <italic>Arabidopsis</italic> (<xref ref-type="bibr" rid="B76">Yanofsky et&#xa0;al., 1990</xref>). These results confirmed that <italic>BnaAG</italic> genes were involved in the development of third and fourth whorls in flowers, suggesting that there may be functional redundancy among the four <italic>BnaAG</italic> genes.</p>
</sec>
<sec id="s4_5">
<title>
<italic>BnaAG</italic> may be a sex-identification marker gene in <italic>B. napus</italic>
</title>
<p>
<italic>AG</italic> is responsible for the floral organ sex determination of plants (<xref ref-type="bibr" rid="B83">Zhang et&#xa0;al., 2020</xref>; <xref ref-type="bibr" rid="B67">Wang et&#xa0;al., 2021</xref>). The flowers of <italic>B. napus</italic> are monoecious, and the creation and application of male sterile materials in rapeseed can greatly enrich the utilization of heterosis. The <italic>feml</italic> phenotype, similar to the female flower, was found in the T0 generation after editing <italic>BnaAG.</italic> Although the carpel was deformed, a few seeds could be obtained by cross-pollination, implying that the <italic>feml</italic> was a female flower without stamens. Thus, <italic>BnaAG</italic> may be a sex-determining marker gene in <italic>B. napus.</italic>
</p>
</sec>
</sec>
<sec id="s5" sec-type="conclusions">
<title>Conclusions</title>
<p>In conclusion, 1430 MADS-box genes were identified in the six U&#x2019;s triangle species and classified into M-type and MIKC-type based on their evolutionary relationships. Gene structure, conserved motifs, duplication events, and synteny between the subgenomes of different MIKC-type genes were analyzed. The expression profiles of different tissues revealed that the MIKC-type genes exhibited tissue-specific expression. Transcriptome analysis of genes induced by abiotic and biotic stress showed that MIKC-type MADS-box genes responded to external stimuli. Moreover, four types of floral organ mutants were created by editing <italic>BnaAG</italic> homologous genes, which revealed the mechanisms by which <italic>BnaAG</italic> regulates floral organ development in rapeseed. Our study provides novel insights into the regulation of floral organ development in <italic>Brassica</italic> species and may help develop new genetic varieties.</p>
</sec>
<sec id="s6" sec-type="data-availability">
<title>Data availability statement</title>
<p>The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/<xref ref-type="supplementary-material" rid="SM1">
<bold>Supplementary material</bold>
</xref>.</p>
</sec>
<sec id="s7" sec-type="author-contributions">
<title>Author contributions</title>
<p>SWH designed the experiments. MS wrote the manuscript. MS and YFZ executed the experiments. QJ and SHH analyzed the data. RA and NC prepared the figures. JM and YTZ revised the manuscript. All authors contributed to the article and approved the submitted version.</p>
</sec>
</body>
<back>
<sec id="s8" sec-type="funding-information">
<title>Funding</title>
<p>This research was funded by the Shaanxi Creative Talents Promotion Plan-Technological Innovation Team (2020TD-051), the Scientific Research and Sharing Platform Construction Project of Shaanxi Province (2021PT-036), the Key Research and Development Program of Henan Province (221111110200), the Key Research and Development Program of Yangling Seed Industry Innovation Center (Ylzy-yc-2021-02), and the National Key Research and Development Program of China (2016YFD0101900).</p>
</sec>
<ack>
<title>Acknowledgments</title>
<p>We are thankful to Qijun Chen (China Agricultural University) for providing the pHSE401 vector.</p>
</ack>
<sec id="s9" sec-type="COI-statement">
<title>Conflict of interest</title>
<p>The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.</p>
</sec>
<sec id="s10" sec-type="disclaimer">
<title>Publisher&#x2019;s note</title>
<p>All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article, or claim that may be made by its manufacturer, is not guaranteed or endorsed by the publisher.</p>
</sec>
<sec id="s11" sec-type="supplementary-material">
<title>Supplementary material</title>
<p>The Supplementary Material for this article can be found online at: <ext-link ext-link-type="uri" xlink:href="https://www.frontiersin.org/articles/10.3389/fpls.2022.1115513/full#supplementary-material">https://www.frontiersin.org/articles/10.3389/fpls.2022.1115513/full#supplementary-material</ext-link>
</p>
<supplementary-material xlink:href="Image_1.tiff" id="SF1" mimetype="image/tiff">
<label>Supplementary Figure&#xa0;1</label>
<caption>
<p>Gene structure and conserved motifs of MIKC-type subclades except for AG, AP1, CAL, AP3, PI, and SEP subclades.</p>
</caption>
</supplementary-material>
<supplementary-material xlink:href="Image_2.tiff" id="SF2" mimetype="image/tiff">
<label>Supplementary Figure&#xa0;2</label>
<caption>
<p>Editing efficiency of sgRNA-1 and sgRNA-2.</p>
</caption>
</supplementary-material>
<supplementary-material xlink:href="Image_3.tiff" id="SF3" mimetype="image/tiff">
<label>Supplementary Figure&#xa0;3</label>
<caption>
<p>Multiple sequence alignment of BnaAG.A01 in WT and <italic>feml</italic>.</p>
</caption>
</supplementary-material>
<supplementary-material xlink:href="DataSheet_1.pdf" id="SM2" mimetype="application/pdf"/>
<supplementary-material xlink:href="Table_1.xlsx" id="SM1" mimetype="application/vnd.openxmlformats-officedocument.spreadsheetml.sheet"/>
</sec>
<ref-list>
<title>References</title>
<ref id="B1">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Alvarez-Buylla</surname> <given-names>E. R.</given-names>
</name>
<name>
<surname>Garcia-Ponce</surname> <given-names>B.</given-names>
</name>
<name>
<surname>Sanchez</surname> <given-names>M. P.</given-names>
</name>
<name>
<surname>Espinosa-Soto</surname> <given-names>C.</given-names>
</name>
<name>
<surname>Garcia-Gomez</surname> <given-names>M. L.</given-names>
</name>
<name>
<surname>Pineyro-Nelson</surname> <given-names>A.</given-names>
</name>
<etal/>
</person-group>. (<year>2019</year>). <article-title>MADS-box genes underground becoming mainstream: plant root developmental mechanisms</article-title>. <source>New Phytol.</source> <volume>223</volume>, <fpage>1143</fpage>&#x2013;<lpage>1158</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1111/nph.15793</pub-id>
</citation>
</ref>
<ref id="B2">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Arora</surname> <given-names>R.</given-names>
</name>
<name>
<surname>Agarwal</surname> <given-names>P.</given-names>
</name>
<name>
<surname>Ray</surname> <given-names>S.</given-names>
</name>
<name>
<surname>Singh</surname> <given-names>A. K.</given-names>
</name>
<name>
<surname>Singh</surname> <given-names>V. P.</given-names>
</name>
<name>
<surname>Tyagi</surname> <given-names>A. K.</given-names>
</name>
<etal/>
</person-group>. (<year>2007</year>). <article-title>MADS-box gene family in rice: Genome-wide identification, organization and expression profiling during reproductive development and stress</article-title>. <source>BMC Genomics</source> <volume>8</volume>, <elocation-id>242</elocation-id>. doi:&#xa0;<pub-id pub-id-type="doi">10.1186/1471-2164-8-242</pub-id>
</citation>
</ref>
<ref id="B3">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Bailey</surname> <given-names>T. L.</given-names>
</name>
<name>
<surname>Boden</surname> <given-names>M.</given-names>
</name>
<name>
<surname>Buske</surname> <given-names>F. A.</given-names>
</name>
<name>
<surname>Frith</surname> <given-names>M.</given-names>
</name>
<name>
<surname>Grant</surname> <given-names>C. E.</given-names>
</name>
<name>
<surname>Clementi</surname> <given-names>L.</given-names>
</name>
<etal/>
</person-group>. (<year>2009</year>). <article-title>MEME SUITE: Tools for motif discovery and searching</article-title>. <source>Nucleic Acids Res.</source> <volume>37</volume>, <fpage>W202</fpage>&#x2013;<lpage>W208</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1093/nar/gkp335</pub-id>
</citation>
</ref>
<ref id="B4">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Becker</surname> <given-names>A.</given-names>
</name>
<name>
<surname>Winter</surname> <given-names>K. U.</given-names>
</name>
<name>
<surname>Meyer</surname> <given-names>B.</given-names>
</name>
<name>
<surname>Saedler</surname> <given-names>H.</given-names>
</name>
<name>
<surname>Theissen</surname> <given-names>G.</given-names>
</name>
</person-group> (<year>2000</year>). <article-title>MADS-box gene diversity in seed plants 300 million years ago</article-title>. <source>Mol. Biol. Evol.</source> <volume>17</volume>, <fpage>1425</fpage>&#x2013;<lpage>1434</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1093/oxfordjournals.molbev.a026243</pub-id>
</citation>
</ref>
<ref id="B5">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Bhalla</surname> <given-names>P. L.</given-names>
</name>
<name>
<surname>Singh</surname> <given-names>M. B.</given-names>
</name>
</person-group> (<year>2008</year>). <article-title>Agrobacterium-mediated transformation of brassica napus and brassica oleracea</article-title>. <source>Nat. Protoc.</source> <volume>3</volume>, <fpage>181</fpage>&#x2013;<lpage>189</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1038/nprot.2007.527</pub-id>
</citation>
</ref>
<ref id="B6">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Cai</surname> <given-names>C.</given-names>
</name>
<name>
<surname>Wang</surname> <given-names>X.</given-names>
</name>
<name>
<surname>Liu</surname> <given-names>B.</given-names>
</name>
<name>
<surname>Wu</surname> <given-names>J.</given-names>
</name>
<name>
<surname>Liang</surname> <given-names>J.</given-names>
</name>
<name>
<surname>Cui</surname> <given-names>Y.</given-names>
</name>
<etal/>
</person-group>. (<year>2017</year>). <article-title>Brassica rapa genome 2.0: A reference upgrade through sequence re-assembly and gene re-annotation</article-title>. <source>Mol. Plant</source> <volume>10</volume>, <fpage>649</fpage>&#x2013;<lpage>651</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1016/j.molp.2016.11.008</pub-id>
</citation>
</ref>
<ref id="B7">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Cai</surname> <given-names>X.</given-names>
</name>
<name>
<surname>Wu</surname> <given-names>J.</given-names>
</name>
<name>
<surname>Liang</surname> <given-names>J.</given-names>
</name>
<name>
<surname>Lin</surname> <given-names>R.</given-names>
</name>
<name>
<surname>Zhang</surname> <given-names>K.</given-names>
</name>
<name>
<surname>Cheng</surname> <given-names>F.</given-names>
</name>
<etal/>
</person-group>. (<year>2020</year>). <article-title>Improved brassica oleracea JZS assembly reveals significant changing of LTR-RT dynamics in different morphotypes</article-title>. <source>Theor. Appl. Genet.</source> <volume>133</volume>, <fpage>3187</fpage>&#x2013;<lpage>3199</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1007/s00122-020-03664-3</pub-id>
</citation>
</ref>
<ref id="B8">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Camacho</surname> <given-names>C.</given-names>
</name>
<name>
<surname>Coulouris</surname> <given-names>G.</given-names>
</name>
<name>
<surname>Avagyan</surname> <given-names>V.</given-names>
</name>
<name>
<surname>Ma</surname> <given-names>N.</given-names>
</name>
<name>
<surname>Papadopoulos</surname> <given-names>J.</given-names>
</name>
<name>
<surname>Bealer</surname> <given-names>K.</given-names>
</name>
<etal/>
</person-group>. (<year>2009</year>). <article-title>BLAST+: Architecture and applications</article-title>. <source>BMC Bioinf.</source> <volume>10</volume>, <elocation-id>421</elocation-id>. doi:&#xa0;<pub-id pub-id-type="doi">10.1186/1471-2105-10-421</pub-id>
</citation>
</ref>
<ref id="B9">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Chalhoub</surname> <given-names>B.</given-names>
</name>
<name>
<surname>Denoeud</surname> <given-names>F.</given-names>
</name>
<name>
<surname>Liu</surname> <given-names>S.</given-names>
</name>
<name>
<surname>Parkin</surname> <given-names>I. A.</given-names>
</name>
<name>
<surname>Tang</surname> <given-names>H.</given-names>
</name>
<name>
<surname>Wang</surname> <given-names>X.</given-names>
</name>
<etal/>
</person-group>. (<year>2014</year>). <article-title>Plant genetics. early allopolyploid evolution in the post-neolithic brassica napus oilseed genome</article-title>. <source>Science</source> <volume>345</volume>, <fpage>950</fpage>&#x2013;<lpage>953</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1126/science.1253435</pub-id>
</citation>
</ref>
<ref id="B10">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Chen</surname> <given-names>C.</given-names>
</name>
<name>
<surname>Chen</surname> <given-names>H.</given-names>
</name>
<name>
<surname>Zhang</surname> <given-names>Y.</given-names>
</name>
<name>
<surname>Thomas</surname> <given-names>H. R.</given-names>
</name>
<name>
<surname>Frank</surname> <given-names>M. H.</given-names>
</name>
<name>
<surname>He</surname> <given-names>Y.</given-names>
</name>
<etal/>
</person-group>. (<year>2020</year>). <article-title>TBtools: An integrative toolkit developed for interactive analyses of big biological data</article-title>. <source>Mol. Plant</source> <volume>13</volume>, <fpage>1194</fpage>&#x2013;<lpage>1202</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1016/j.molp.2020.06.009</pub-id>
</citation>
</ref>
<ref id="B11">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Cheng</surname> <given-names>F.</given-names>
</name>
<name>
<surname>Mandakova</surname> <given-names>T.</given-names>
</name>
<name>
<surname>Wu</surname> <given-names>J.</given-names>
</name>
<name>
<surname>Xie</surname> <given-names>Q.</given-names>
</name>
<name>
<surname>Lysak</surname> <given-names>M. A.</given-names>
</name>
<name>
<surname>Wang</surname> <given-names>X.</given-names>
</name>
</person-group> (<year>2013</year>). <article-title>Deciphering the diploid ancestral genome of the mesohexaploid brassica rapa</article-title>. <source>Plant Cell</source> <volume>25</volume>, <fpage>1541</fpage>&#x2013;<lpage>1554</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1105/tpc.113.110486</pub-id>
</citation>
</ref>
<ref id="B12">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Chen</surname> <given-names>X.</given-names>
</name>
<name>
<surname>Tong</surname> <given-names>C.</given-names>
</name>
<name>
<surname>Zhang</surname> <given-names>X.</given-names>
</name>
<name>
<surname>Song</surname> <given-names>A.</given-names>
</name>
<name>
<surname>Hu</surname> <given-names>M.</given-names>
</name>
<name>
<surname>Dong</surname> <given-names>W.</given-names>
</name>
<etal/>
</person-group>. (<year>2021</year>). <article-title>A high-quality brassica napus genome reveals expansion of transposable elements, subgenome evolution and disease resistance</article-title>. <source>Plant Biotechnol. J.</source> <volume>19</volume>, <fpage>615</fpage>&#x2013;<lpage>630</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1111/pbi.13493</pub-id>
</citation>
</ref>
<ref id="B13">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Coen</surname> <given-names>E. S.</given-names>
</name>
<name>
<surname>Meyerowitz</surname> <given-names>E. M.</given-names>
</name>
</person-group> (<year>1991</year>). <article-title>The war of the whorls: Genetic interactions controlling flower development</article-title>. <source>Nature</source> <volume>353</volume>, <fpage>31</fpage>&#x2013;<lpage>37</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1038/353031a0</pub-id>
</citation>
</ref>
<ref id="B14">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Coen</surname> <given-names>O.</given-names>
</name>
<name>
<surname>Fiume</surname> <given-names>E.</given-names>
</name>
<name>
<surname>Xu</surname> <given-names>W.</given-names>
</name>
<name>
<surname>De Vos</surname> <given-names>D.</given-names>
</name>
<name>
<surname>Lu</surname> <given-names>J.</given-names>
</name>
<name>
<surname>Pechoux</surname> <given-names>C.</given-names>
</name>
<etal/>
</person-group>. (<year>2017</year>). <article-title>Developmental patterning of the sub-epidermal integument cell layer in arabidopsis seeds</article-title>. <source>Development</source> <volume>144</volume>, <fpage>1490</fpage>&#x2013;<lpage>1497</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1242/dev.146274</pub-id>
</citation>
</ref>
<ref id="B15">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Di Marzo</surname> <given-names>M.</given-names>
</name>
<name>
<surname>Viana</surname> <given-names>V. E.</given-names>
</name>
<name>
<surname>Banfi</surname> <given-names>C.</given-names>
</name>
<name>
<surname>Cassina</surname> <given-names>V.</given-names>
</name>
<name>
<surname>Corti</surname> <given-names>R.</given-names>
</name>
<name>
<surname>Herrera-Ubaldo</surname> <given-names>H.</given-names>
</name>
<etal/>
</person-group>. (<year>2022</year>). <article-title>Cell wall modifications by alpha-XYLOSIDASE1 are required for control of seed and fruit size in arabidopsis</article-title>. <source>J. Exp. Bot.</source> <volume>73</volume>, <fpage>1499</fpage>&#x2013;<lpage>1515</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1093/jxb/erab514</pub-id>
</citation>
</ref>
<ref id="B16">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Dreni</surname> <given-names>L.</given-names>
</name>
<name>
<surname>Kater</surname> <given-names>M. M.</given-names>
</name>
</person-group> (<year>2014</year>). <article-title>MADS reloaded: evolution of the AGAMOUS subfamily genes</article-title>. <source>New Phytol.</source> <volume>201</volume>, <fpage>717</fpage>&#x2013;<lpage>732</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1111/nph.12555</pub-id>
</citation>
</ref>
<ref id="B17">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Duan</surname> <given-names>W.</given-names>
</name>
<name>
<surname>Song</surname> <given-names>X.</given-names>
</name>
<name>
<surname>Liu</surname> <given-names>T.</given-names>
</name>
<name>
<surname>Huang</surname> <given-names>Z.</given-names>
</name>
<name>
<surname>Ren</surname> <given-names>J.</given-names>
</name>
<name>
<surname>Hou</surname> <given-names>X.</given-names>
</name>
<etal/>
</person-group>. (<year>2015</year>). <article-title>Genome-wide analysis of the MADS-box gene family in brassica rapa (Chinese cabbage)</article-title>. <source>Mol. Genet. Genomics</source> <volume>290</volume>, <fpage>239</fpage>&#x2013;<lpage>255</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1007/s00438-014-0912-7</pub-id>
</citation>
</ref>
<ref id="B18">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Egea-Cortines</surname> <given-names>M.</given-names>
</name>
<name>
<surname>Saedler</surname> <given-names>H.</given-names>
</name>
<name>
<surname>Sommer</surname> <given-names>H.</given-names>
</name>
</person-group> (<year>1999</year>). <article-title>Ternary complex formation between the MADS-box proteins SQUAMOSA, DEFICIENS and GLOBOSA is involved in the control of floral architecture in antirrhinum majus</article-title>. <source>EMBO J.</source> <volume>18</volume>, <fpage>5370</fpage>&#x2013;<lpage>5379</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1093/emboj/18.19.5370</pub-id>
</citation>
</ref>
<ref id="B19">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Fan</surname> <given-names>H. Y.</given-names>
</name>
<name>
<surname>Hu</surname> <given-names>Y.</given-names>
</name>
<name>
<surname>Tudor</surname> <given-names>M.</given-names>
</name>
<name>
<surname>Ma</surname> <given-names>H.</given-names>
</name>
</person-group> (<year>1997</year>). <article-title>Specific interactions between the K domains of AG and AGLs, members of the MADS domain family of DNA binding proteins</article-title>. <source>Plant J.</source> <volume>12</volume>, <fpage>999</fpage>&#x2013;<lpage>1010</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1046/j.1365-313x.1997.12050999.x</pub-id>
</citation>
</ref>
<ref id="B20">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Ferrandiz</surname> <given-names>C.</given-names>
</name>
<name>
<surname>Liljegren</surname> <given-names>S. J.</given-names>
</name>
<name>
<surname>Yanofsky</surname> <given-names>M. F.</given-names>
</name>
</person-group> (<year>2000</year>). <article-title>Negative regulation of the SHATTERPROOF genes by FRUITFULL during arabidopsis fruit development</article-title>. <source>Science</source> <volume>289</volume>, <fpage>436</fpage>&#x2013;<lpage>438</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1126/science.289.5478.436</pub-id>
</citation>
</ref>
<ref id="B21">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Garay-Arroyo</surname> <given-names>A.</given-names>
</name>
<name>
<surname>Ortiz-Moreno</surname> <given-names>E.</given-names>
</name>
<name>
<surname>de la Paz Sanchez</surname> <given-names>M.</given-names>
</name>
<name>
<surname>Murphy</surname> <given-names>A. S.</given-names>
</name>
<name>
<surname>Garcia-Ponce</surname> <given-names>B.</given-names>
</name>
<name>
<surname>Marsch-Martinez</surname> <given-names>N.</given-names>
</name>
<etal/>
</person-group>. (<year>2013</year>). <article-title>The MADS transcription factor XAL2/AGL14 modulates auxin transport during arabidopsis root development by regulating PIN expression</article-title>. <source>EMBO J.</source> <volume>32</volume>, <fpage>2884</fpage>&#x2013;<lpage>2895</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1038/emboj.2013.216</pub-id>
</citation>
</ref>
<ref id="B22">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Gasteiger</surname> <given-names>E.</given-names>
</name>
<name>
<surname>Gattiker</surname> <given-names>A.</given-names>
</name>
<name>
<surname>Hoogland</surname> <given-names>C.</given-names>
</name>
<name>
<surname>Ivanyi</surname> <given-names>I.</given-names>
</name>
<name>
<surname>Appel</surname> <given-names>R. D.</given-names>
</name>
<name>
<surname>Bairoch</surname> <given-names>A.</given-names>
</name>
</person-group> (<year>2003</year>). <article-title>ExPASy: The proteomics server for in-depth protein knowledge and analysis</article-title>. <source>Nucleic Acids Res.</source> <volume>31</volume>, <fpage>3784</fpage>&#x2013;<lpage>3788</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1093/nar/gkg563</pub-id>
</citation>
</ref>
<ref id="B23">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Goto</surname> <given-names>K.</given-names>
</name>
<name>
<surname>Meyerowitz</surname> <given-names>E. M.</given-names>
</name>
</person-group> (<year>1994</year>). <article-title>Function and regulation of the arabidopsis floral homeotic gene PISTILLATA</article-title>. <source>Genes Dev.</source> <volume>8</volume>, <fpage>1548</fpage>&#x2013;<lpage>1560</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1101/gad.8.13.1548</pub-id>
</citation>
</ref>
<ref id="B24">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Guo</surname> <given-names>N.</given-names>
</name>
<name>
<surname>Wang</surname> <given-names>S.</given-names>
</name>
<name>
<surname>Gao</surname> <given-names>L.</given-names>
</name>
<name>
<surname>Liu</surname> <given-names>Y.</given-names>
</name>
<name>
<surname>Wang</surname> <given-names>X.</given-names>
</name>
<name>
<surname>Lai</surname> <given-names>E.</given-names>
</name>
<etal/>
</person-group>. (<year>2021</year>). <article-title>Genome sequencing sheds light on the contribution of structural variants to brassica oleracea diversification</article-title>. <source>BMC Biol.</source> <volume>19</volume>, <fpage>93</fpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1186/s12915-021-01031-2</pub-id>
</citation>
</ref>
<ref id="B25">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Hartmann</surname> <given-names>U.</given-names>
</name>
<name>
<surname>Hohmann</surname> <given-names>S.</given-names>
</name>
<name>
<surname>Nettesheim</surname> <given-names>K.</given-names>
</name>
<name>
<surname>Wisman</surname> <given-names>E.</given-names>
</name>
<name>
<surname>Saedler</surname> <given-names>H.</given-names>
</name>
<name>
<surname>Huijser</surname> <given-names>P.</given-names>
</name>
</person-group> (<year>2000</year>). <article-title>Molecular cloning of SVP: A negative regulator of the floral transition in arabidopsis</article-title>. <source>Plant J.</source> <volume>21</volume>, <fpage>351</fpage>&#x2013;<lpage>360</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1046/j.1365-313x.2000.00682.x</pub-id>
</citation>
</ref>
<ref id="B26">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Henschel</surname> <given-names>K.</given-names>
</name>
<name>
<surname>Kofuji</surname> <given-names>R.</given-names>
</name>
<name>
<surname>Hasebe</surname> <given-names>M.</given-names>
</name>
<name>
<surname>Saedler</surname> <given-names>H.</given-names>
</name>
<name>
<surname>Munster</surname> <given-names>T.</given-names>
</name>
<name>
<surname>Theissen</surname> <given-names>G.</given-names>
</name>
</person-group> (<year>2002</year>). <article-title>Two ancient classes of MIKC-type MADS-box genes are present in the moss physcomitrella patens</article-title>. <source>Mol. Biol. Evol.</source> <volume>19</volume>, <fpage>801</fpage>&#x2013;<lpage>814</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1093/oxfordjournals.molbev.a004137</pub-id>
</citation>
</ref>
<ref id="B27">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Honma</surname> <given-names>T.</given-names>
</name>
<name>
<surname>Goto</surname> <given-names>K.</given-names>
</name>
</person-group> (<year>2001</year>). <article-title>Complexes of MADS-box proteins are sufficient to convert leaves into floral organs</article-title>. <source>Nature</source> <volume>409</volume>, <fpage>525</fpage>&#x2013;<lpage>529</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1038/35054083</pub-id>
</citation>
</ref>
<ref id="B28">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Hwang</surname> <given-names>K.</given-names>
</name>
<name>
<surname>Susila</surname> <given-names>H.</given-names>
</name>
<name>
<surname>Nasim</surname> <given-names>Z.</given-names>
</name>
<name>
<surname>Jung</surname> <given-names>J. Y.</given-names>
</name>
<name>
<surname>Ahn</surname> <given-names>J. H.</given-names>
</name>
</person-group> (<year>2019</year>). <article-title>Arabidopsis ABF3 and ABF4 transcription factors act with the NF-YC complex to regulate SOC1 expression and mediate drought-accelerated flowering</article-title>. <source>Mol. Plant</source> <volume>12</volume>, <fpage>489</fpage>&#x2013;<lpage>505</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1016/j.molp.2019.01.002</pub-id>
</citation>
</ref>
<ref id="B29">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Immink</surname> <given-names>R. G.</given-names>
</name>
<name>
<surname>Gadella</surname> <given-names>T. W.</given-names>
<suffix>Jr.</suffix>
</name>
<name>
<surname>Ferrario</surname> <given-names>S.</given-names>
</name>
<name>
<surname>Busscher</surname> <given-names>M.</given-names>
</name>
<name>
<surname>Angenent</surname> <given-names>G. C.</given-names>
</name>
</person-group> (<year>2002</year>). <article-title>Analysis of MADS box protein-protein interactions in living plant cells</article-title>. <source>Proc. Natl. Acad. Sci. U S A.</source> <volume>99</volume>, <fpage>2416</fpage>&#x2013;<lpage>2421</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1073/pnas.042677699</pub-id>
</citation>
</ref>
<ref id="B30">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Jack</surname> <given-names>T.</given-names>
</name>
</person-group> (<year>2001</year>). <article-title>Plant development going MADS</article-title>. <source>Plant Mol. Biol.</source> <volume>46</volume>, <fpage>515</fpage>&#x2013;<lpage>520</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1023/a:1010689126632</pub-id>
</citation>
</ref>
<ref id="B31">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Katoh</surname> <given-names>K.</given-names>
</name>
<name>
<surname>Rozewicki</surname> <given-names>J.</given-names>
</name>
<name>
<surname>Yamada</surname> <given-names>K. D.</given-names>
</name>
</person-group> (<year>2019</year>). <article-title>MAFFT online service: Multiple sequence alignment, interactive sequence choice and visualization</article-title>. <source>Brief Bioinform.</source> <volume>20</volume>, <fpage>1160</fpage>&#x2013;<lpage>1166</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1093/bib/bbx108</pub-id>
</citation>
</ref>
<ref id="B32">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Kim</surname> <given-names>D.</given-names>
</name>
<name>
<surname>Langmead</surname> <given-names>B.</given-names>
</name>
<name>
<surname>Salzberg</surname> <given-names>S. L.</given-names>
</name>
</person-group> (<year>2015</year>). <article-title>HISAT: A fast spliced aligner with low memory requirements</article-title>. <source>Nat. Methods</source> <volume>12</volume>, <fpage>357</fpage>&#x2013;<lpage>360</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1038/nmeth.3317</pub-id>
</citation>
</ref>
<ref id="B33">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Kim</surname> <given-names>H. A.</given-names>
</name>
<name>
<surname>Lim</surname> <given-names>C. J.</given-names>
</name>
<name>
<surname>Kim</surname> <given-names>S.</given-names>
</name>
<name>
<surname>Choe</surname> <given-names>J. K.</given-names>
</name>
<name>
<surname>Jo</surname> <given-names>S. H.</given-names>
</name>
<name>
<surname>Baek</surname> <given-names>N.</given-names>
</name>
<etal/>
</person-group>. (<year>2014</year>). <article-title>High-throughput sequencing and <italic>de novo</italic> assembly of brassica oleracea var. capitata l. for transcriptome analysis</article-title>. <source>PLoS One</source> <volume>9</volume>, <elocation-id>e92087</elocation-id>. doi:&#xa0;<pub-id pub-id-type="doi">10.1371/journal.pone.0092087</pub-id>
</citation>
</ref>
<ref id="B34">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Kofuji</surname> <given-names>R.</given-names>
</name>
<name>
<surname>Sumikawa</surname> <given-names>N.</given-names>
</name>
<name>
<surname>Yamasaki</surname> <given-names>M.</given-names>
</name>
<name>
<surname>Kondo</surname> <given-names>K.</given-names>
</name>
<name>
<surname>Ueda</surname> <given-names>K.</given-names>
</name>
<name>
<surname>Ito</surname> <given-names>M.</given-names>
</name>
<etal/>
</person-group>. (<year>2003</year>). <article-title>Evolution and divergence of the MADS-box gene family based on genome-wide expression analyses</article-title>. <source>Mol. Biol. Evol.</source> <volume>20</volume>, <fpage>1963</fpage>&#x2013;<lpage>1977</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1093/molbev/msg216</pub-id>
</citation>
</ref>
<ref id="B35">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Krzywinski</surname> <given-names>M.</given-names>
</name>
<name>
<surname>Schein</surname> <given-names>J.</given-names>
</name>
<name>
<surname>Birol</surname> <given-names>I.</given-names>
</name>
<name>
<surname>Connors</surname> <given-names>J.</given-names>
</name>
<name>
<surname>Gascoyne</surname> <given-names>R.</given-names>
</name>
<name>
<surname>Horsman</surname> <given-names>D.</given-names>
</name>
<etal/>
</person-group>. (<year>2009</year>). <article-title>Circos: an information aesthetic for comparative genomics</article-title>. <source>Genome Res.</source> <volume>19</volume>, <fpage>1639</fpage>&#x2013;<lpage>1645</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1101/gr.092759.109</pub-id>
</citation>
</ref>
<ref id="B36">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Lee</surname> <given-names>J.</given-names>
</name>
<name>
<surname>Lee</surname> <given-names>I.</given-names>
</name>
</person-group> (<year>2010</year>). <article-title>Regulation and function of SOC1, a flowering pathway integrator</article-title>. <source>J. Exp. Bot.</source> <volume>61</volume>, <fpage>2247</fpage>&#x2013;<lpage>2254</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1093/jxb/erq098</pub-id>
</citation>
</ref>
<ref id="B37">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Letunic</surname> <given-names>I.</given-names>
</name>
<name>
<surname>Bork</surname> <given-names>P.</given-names>
</name>
</person-group> (<year>2007</year>). <article-title>Interactive tree of life (iTOL): An online tool for phylogenetic tree display and annotation</article-title>. <source>Bioinformatics</source> <volume>23</volume>, <fpage>127</fpage>&#x2013;<lpage>128</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1093/bioinformatics/btl529</pub-id>
</citation>
</ref>
<ref id="B38">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Letunic</surname> <given-names>I.</given-names>
</name>
<name>
<surname>Bork</surname> <given-names>P.</given-names>
</name>
</person-group> (<year>2018</year>). <article-title>20 years of the SMART protein domain annotation resource</article-title>. <source>Nucleic Acids Res.</source> <volume>46</volume>, <fpage>D493</fpage>&#x2013;<lpage>D496</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1093/nar/gkx922</pub-id>
</citation>
</ref>
<ref id="B39">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Liao</surname> <given-names>Y.</given-names>
</name>
<name>
<surname>Smyth</surname> <given-names>G. K.</given-names>
</name>
<name>
<surname>Shi</surname> <given-names>W.</given-names>
</name>
</person-group> (<year>2014</year>). <article-title>featureCounts: an efficient general purpose program for assigning sequence reads to genomic features</article-title>. <source>Bioinformatics</source> <volume>30</volume>, <fpage>923</fpage>&#x2013;<lpage>930</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1093/bioinformatics/btt656</pub-id>
</citation>
</ref>
<ref id="B40">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Liljegren</surname> <given-names>S. J.</given-names>
</name>
<name>
<surname>Ditta</surname> <given-names>G. S.</given-names>
</name>
<name>
<surname>Eshed</surname> <given-names>Y.</given-names>
</name>
<name>
<surname>Savidge</surname> <given-names>B.</given-names>
</name>
<name>
<surname>Bowman</surname> <given-names>J. L.</given-names>
</name>
<name>
<surname>Yanofsky</surname> <given-names>M. F.</given-names>
</name>
</person-group> (<year>2000</year>). <article-title>SHATTERPROOF MADS-box genes control seed dispersal in arabidopsis</article-title>. <source>Nature</source> <volume>404</volume>, <fpage>766</fpage>&#x2013;<lpage>770</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1038/35008089</pub-id>
</citation>
</ref>
<ref id="B41">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Liu</surname> <given-names>S.</given-names>
</name>
<name>
<surname>Liu</surname> <given-names>Y.</given-names>
</name>
<name>
<surname>Yang</surname> <given-names>X.</given-names>
</name>
<name>
<surname>Tong</surname> <given-names>C.</given-names>
</name>
<name>
<surname>Edwards</surname> <given-names>D.</given-names>
</name>
<name>
<surname>Parkin</surname> <given-names>I. A.</given-names>
</name>
<etal/>
</person-group>. (<year>2014</year>). <article-title>The brassica oleracea genome reveals the asymmetrical evolution of polyploid genomes</article-title>. <source>Nat. Commun.</source> <volume>5</volume>, <fpage>3930</fpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1038/ncomms4930</pub-id>
</citation>
</ref>
<ref id="B42">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Lu</surname> <given-names>S.</given-names>
</name>
<name>
<surname>Wang</surname> <given-names>J.</given-names>
</name>
<name>
<surname>Chitsaz</surname> <given-names>F.</given-names>
</name>
<name>
<surname>Derbyshire</surname> <given-names>M. K.</given-names>
</name>
<name>
<surname>Geer</surname> <given-names>R. C.</given-names>
</name>
<name>
<surname>Gonzales</surname> <given-names>N. R.</given-names>
</name>
<etal/>
</person-group>. (<year>2020</year>). <article-title>CDD/SPARCLE: the conserved domain database in 2020</article-title>. <source>Nucleic Acids Res.</source> <volume>48</volume>, <fpage>D265</fpage>&#x2013;<lpage>D268</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1093/nar/gkz991</pub-id>
</citation>
</ref>
<ref id="B43">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Ma</surname> <given-names>J.</given-names>
</name>
<name>
<surname>Yang</surname> <given-names>Y.</given-names>
</name>
<name>
<surname>Luo</surname> <given-names>W.</given-names>
</name>
<name>
<surname>Yang</surname> <given-names>C.</given-names>
</name>
<name>
<surname>Ding</surname> <given-names>P.</given-names>
</name>
<name>
<surname>Liu</surname> <given-names>Y.</given-names>
</name>
<etal/>
</person-group>. (<year>2017</year>). <article-title>Genome-wide identification and analysis of the MADS-box gene family in bread wheat (Triticum aestivum l.)</article-title>. <source>PLoS One</source> <volume>12</volume>, <elocation-id>e0181443</elocation-id>. doi:&#xa0;<pub-id pub-id-type="doi">10.1371/journal.pone.0181443</pub-id>
</citation>
</ref>
<ref id="B44">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Mun</surname> <given-names>J. H.</given-names>
</name>
<name>
<surname>Kwon</surname> <given-names>S. J.</given-names>
</name>
<name>
<surname>Seol</surname> <given-names>Y. J.</given-names>
</name>
<name>
<surname>Kim</surname> <given-names>J. A.</given-names>
</name>
<name>
<surname>Jin</surname> <given-names>M.</given-names>
</name>
<name>
<surname>Kim</surname> <given-names>J. S.</given-names>
</name>
<etal/>
</person-group>. (<year>2010</year>). <article-title>Sequence and structure of brassica rapa chromosome A3</article-title>. <source>Genome Biol.</source> <volume>11</volume>, <fpage>R94</fpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1186/gb-2010-11-9-r94</pub-id>
</citation>
</ref>
<ref id="B45">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Nagaharu</surname> <given-names>U.</given-names>
</name>
<name>
<surname>Nagaharu</surname> <given-names>N. J. J. J. B.</given-names>
</name>
</person-group> (<year>1935</year>). <article-title>Genome analysis in brassica with special reference to the experimental formation of b. napus and peculiar mode of fertilization</article-title>. <source>Jpn J. Bot.</source> <volume>7</volume>, <fpage>389</fpage>&#x2013;<lpage>452</lpage>.</citation>
</ref>
<ref id="B46">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Okada</surname> <given-names>K.</given-names>
</name>
<name>
<surname>Shimura</surname> <given-names>Y.</given-names>
</name>
</person-group> (<year>1994</year>). <article-title>Genetic analyses of signalling in flower development using arabidopsis</article-title>. <source>Plant Mol. Biol.</source> <volume>26</volume>, <fpage>1357</fpage>&#x2013;<lpage>1377</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1007/BF00016480</pub-id>
</citation>
</ref>
<ref id="B47">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Parenicova</surname> <given-names>L.</given-names>
</name>
<name>
<surname>de Folter</surname> <given-names>S.</given-names>
</name>
<name>
<surname>Kieffer</surname> <given-names>M.</given-names>
</name>
<name>
<surname>Horner</surname> <given-names>D. S.</given-names>
</name>
<name>
<surname>Favalli</surname> <given-names>C.</given-names>
</name>
<name>
<surname>Busscher</surname> <given-names>J.</given-names>
</name>
<etal/>
</person-group>. (<year>2003</year>). <article-title>Molecular and phylogenetic analyses of the complete MADS-box transcription factor family in arabidopsis: New openings to the MADS world</article-title>. <source>Plant Cell</source> <volume>15</volume>, <fpage>1538</fpage>&#x2013;<lpage>1551</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1105/tpc.011544</pub-id>
</citation>
</ref>
<ref id="B48">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Paritosh</surname> <given-names>K.</given-names>
</name>
<name>
<surname>Pradhan</surname> <given-names>A. K.</given-names>
</name>
<name>
<surname>Pental</surname> <given-names>D.</given-names>
</name>
</person-group> (<year>2020</year>). <article-title>A highly contiguous genome assembly of brassica nigra (BB) and revised nomenclature for the pseudochromosomes</article-title>. <source>BMC Genomics</source> <volume>21</volume>, <fpage>887</fpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1186/s12864-020-07271-w</pub-id>
</citation>
</ref>
<ref id="B49">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Paritosh</surname> <given-names>K.</given-names>
</name>
<name>
<surname>Yadava</surname> <given-names>S. K.</given-names>
</name>
<name>
<surname>Singh</surname> <given-names>P.</given-names>
</name>
<name>
<surname>Bhayana</surname> <given-names>L.</given-names>
</name>
<name>
<surname>Mukhopadhyay</surname> <given-names>A.</given-names>
</name>
<name>
<surname>Gupta</surname> <given-names>V.</given-names>
</name>
<etal/>
</person-group>. (<year>2021</year>). <article-title>A chromosome-scale assembly of allotetraploid brassica juncea (AABB) elucidates comparative architecture of the a and b genomes</article-title>. <source>Plant Biotechnol. J.</source> <volume>19</volume>, <fpage>602</fpage>&#x2013;<lpage>614</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1111/pbi.13492</pub-id>
</citation>
</ref>
<ref id="B50">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Parkin</surname> <given-names>I. A.</given-names>
</name>
<name>
<surname>Koh</surname> <given-names>C.</given-names>
</name>
<name>
<surname>Tang</surname> <given-names>H.</given-names>
</name>
<name>
<surname>Robinson</surname> <given-names>S. J.</given-names>
</name>
<name>
<surname>Kagale</surname> <given-names>S.</given-names>
</name>
<name>
<surname>Clarke</surname> <given-names>W. E.</given-names>
</name>
<etal/>
</person-group>. (<year>2014</year>). <article-title>Transcriptome and methylome profiling reveals relics of genome dominance in the mesopolyploid brassica oleracea</article-title>. <source>Genome Biol.</source> <volume>15</volume>, <fpage>R77</fpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1186/gb-2014-15-6-r77</pub-id>
</citation>
</ref>
<ref id="B51">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Paul</surname> <given-names>P.</given-names>
</name>
<name>
<surname>Joshi</surname> <given-names>S.</given-names>
</name>
<name>
<surname>Tian</surname> <given-names>R.</given-names>
</name>
<name>
<surname>Diogo Junior</surname> <given-names>R.</given-names>
</name>
<name>
<surname>Chakrabarti</surname> <given-names>M.</given-names>
</name>
<name>
<surname>Perry</surname> <given-names>S. E.</given-names>
</name>
</person-group> (<year>2022</year>). <article-title>The MADS-domain factor AGAMOUS-Like18 promotes somatic embryogenesis</article-title>. <source>Plant Physiol.</source> <volume>188</volume>, <fpage>1617</fpage>&#x2013;<lpage>1631</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1093/plphys/kiab553</pub-id>
</citation>
</ref>
<ref id="B52">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Perumal</surname> <given-names>S.</given-names>
</name>
<name>
<surname>Koh</surname> <given-names>C. S.</given-names>
</name>
<name>
<surname>Jin</surname> <given-names>L.</given-names>
</name>
<name>
<surname>Buchwaldt</surname> <given-names>M.</given-names>
</name>
<name>
<surname>Higgins</surname> <given-names>E. E.</given-names>
</name>
<name>
<surname>Zheng</surname> <given-names>C.</given-names>
</name>
<etal/>
</person-group>. (<year>2020</year>). <article-title>A high-contiguity brassica nigra genome localizes active centromeres and defines the ancestral brassica genome</article-title>. <source>Nat. Plants</source> <volume>6</volume>, <fpage>929</fpage>&#x2013;<lpage>941</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1038/s41477-020-0735-y</pub-id>
</citation>
</ref>
<ref id="B53">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Pinyopich</surname> <given-names>A.</given-names>
</name>
<name>
<surname>Ditta</surname> <given-names>G. S.</given-names>
</name>
<name>
<surname>Savidge</surname> <given-names>B.</given-names>
</name>
<name>
<surname>Liljegren</surname> <given-names>S. J.</given-names>
</name>
<name>
<surname>Baumann</surname> <given-names>E.</given-names>
</name>
<name>
<surname>Wisman</surname> <given-names>E.</given-names>
</name>
<etal/>
</person-group>. (<year>2003</year>). <article-title>Assessing the redundancy of MADS-box genes during carpel and ovule development</article-title>. <source>Nature</source> <volume>424</volume>, <fpage>85</fpage>&#x2013;<lpage>88</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1038/nature01741</pub-id>
</citation>
</ref>
<ref id="B54">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Price</surname> <given-names>M. N.</given-names>
</name>
<name>
<surname>Dehal</surname> <given-names>P. S.</given-names>
</name>
<name>
<surname>Arkin</surname> <given-names>A. P.</given-names>
</name>
</person-group> (<year>2009</year>). <article-title>FastTree: Computing large minimum evolution trees with profiles instead of a distance matrix</article-title>. <source>Mol. Biol. Evol.</source> <volume>26</volume>, <fpage>1641</fpage>&#x2013;<lpage>1650</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1093/molbev/msp077</pub-id>
</citation>
</ref>
<ref id="B55">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Riechmann</surname> <given-names>J. L.</given-names>
</name>
<name>
<surname>Meyerowitz</surname> <given-names>E. M.</given-names>
</name>
</person-group> (<year>1997</year>). <article-title>Determination of floral organ identity by arabidopsis MADS domain homeotic proteins AP1, AP3, PI, and AG is independent of their DNA-binding specificity</article-title>. <source>Mol. Biol. Cell</source> <volume>8</volume>, <fpage>1243</fpage>&#x2013;<lpage>1259</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1091/mbc.8.7.1243</pub-id>
</citation>
</ref>
<ref id="B56">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Schilling</surname> <given-names>S.</given-names>
</name>
<name>
<surname>Kennedy</surname> <given-names>A.</given-names>
</name>
<name>
<surname>Pan</surname> <given-names>S.</given-names>
</name>
<name>
<surname>Jermiin</surname> <given-names>L. S.</given-names>
</name>
<name>
<surname>Melzer</surname> <given-names>R.</given-names>
</name>
</person-group> (<year>2020</year>). <article-title>Genome-wide analysis of MIKC-type MADS-box genes in wheat: Pervasive duplications, functional conservation and putative neofunctionalization</article-title>. <source>New Phytol.</source> <volume>225</volume>, <fpage>511</fpage>&#x2013;<lpage>529</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1111/nph.16122</pub-id>
</citation>
</ref>
<ref id="B57">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Searle</surname> <given-names>I.</given-names>
</name>
<name>
<surname>He</surname> <given-names>Y.</given-names>
</name>
<name>
<surname>Turck</surname> <given-names>F.</given-names>
</name>
<name>
<surname>Vincent</surname> <given-names>C.</given-names>
</name>
<name>
<surname>Fornara</surname> <given-names>F.</given-names>
</name>
<name>
<surname>Krober</surname> <given-names>S.</given-names>
</name>
<etal/>
</person-group>. (<year>2006</year>). <article-title>The transcription factor FLC confers a flowering response to vernalization by repressing meristem competence and systemic signaling in arabidopsis</article-title>. <source>Genes Dev.</source> <volume>20</volume>, <fpage>898</fpage>&#x2013;<lpage>912</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1101/gad.373506</pub-id>
</citation>
</ref>
<ref id="B58">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Shao</surname> <given-names>Z.</given-names>
</name>
<name>
<surname>He</surname> <given-names>M.</given-names>
</name>
<name>
<surname>Zeng</surname> <given-names>Z.</given-names>
</name>
<name>
<surname>Chen</surname> <given-names>Y.</given-names>
</name>
<name>
<surname>Hanna</surname> <given-names>A. D.</given-names>
</name>
<name>
<surname>Zhu</surname> <given-names>H.</given-names>
</name>
</person-group> (<year>2021</year>). <article-title>Genome-wide identification and expression analysis of the MADS-box gene family in sweet potato [Ipomoea batatas (L.) lam]</article-title>. <source>Front. Genet.</source> <volume>12(1664-8021</volume> (<issue>1664-8021 (Print</issue>). doi:&#xa0;<pub-id pub-id-type="doi">10.3389/fgene.2021.750137</pub-id>
</citation>
</ref>
<ref id="B59">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Sheng</surname> <given-names>X. G.</given-names>
</name>
<name>
<surname>Zhao</surname> <given-names>Z. Q.</given-names>
</name>
<name>
<surname>Wang</surname> <given-names>J. S.</given-names>
</name>
<name>
<surname>Yu</surname> <given-names>H. F.</given-names>
</name>
<name>
<surname>Shen</surname> <given-names>Y. S.</given-names>
</name>
<name>
<surname>Zeng</surname> <given-names>X. Y.</given-names>
</name>
<etal/>
</person-group>. (<year>2019</year>). <article-title>Genome wide analysis of MADS-box gene family in brassica oleracea reveals conservation and variation in flower development</article-title>. <source>BMC Plant Biol.</source> <volume>19</volume>, <fpage>106</fpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1186/s12870-019-1717-y</pub-id>
</citation>
</ref>
<ref id="B60">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Silva</surname> <given-names>C. S.</given-names>
</name>
<name>
<surname>Puranik</surname> <given-names>S.</given-names>
</name>
<name>
<surname>Round</surname> <given-names>A.</given-names>
</name>
<name>
<surname>Brennich</surname> <given-names>M.</given-names>
</name>
<name>
<surname>Jourdain</surname> <given-names>A.</given-names>
</name>
<name>
<surname>Parcy</surname> <given-names>F.</given-names>
</name>
<etal/>
</person-group>. (<year>2015</year>). <article-title>Evolution of the plant reproduction master regulators LFY and the MADS transcription factors: The role of protein structure in the evolutionary development of the flower</article-title>. <source>Front. Plant Sci.</source> <volume>6</volume>. doi:&#xa0;<pub-id pub-id-type="doi">10.3389/fpls.2015.01193</pub-id>
</citation>
</ref>
<ref id="B61">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Song</surname> <given-names>J. M.</given-names>
</name>
<name>
<surname>Guan</surname> <given-names>Z.</given-names>
</name>
<name>
<surname>Hu</surname> <given-names>J.</given-names>
</name>
<name>
<surname>Guo</surname> <given-names>C.</given-names>
</name>
<name>
<surname>Yang</surname> <given-names>Z.</given-names>
</name>
<name>
<surname>Wang</surname> <given-names>S.</given-names>
</name>
<etal/>
</person-group>. (<year>2020</year>). <article-title>Eight high-quality genomes reveal pan-genome architecture and ecotype differentiation of brassica napus</article-title>. <source>Nat. Plants</source> <volume>6</volume>, <fpage>34</fpage>&#x2013;<lpage>45</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1038/s41477-019-0577-7</pub-id>
</citation>
</ref>
<ref id="B62">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Song</surname> <given-names>X.</given-names>
</name>
<name>
<surname>Wei</surname> <given-names>Y.</given-names>
</name>
<name>
<surname>Xiao</surname> <given-names>D.</given-names>
</name>
<name>
<surname>Gong</surname> <given-names>K.</given-names>
</name>
<name>
<surname>Sun</surname> <given-names>P.</given-names>
</name>
<name>
<surname>Ren</surname> <given-names>Y.</given-names>
</name>
<etal/>
</person-group>. (<year>2021</year>). <article-title>Brassica carinata genome characterization clarifies u's triangle model of evolution and polyploidy in brassica</article-title>. <source>Plant Physiol.</source> <volume>186</volume>, <fpage>388</fpage>&#x2013;<lpage>406</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1093/plphys/kiab048</pub-id>
</citation>
</ref>
<ref id="B63">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Sun</surname> <given-names>F. M.</given-names>
</name>
<name>
<surname>Fan</surname> <given-names>G. Y.</given-names>
</name>
<name>
<surname>Hu</surname> <given-names>Q.</given-names>
</name>
<name>
<surname>Zhou</surname> <given-names>Y. M.</given-names>
</name>
<name>
<surname>Guan</surname> <given-names>M.</given-names>
</name>
<name>
<surname>Tong</surname> <given-names>C. B.</given-names>
</name>
<etal/>
</person-group>. (<year>2017</year>). <article-title>The high-quality genome of brassica napus cultivar 'ZS11' reveals the introgression history in semi-winter morphotype</article-title>. <source>Plant J.</source> <volume>92</volume>, <fpage>452</fpage>&#x2013;<lpage>468</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1111/tpj.13669</pub-id>
</citation>
</ref>
<ref id="B64">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Theissen</surname> <given-names>G.</given-names>
</name>
<name>
<surname>Becker</surname> <given-names>A.</given-names>
</name>
<name>
<surname>Di Rosa</surname> <given-names>A.</given-names>
</name>
<name>
<surname>Kanno</surname> <given-names>A.</given-names>
</name>
<name>
<surname>Kim</surname> <given-names>J. T.</given-names>
</name>
<name>
<surname>Munster</surname> <given-names>T.</given-names>
</name>
<etal/>
</person-group>. (<year>2000</year>). <article-title>A short history of MADS-box genes in plants</article-title>. <source>Plant Mol. Biol.</source> <volume>42</volume>, <fpage>115</fpage>&#x2013;<lpage>149</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1023/A:1006332105728</pub-id>
</citation>
</ref>
<ref id="B65">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Tsutsui</surname> <given-names>H.</given-names>
</name>
<name>
<surname>Higashiyama</surname> <given-names>T.</given-names>
</name>
</person-group> (<year>2017</year>). <article-title>pKAMA-ITACHI vectors for highly efficient CRISPR/Cas9-mediated gene knockout in arabidopsis thaliana</article-title>. <source>Plant Cell Physiol.</source> <volume>58</volume>, <fpage>46</fpage>&#x2013;<lpage>56</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1093/pcp/pcw191</pub-id>
</citation>
</ref>
<ref id="B66">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Waadt</surname> <given-names>R.</given-names>
</name>
<name>
<surname>Seller</surname> <given-names>C. A.</given-names>
</name>
<name>
<surname>Hsu</surname> <given-names>P. K.</given-names>
</name>
<name>
<surname>Takahashi</surname> <given-names>Y.</given-names>
</name>
<name>
<surname>Munemasa</surname> <given-names>S.</given-names>
</name>
<name>
<surname>Schroeder</surname> <given-names>J. I.</given-names>
</name>
</person-group> (<year>2022</year>). <article-title>Plant hormone regulation of abiotic stress responses</article-title>. <source>Nat. Rev. Mol. Cell Biol.</source> <volume>23</volume>, <fpage>680</fpage>&#x2013;<lpage>694</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1038/s41580-022-00479-6</pub-id>
</citation>
</ref>
<ref id="B67">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Wang</surname> <given-names>X.</given-names>
</name>
<name>
<surname>Song</surname> <given-names>M.</given-names>
</name>
<name>
<surname>Flaishman</surname> <given-names>M. A.</given-names>
</name>
<name>
<surname>Chen</surname> <given-names>S.</given-names>
</name>
<name>
<surname>Ma</surname> <given-names>H.</given-names>
</name>
</person-group> (<year>2021</year>). <article-title>AGAMOUS gene as a new sex-identification marker in fig (Ficus carica l.) is more efficient than RAN1</article-title>. <source>Front. Plant Sci.</source> <volume>12(1664-462X</volume> (<issue>1664-462X (Print</issue>). doi:&#xa0;<pub-id pub-id-type="doi">10.3389/fpls.2021.755358</pub-id>
</citation>
</ref>
<ref id="B68">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Wang</surname> <given-names>Y.</given-names>
</name>
<name>
<surname>Tang</surname> <given-names>H.</given-names>
</name>
<name>
<surname>Debarry</surname> <given-names>J. D.</given-names>
</name>
<name>
<surname>Tan</surname> <given-names>X.</given-names>
</name>
<name>
<surname>Li</surname> <given-names>J.</given-names>
</name>
<name>
<surname>Wang</surname> <given-names>X.</given-names>
</name>
<etal/>
</person-group>. (<year>2012</year>). <article-title>MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity</article-title>. <source>Nucleic Acids Res.</source> <volume>40</volume>, <elocation-id>e49</elocation-id>. doi:&#xa0;<pub-id pub-id-type="doi">10.1093/nar/gkr1293</pub-id>
</citation>
</ref>
<ref id="B69">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Wang</surname> <given-names>X.</given-names>
</name>
<name>
<surname>Wang</surname> <given-names>H.</given-names>
</name>
<name>
<surname>Wang</surname> <given-names>J.</given-names>
</name>
<name>
<surname>Sun</surname> <given-names>R.</given-names>
</name>
<name>
<surname>Wu</surname> <given-names>J.</given-names>
</name>
<name>
<surname>Liu</surname> <given-names>S.</given-names>
</name>
<etal/>
</person-group>. (<year>2011</year>). <article-title>The genome of the mesopolyploid crop species brassica rapa</article-title>. <source>Nat. Genet.</source> <volume>43</volume>, <fpage>1035</fpage>&#x2013;<lpage>1039</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1038/ng.919</pub-id>
</citation>
</ref>
<ref id="B70">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Wang</surname> <given-names>Y.</given-names>
</name>
<name>
<surname>Zhang</surname> <given-names>J.</given-names>
</name>
<name>
<surname>Hu</surname> <given-names>Z.</given-names>
</name>
<name>
<surname>Guo</surname> <given-names>X.</given-names>
</name>
<name>
<surname>Tian</surname> <given-names>S.</given-names>
</name>
<name>
<surname>Chen</surname> <given-names>G.</given-names>
</name>
</person-group> (<year>2019</year>). <article-title>Genome-wide analysis of the MADS-box transcription factor family in solanum lycopersicum</article-title>. <source>Int. J. Mol. Sci.</source> <volume>20</volume>, <fpage>2961</fpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.3390/ijms20122961</pub-id>
</citation>
</ref>
<ref id="B71">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Woodhouse</surname> <given-names>M. R.</given-names>
</name>
<name>
<surname>Cheng</surname> <given-names>F.</given-names>
</name>
<name>
<surname>Pires</surname> <given-names>J. C.</given-names>
</name>
<name>
<surname>Lisch</surname> <given-names>D.</given-names>
</name>
<name>
<surname>Freeling</surname> <given-names>M.</given-names>
</name>
<name>
<surname>Wang</surname> <given-names>X.</given-names>
</name>
</person-group> (<year>2014</year>). <article-title>Origin, inheritance, and gene regulatory consequences of genome dominance in polyploids</article-title>. <source>Proc. Natl. Acad. Sci. U.S.A.</source> <volume>111</volume>, <fpage>5283</fpage>&#x2013;<lpage>5288</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1073/pnas.1402475111</pub-id>
</citation>
</ref>
<ref id="B72">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Wu</surname> <given-names>Y.</given-names>
</name>
<name>
<surname>Ke</surname> <given-names>Y.</given-names>
</name>
<name>
<surname>Wen</surname> <given-names>J.</given-names>
</name>
<name>
<surname>Guo</surname> <given-names>P.</given-names>
</name>
<name>
<surname>Ran</surname> <given-names>F.</given-names>
</name>
<name>
<surname>Wang</surname> <given-names>M.</given-names>
</name>
<etal/>
</person-group>. (<year>2018</year>). <article-title>Evolution and expression analyses of the MADS-box gene family in brassica napus</article-title>. <source>PLoS One</source> <volume>13</volume>, <elocation-id>e0200762</elocation-id>. doi:&#xa0;<pub-id pub-id-type="doi">10.1371/journal.pone.0200762</pub-id>
</citation>
</ref>
<ref id="B73">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Xing</surname> <given-names>H. L.</given-names>
</name>
<name>
<surname>Dong</surname> <given-names>L.</given-names>
</name>
<name>
<surname>Wang</surname> <given-names>Z. P.</given-names>
</name>
<name>
<surname>Zhang</surname> <given-names>H. Y.</given-names>
</name>
<name>
<surname>Han</surname> <given-names>C. Y.</given-names>
</name>
<name>
<surname>Liu</surname> <given-names>B.</given-names>
</name>
<etal/>
</person-group>. (<year>2014</year>). <article-title>A CRISPR/Cas9 toolkit for multiplex genome editing in plants</article-title>. <source>BMC Plant Biol.</source> <volume>14</volume>, <elocation-id>327</elocation-id>. doi:&#xa0;<pub-id pub-id-type="doi">10.1186/s12870-014-0327-y</pub-id>
</citation>
</ref>
<ref id="B74">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Yang</surname> <given-names>Y.</given-names>
</name>
<name>
<surname>Jack</surname> <given-names>T.</given-names>
</name>
</person-group> (<year>2004</year>). <article-title>Defining subdomains of the K domain important for protein-protein interactions of plant MADS proteins</article-title>. <source>Plant Mol. Biol.</source> <volume>55</volume>, <fpage>45</fpage>&#x2013;<lpage>59</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1007/s11103-004-0416-7</pub-id>
</citation>
</ref>
<ref id="B75">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Yang</surname> <given-names>J.</given-names>
</name>
<name>
<surname>Liu</surname> <given-names>D.</given-names>
</name>
<name>
<surname>Wang</surname> <given-names>X.</given-names>
</name>
<name>
<surname>Ji</surname> <given-names>C.</given-names>
</name>
<name>
<surname>Cheng</surname> <given-names>F.</given-names>
</name>
<name>
<surname>Liu</surname> <given-names>B.</given-names>
</name>
<etal/>
</person-group>. (<year>2016</year>). <article-title>The genome sequence of allopolyploid brassica juncea and analysis of differential homoeolog gene expression influencing selection</article-title>. <source>Nat. Genet.</source> <volume>48</volume>, <fpage>1225</fpage>&#x2013;<lpage>1232</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1038/ng.3657</pub-id>
</citation>
</ref>
<ref id="B76">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Yanofsky</surname> <given-names>M. F.</given-names>
</name>
<name>
<surname>Ma</surname> <given-names>H.</given-names>
</name>
<name>
<surname>Bowman</surname> <given-names>J. L.</given-names>
</name>
<name>
<surname>Drews</surname> <given-names>G. N.</given-names>
</name>
<name>
<surname>Feldmann</surname> <given-names>K. A.</given-names>
</name>
<name>
<surname>Meyerowitz</surname> <given-names>E. M.</given-names>
</name>
</person-group> (<year>1990</year>). <article-title>The protein encoded by the arabidopsis homeotic gene agamous resembles transcription factors</article-title>. <source>Nature</source> <volume>346</volume>, <fpage>35</fpage>&#x2013;<lpage>39</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1038/346035a0</pub-id>
</citation>
</ref>
<ref id="B77">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Yim</surname> <given-names>W. C.</given-names>
</name>
<name>
<surname>Swain</surname> <given-names>M. L.</given-names>
</name>
<name>
<surname>Ma</surname> <given-names>D.</given-names>
</name>
<name>
<surname>An</surname> <given-names>H.</given-names>
</name>
<name>
<surname>Bird</surname> <given-names>K. A.</given-names>
</name>
<name>
<surname>Curdie</surname> <given-names>D. D.</given-names>
</name>
<etal/>
</person-group>. (<year>2022</year>). <article-title>The final piece of the triangle of U: Evolution of the tetraploid brassica carinata genome</article-title>. <source>Plant Cell</source>. <volume>34</volume>, <page-range>4143&#x2013;4172</page-range>. doi:&#xa0;<pub-id pub-id-type="doi">10.1093/plcell/koac249</pub-id>
</citation>
</ref>
<ref id="B78">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Yu</surname> <given-names>L. H.</given-names>
</name>
<name>
<surname>Miao</surname> <given-names>Z. Q.</given-names>
</name>
<name>
<surname>Qi</surname> <given-names>G. F.</given-names>
</name>
<name>
<surname>Wu</surname> <given-names>J.</given-names>
</name>
<name>
<surname>Cai</surname> <given-names>X. T.</given-names>
</name>
<name>
<surname>Mao</surname> <given-names>J. L.</given-names>
</name>
<etal/>
</person-group>. (<year>2014</year>). <article-title>MADS-box transcription factor AGL21 regulates lateral root development and responds to multiple external and physiological signals</article-title>. <source>Mol. Plant</source> <volume>7</volume>, <fpage>1653</fpage>&#x2013;<lpage>1669</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1093/mp/ssu088</pub-id>
</citation>
</ref>
<ref id="B79">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Zahn</surname> <given-names>L. M.</given-names>
</name>
<name>
<surname>Feng</surname> <given-names>B. M.</given-names>
</name>
<name>
<surname>Ma</surname> <given-names>H.</given-names>
</name>
</person-group> (<year>2006</year>). <article-title>Beyond the ABC-model: Regulation of floral homeotic genes</article-title>. <source>Adv. Botanical Research: Incorporating Adv. Plant Pathol.</source> <volume>44</volume>, <fpage>163</fpage>&#x2013;<lpage>207</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1016/S0065-2296(06)44004-0</pub-id>
</citation>
</ref>
<ref id="B80">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Zhang</surname> <given-names>L.</given-names>
</name>
<name>
<surname>Cai</surname> <given-names>X.</given-names>
</name>
<name>
<surname>Wu</surname> <given-names>J.</given-names>
</name>
<name>
<surname>Liu</surname> <given-names>M.</given-names>
</name>
<name>
<surname>Grob</surname> <given-names>S.</given-names>
</name>
<name>
<surname>Cheng</surname> <given-names>F.</given-names>
</name>
<etal/>
</person-group>. (<year>2018</year>). <article-title>Improved brassica rapa reference genome by single-molecule sequencing and chromosome conformation capture technologies</article-title>. <source>Hortic. Res.</source> <volume>5(2662-6810</volume> (<issue>2662-6810 (Print</issue>), <fpage>50</fpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1038/s41438-018-0071-9</pub-id>
</citation>
</ref>
<ref id="B81">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Zhang</surname> <given-names>H.</given-names>
</name>
<name>
<surname>Gao</surname> <given-names>S.</given-names>
</name>
<name>
<surname>Lercher</surname> <given-names>M. J.</given-names>
</name>
<name>
<surname>Hu</surname> <given-names>S.</given-names>
</name>
<name>
<surname>Chen</surname> <given-names>W. H.</given-names>
</name>
</person-group> (<year>2012</year>). <article-title>EvolView, an online tool for visualizing, annotating and managing phylogenetic trees</article-title>. <source>Nucleic Acids Res.</source> <volume>40</volume> (<issue>Web Server issue</issue>), <fpage>W569</fpage>&#x2013;<lpage>W572</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1093/nar/gks576</pub-id>
</citation>
</ref>
<ref id="B82">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Zhang</surname> <given-names>Z.</given-names>
</name>
<name>
<surname>Guo</surname> <given-names>J.</given-names>
</name>
<name>
<surname>Cai</surname> <given-names>X.</given-names>
</name>
<name>
<surname>Li</surname> <given-names>Y.</given-names>
</name>
<name>
<surname>Xi</surname> <given-names>X.</given-names>
</name>
<name>
<surname>Lin</surname> <given-names>R.</given-names>
</name>
<etal/>
</person-group>. (<year>2022</year>). <article-title>Improved reference genome annotation of brassica rapa by pacific biosciences RNA sequencing</article-title>. <source>Front. Plant Sci.</source> <volume>13(1664-462X</volume> (<issue>1664-462X (Print</issue>). doi:&#xa0;<pub-id pub-id-type="doi">10.3389/fpls.2022.841618</pub-id>
</citation>
</ref>
<ref id="B83">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Zhang</surname> <given-names>X.</given-names>
</name>
<name>
<surname>Wang</surname> <given-names>G.</given-names>
</name>
<name>
<surname>Zhang</surname> <given-names>S.</given-names>
</name>
<name>
<surname>Chen</surname> <given-names>S.</given-names>
</name>
<name>
<surname>Wang</surname> <given-names>Y.</given-names>
</name>
<name>
<surname>Wen</surname> <given-names>P.</given-names>
</name>
<etal/>
</person-group>. (<year>2020</year>). <article-title>Genomes of the banyan tree and pollinator wasp provide insights into fig-wasp coevolution</article-title>. <source>Cell</source> <volume>183</volume>, <fpage>875</fpage>&#x2013;<lpage>889.e817</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1016/j.cell.2020.09.043</pub-id>
</citation>
</ref>
<ref id="B84">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Zhao</surname> <given-names>D.</given-names>
</name>
<name>
<surname>Chen</surname> <given-names>Z.</given-names>
</name>
<name>
<surname>Xu</surname> <given-names>L.</given-names>
</name>
<name>
<surname>Zhang</surname> <given-names>L.</given-names>
</name>
<name>
<surname>Zou</surname> <given-names>Q.</given-names>
</name>
</person-group> (<year>2021</year>a). <article-title>Genome-wide analysis of the MADS-box gene family in maize: Gene structure, evolution, and relationships</article-title>. <source>Genes (Basel)</source> <volume>12</volume>, <elocation-id>1956</elocation-id>. doi:&#xa0;<pub-id pub-id-type="doi">10.3390/genes12121956</pub-id>
</citation>
</ref>
<ref id="B85">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Zhao</surname> <given-names>P. X.</given-names>
</name>
<name>
<surname>Miao</surname> <given-names>Z. Q.</given-names>
</name>
<name>
<surname>Zhang</surname> <given-names>J.</given-names>
</name>
<name>
<surname>Chen</surname> <given-names>S. Y.</given-names>
</name>
<name>
<surname>Liu</surname> <given-names>Q. Q.</given-names>
</name>
<name>
<surname>Xiang</surname> <given-names>C. B.</given-names>
</name>
</person-group> (<year>2020</year>). <article-title>Arabidopsis MADS-box factor AGL16 negatively regulates drought resistance <italic>via</italic> stomatal density and stomatal movement</article-title>. <source>J. Exp. Bot.</source> <volume>71</volume>, <fpage>6092</fpage>&#x2013;<lpage>6106</lpage>. doi:&#xa0;<pub-id pub-id-type="doi">10.1093/jxb/eraa303</pub-id>
</citation>
</ref>
<ref id="B86">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Zhao</surname> <given-names>W.</given-names>
</name>
<name>
<surname>Zhang</surname> <given-names>L. L.</given-names>
</name>
<name>
<surname>Xu</surname> <given-names>Z. S.</given-names>
</name>
<name>
<surname>Fu</surname> <given-names>L.</given-names>
</name>
<name>
<surname>Pang</surname> <given-names>H. X.</given-names>
</name>
<name>
<surname>Ma</surname> <given-names>Y. Z.</given-names>
</name>
<etal/>
</person-group>. (<year>2021</year>b). <article-title>Genome-wide analysis of MADS-box genes in foxtail millet (Setaria italica l.) and functional assessment of the role of SiMADS51 in the drought stress response</article-title>. <source>Front. Plant Sci.</source> <volume>12</volume>. doi:&#xa0;<pub-id pub-id-type="doi">10.3389/fpls.2021.659474</pub-id>
</citation>
</ref>
<ref id="B87">
<citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname>Zhou</surname> <given-names>E.</given-names>
</name>
<name>
<surname>Zhang</surname> <given-names>Y.</given-names>
</name>
<name>
<surname>Wang</surname> <given-names>H.</given-names>
</name>
<name>
<surname>Jia</surname> <given-names>Z.</given-names>
</name>
<name>
<surname>Wang</surname> <given-names>X.</given-names>
</name>
<name>
<surname>Wen</surname> <given-names>J.</given-names>
</name>
<etal/>
</person-group>. (<year>2022</year>). <article-title>Identification and characterization of the MIKC-type MADS-box gene family in brassica napus and its role in floral transition</article-title>. <source>Int. J. Mol. Sci.</source> <volume>23</volume>, <elocation-id>4289</elocation-id>. doi:&#xa0;<pub-id pub-id-type="doi">10.3390/ijms23084289</pub-id>
</citation>
</ref>
</ref-list>
</back>
</article>