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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>
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<article-meta>
<article-id pub-id-type="doi">10.3389/fpls.2023.1272951</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>Inhibition of ethylene involved in resistance to <italic>E. turcicum</italic> in an exotic-derived double haploid maize population</article-title>
</title-group>
<contrib-group>
<contrib contrib-type="author">
<name>
<surname>Lipps</surname>
<given-names>Sarah</given-names>
</name>
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<role content-type="https://credit.niso.org/contributor-roles/methodology/"/>
<role content-type="https://credit.niso.org/contributor-roles/validation/"/>
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</contrib>
<contrib contrib-type="author">
<name>
<surname>Lipka</surname>
<given-names>Alexander E.</given-names>
</name>
<uri xlink:href="https://loop.frontiersin.org/people/448829"/>
<role content-type="https://credit.niso.org/contributor-roles/methodology/"/>
<role content-type="https://credit.niso.org/contributor-roles/validation/"/>
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</contrib>
<contrib contrib-type="author">
<name>
<surname>Mideros</surname>
<given-names>Santiago</given-names>
</name>
<uri xlink:href="https://loop.frontiersin.org/people/1253090"/>
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<contrib contrib-type="author" corresp="yes">
<name>
<surname>Jamann</surname>
<given-names>Tiffany</given-names>
</name>
<xref ref-type="author-notes" rid="fn001">
<sup>*</sup>
</xref>
<uri xlink:href="https://loop.frontiersin.org/people/883352"/>
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</contrib-group>
<aff id="aff1">
<institution>Department of Crop Sciences, University of Illinois</institution>, <addr-line>Urbana, IL</addr-line>, <country>United States</country>
</aff>
<author-notes>
<fn fn-type="edited-by">
<p>Edited by: Kun Zhang, Yangzhou University, China</p>
</fn>
<fn fn-type="edited-by">
<p>Reviewed by: Houxiang Kang, Chinese Academy of Agricultural Sciences (CAAS), China; Qin Yang, Northwest A&amp;F University, China</p>
</fn>
<fn fn-type="corresp" id="fn001">
<p>*Correspondence: Tiffany Jamann, <email xlink:href="mailto:tjamann@illinois.edu">tjamann@illinois.edu</email>
</p>
</fn>
</author-notes>
<pub-date pub-type="epub">
<day>06</day>
<month>10</month>
<year>2023</year>
</pub-date>
<pub-date pub-type="collection">
<year>2023</year>
</pub-date>
<volume>14</volume>
<elocation-id>1272951</elocation-id>
<history>
<date date-type="received">
<day>04</day>
<month>08</month>
<year>2023</year>
</date>
<date date-type="accepted">
<day>19</day>
<month>09</month>
<year>2023</year>
</date>
</history>
<permissions>
<copyright-statement>Copyright &#xa9; 2023 Lipps, Lipka, Mideros and Jamann</copyright-statement>
<copyright-year>2023</copyright-year>
<copyright-holder>Lipps, Lipka, Mideros and Jamann</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>Northern corn leaf blight (NCLB) is an economically important disease of maize. While the genetic architecture of NCLB has been well characterized, the pathogen is known to overcome currently deployed resistance genes, and the role of hormones in resistance to NCLB is an area of active research. The objectives of the study were (i) to identify significant markers associated with resistance to NCLB, (ii) to identify metabolic pathways associated with NCLB resistance, and (iii) to examine role of ethylene in resistance to NCLB. We screened 252 lines from the exotic-derived double haploid BGEM maize population for resistance to NCLB in both field and greenhouse environments. We used a genome wide association study (GWAS) and stepwise regression to identify four markers associated with resistance, followed by a pathway association study tool (PAST) to identify important metabolic pathways associated with disease severity and incubation period. The ethylene synthesis pathway was significant for disease severity and incubation period. We conducted a greenhouse assay in which we inhibited ethylene to examine the role of ethylene in resistance to NCLB. We observed a significant increase in incubation period and a significant decrease in disease severity between plants treated with the ethylene inhibitor and mock-treated plants. Our study confirms the potential of the BGEM population as a source of novel alleles for resistance. We also confirm the role of ethylene in resistance to NCLB and contribute to the growing body of literature on ethylene and disease resistance in monocots.</p>
</abstract>
<kwd-group>
<kwd>
<italic>Exserohilum turcicum</italic>
</kwd>
<kwd>maize</kwd>
<kwd>BGEM</kwd>
<kwd>ethylene</kwd>
<kwd>disease resistance</kwd>
<kwd>quantitative disease resistance</kwd>
<kwd>GWAS</kwd>
</kwd-group>
<contract-sponsor id="cn001">U.S. Department of Energy<named-content content-type="fundref-id">10.13039/100000015</named-content>
</contract-sponsor>
<counts>
<fig-count count="4"/>
<table-count count="8"/>
<equation-count count="2"/>
<ref-count count="79"/>
<page-count count="16"/>
<word-count count="9496"/>
</counts>
<custom-meta-wrap>
<custom-meta>
<meta-name>section-in-acceptance</meta-name>
<meta-value>Plant Pathogen Interactions</meta-value>
</custom-meta>
</custom-meta-wrap>
</article-meta>
</front>
<body>
<sec id="s1" sec-type="intro">
<label>1</label>
<title>Introduction</title>
<p>Northern corn leaf blight (NCLB), caused by the fungus <italic>Exserohilum turcicum</italic> (Pass.) K. J. Leonard and Suggs [syn<italic>. Setosphaeria turcica</italic> (Luttr.) K. J. Leonard and Suggs.], is one of the most important diseases of maize. <italic>E. turcicum</italic> is well-adapted to most maize growing regions in the world and causes yield losses globally (<xref ref-type="bibr" rid="B48">Savary et&#xa0;al., 2019</xref>). Over 7.62 million metric tons (300 million bushels) have been lost due to NCLB between 2016 and 2019 in the United States and Ontario, Canada (<xref ref-type="bibr" rid="B32">Mueller et&#xa0;al., 2020</xref>). The cost of economic losses due to damage from NCLB was estimated in one study examining hybrids with a range of resistance levels to be from $122.00 ha<sup>-1</sup> to $353.20 ha<sup>-1</sup> in fields managed for optimized yield (<xref ref-type="bibr" rid="B11">De Rossi et&#xa0;al., 2022</xref>). Furthermore, <italic>E. turcicum</italic> has a high evolutionary potential, as the fungus has high genetic variability and undergoes sexual reproduction in the field. Thus, there is the potential for widespread loss of resistance to <italic>E. turcicum</italic> (<xref ref-type="bibr" rid="B30">McDonald and Linde, 2002</xref>; <xref ref-type="bibr" rid="B15">Galiano-Carneiro and Miedaner, 2017</xref>; <xref ref-type="bibr" rid="B35">Munoz-Zavala et&#xa0;al., 2023</xref>).</p>
<p>The disease cycle and pathogenesis process of <italic>E. turcicum</italic> have been well characterized (<xref ref-type="bibr" rid="B26">Kotze et&#xa0;al., 2019</xref>; <xref ref-type="bibr" rid="B36">Navarro et&#xa0;al., 2020</xref>). <italic>E. turcicum</italic> is a hemibiotroph with a biotrophic and a necrotrophic phase. The fungus overwinters as mycelia in crop residue. Conidia are spread to the host by wind and rain. In the biotrophic phase, an appressorium-like structure is formed, and the fungus penetrates the cuticle, grows through the mesophyll, then colonizes the xylem (<xref ref-type="bibr" rid="B36">Navarro et&#xa0;al., 2020</xref>). The necrotrophic phase of the disease cycle begins when the fungus exits the xylem and colonizes the mesophyll, resulting in cell death. Eventually, <italic>E. turcicum</italic> forms conidiophores resulting in polycyclic disease over the course of the growing season (<xref ref-type="bibr" rid="B26">Kotze et&#xa0;al., 2019</xref>; <xref ref-type="bibr" rid="B36">Navarro et&#xa0;al., 2020</xref>). The first symptoms of infection are tan flecks that develop into tan-grey ovular lesions. The most severe epiphytotics are observed when disease symptoms occur before flowering time and in warm, humid environments (<xref ref-type="bibr" rid="B55">Ullstrup and Miles, 1957</xref>; <xref ref-type="bibr" rid="B42">Raymundo and Hooker, 1981a</xref>; <xref ref-type="bibr" rid="B38">Perkins and Pedersen, 1987</xref>).</p>
<p>An integrated NCLB management program includes host resistance, fungicides, and cultural methods. Host resistance is an important management technique as it does not increase the cost of production and does not harm the environment (<xref ref-type="bibr" rid="B15">Galiano-Carneiro and Miedaner, 2017</xref>). Both qualitative resistance, conferred by a single gene, and quantitative resistance, conferred by multiple genes, have been characterized in maize. Qualitative resistance genes effective for managing <italic>E. turcicum</italic> include <italic>Ht1, Ht2, Ht3</italic>, and <italic>HtN1</italic> (<xref ref-type="bibr" rid="B64">Welz and Geiger, 2000</xref>; <xref ref-type="bibr" rid="B21">Hurni et&#xa0;al., 2015</xref>; <xref ref-type="bibr" rid="B15">Galiano-Carneiro and Miedaner, 2017</xref>). <italic>Ht2, Ht3</italic>, and <italic>HtN1</italic> are allelic and encode a wall-associated protein kinase (<xref ref-type="bibr" rid="B21">Hurni et&#xa0;al., 2015</xref>; <xref ref-type="bibr" rid="B72">Yang et&#xa0;al., 2021</xref>). <italic>Ht1</italic> encodes a nucleotide-binding leucine-rich repeat receptor, <italic>PH4GP- Ht1</italic> (<xref ref-type="bibr" rid="B53">Thatcher et&#xa0;al., 2022</xref>). In this pathosystem, the qualitative genes do not confer complete resistance, but instead delay the onset of symptoms after initial infection and or dramatically reduce the severity of symptoms.</p>
<p>Many quantitative trait loci (QTL) effective against NCLB have been identified in maize (<xref ref-type="bibr" rid="B67">Wisser et&#xa0;al., 2006</xref>). A recent meta-analysis evaluating 110 studies identified chromosomes 10, 6, 5, 1, and 2 as having the highest odds of contributing a major-effect QTL for resistance to fungal and viral diseases, with chromosome 10 have the highest likelihood and chromosome 2 having the lowest likelihood (<xref ref-type="bibr" rid="B46">Rossi et&#xa0;al., 2019</xref>). In addition to regions associated with resistance, progress has been made on identifying potential quantitative resistance mechanisms to <italic>E. turcicum.</italic> Receptor-like kinases (RLKs) have been implicated in resistance to NCLB and other diseases. Three FERONIA-like receptors (FLRs), a type of RLK, have been identified as conferring resistance to multiple fungal foliar diseases, including NCLB (<xref ref-type="bibr" rid="B73">Yu et&#xa0;al., 2022</xref>). Originally <italic>pan1</italic>, an RLK, was implicated in increasing susceptibility to <italic>E. turcicum</italic>, as well as <italic>Pantoea stewartii</italic>, in maize on bin 1.06 (<xref ref-type="bibr" rid="B23">Jamann et&#xa0;al., 2014</xref>). However, a recent study revealed that <italic>pan1</italic> is not responsible for the altered resistance but potentially an aldo-ketoreductase is responsible instead (<xref ref-type="bibr" rid="B12">Doblas-Ib&#xe1;&#xf1;ez et&#xa0;al., 2019</xref>). Additionally, a remorin gene, <italic>ZmREM6.3</italic>, on bin 1.02 was implicated in resistance to <italic>E. turcicum, P. stewartii</italic> and <italic>Puccinia sorghi</italic> (<xref ref-type="bibr" rid="B22">Jamann et&#xa0;al., 2016</xref>). Recently, a transcription repressor, <italic>ZmMM1</italic>, was cloned in maize from teosinte, and found to confer a lesion mimic phenotype, as well as resistance to NCLB and other fungal diseases (<xref ref-type="bibr" rid="B60">Wang et&#xa0;al., 2021</xref>). Other biochemical processes, such as the production of phenylpropanoids, have also been implicated as mechanisms of resistance. In bin 9.02, a maize caffeoyl-CoA <italic>O-</italic>methyltransferase encoded by <italic>ZmCCoAOMT2</italic>, is involved in the production of phenylpropanoids and lignin and is associated with resistance to multiple diseases (<xref ref-type="bibr" rid="B71">Yang et&#xa0;al., 2017</xref>). The recent advances in understanding NCLB have elucidated both regions associated with and mechanism of resistance.</p>
<p>The role of hormones in pathogen defense has been reviewed (<xref ref-type="bibr" rid="B16">Glazebrook, 2005</xref>; <xref ref-type="bibr" rid="B45">Robert-Seilaniantz et&#xa0;al., 2011</xref>; <xref ref-type="bibr" rid="B10">Denance et&#xa0;al., 2013</xref>). Three hormone pathways have been well discussed regarding their overlapping roles in abiotic and biotic stress: salicylic acid (SA), jasmonates (JA), and ethylene (ET). In Arabidopsis, SA is typically associated with biotrophic pathogens, and JA and ET are associated with necrotrophic pathogens (<xref ref-type="bibr" rid="B16">Glazebrook, 2005</xref>). Resistance to biotrophic and necrotrophic pathogens has been thought of as antagonistic, meaning that heightened resistance to biotrophic pathogens is typically associated with increased susceptibility to necrotrophic pathogens (<xref ref-type="bibr" rid="B45">Robert-Seilaniantz et&#xa0;al., 2011</xref>). However, the relationship between phytohormones and pathogen resistance is complex. Some fungi are able to mimic phytohormones or produce effectors that interfere with <italic>in planta</italic> hormone signaling (<xref ref-type="bibr" rid="B10">Denance et&#xa0;al., 2013</xref>). Additionally, pathogens are able to disrupt the balance of active hormones by targeting the regulatory aspects of hormonal pathways or inducing <italic>in planta</italic> hormone production (<xref ref-type="bibr" rid="B45">Robert-Seilaniantz et&#xa0;al., 2011</xref>).</p>
<p>The role of ethylene in disease resistance is complex. Ethylene is produced <italic>in planta</italic> in response to abiotic or biotic stress, which can be sensed by receptors located in the endoplasmic reticulum (<xref ref-type="bibr" rid="B33">Muller and Munne-Bosch, 2015</xref>). The ethylene pathway was first characterized in horticultural crops. It is synthesized from methionine which is converted into S-adenosyl-L-methionine (SAM) by SAM synthase. SAM is converted to 1-aminocyclopropane-1-carboxylate (ACC) via ACC synthase (ACS), and ACC is finally converted to ethylene via ACC oxidase (ACO) (<xref ref-type="bibr" rid="B70">Yang, 1985</xref>; <xref ref-type="bibr" rid="B69">Xu and Zhang, 2015</xref>). When activated, ethylene response factors link ethylene sensing and the activation of pathogen related genes (<xref ref-type="bibr" rid="B20">Huang et&#xa0;al., 2016</xref>).</p>
<p>The role of ethylene in plant-pathogen interactions has been extensively studied in dicots. However, several recent studies have focused on the role of ethylene in resistance against necrotrophic pathogens in maize. In maize, there are five known ACS genes and 13 ACO gene family members (<xref ref-type="bibr" rid="B37">Park et&#xa0;al., 2021</xref>). In kernels treated with <italic>Fusarium verticillioides</italic>, it was found that several ethylene production genes were induced upon infection, and ethylene production was associated with disease progression (<xref ref-type="bibr" rid="B37">Park et&#xa0;al., 2021</xref>). A similar trend was found in kernels inoculated with <italic>Aspergillus flavus</italic>, where ethylene production encouraged fungal conidiation and sporulation (<xref ref-type="bibr" rid="B61">Wang et&#xa0;al., 2017</xref>). Additionally, an ethylene signaling gene, <italic>ZmEIN2</italic>, regulated the abundance of metabolites associated with resistance to <italic>Fusarium graminearum</italic> in maize seedlings (<xref ref-type="bibr" rid="B79">Zhou et&#xa0;al., 2019</xref>). The bulk of research regarding ethylene in maize-pathogen interactions has focused on necrotrophic pathogens. Less is known about the role of hormone signaling and resistance to <italic>E. turicucm</italic>, a hemibiotrophic plant pathogen. Recently, an ethylene response factor, <italic>ZmERF061</italic>, was implicated in resistance against <italic>E. turcicum</italic> in maize (<xref ref-type="bibr" rid="B74">Zang et&#xa0;al., 2020</xref>; <xref ref-type="bibr" rid="B75">Zang et&#xa0;al., 2021</xref>). The plant&#x2019;s ability to sense and respond to ethylene is likely important in defense against hemibiotrophic pathogens like <italic>E. turcicum</italic>, but this hypothesis needs further investigation.</p>
<p>Recent research shows that pathogens are increasing in complexity. In the case of <italic>E. turcicum</italic>, this increased complexity enables certain strains to overcome multiple, and occasionally, all available qualitative disease resistance genes (<xref ref-type="bibr" rid="B62">Weems and Bradley, 2018</xref>; <xref ref-type="bibr" rid="B25">Jindal et&#xa0;al., 2019</xref>; <xref ref-type="bibr" rid="B34">Mu&#xf1;oz-Zavala et&#xa0;al., 2022</xref>). The emergence of novel physiological races of <italic>E. turcicum</italic> requires further development and utilization of host resistance to effectively manage NCLB (<xref ref-type="bibr" rid="B34">Mu&#xf1;oz-Zavala et&#xa0;al., 2022</xref>). The endemic region of <italic>E. turcicum</italic> has expanded due to global warming; thus, it is likely that NCLB prevalence and severity are increasing in regions where it was previously a less common disease (<xref ref-type="bibr" rid="B31">Miedaner and Juroszek, 2021</xref>). With the increased complexity and ability of <italic>E. turicucm</italic> to overcome resistance in maize, it is imperative to continue identifying novel sources of resistance in maize. One effective approach to discover novel resistance alleles is by screening exotic-derived materials to identify previously unknown sources of resistance.</p>
<p>The germplasm enhancement of maize (GEM) program was established in 1995 to increase allelic diversity in temperate maize through the release of exotic-derived germplasm (<xref ref-type="bibr" rid="B40">Pollak and Salhuana, 2001</xref>). The BGEM population is an exotic-derived double haploid (DH) population developed by Iowa State University in collaboration with the GEM program (<xref ref-type="bibr" rid="B6">Brenner et&#xa0;al., 2012</xref>). In total, the BGEM population is derived from 67 landraces originating from 13 different countries (<xref ref-type="bibr" rid="B47">Sanchez et&#xa0;al., 2018</xref>). The BGEM population has previously been evaluated for flowering traits, kernel quality, and root architecture (<xref ref-type="bibr" rid="B47">Sanchez et&#xa0;al., 2018</xref>; <xref ref-type="bibr" rid="B57">Vanous et&#xa0;al., 2018</xref>; <xref ref-type="bibr" rid="B58">Vanous et&#xa0;al., 2019</xref>). We selected the BGEM population for this study as it is adapted to temperate climates and is a source of novel alleles not currently present in midwestern United States commercial germplasm.</p>
<p>The goals of this study were to (i) identify markers associated with resistance to NCLB in the BGEM population, (ii) identify potential metabolic pathways associated with resistance, and (iii) confirm the role of <italic>in planta</italic> ethylene production in NCLB resistance. We hypothesized that allelic diversity in the BGEM population would confer a range of resistance responses sufficient for genetic mapping when challenged with <italic>E. turcicum.</italic> Subsequently, we used the pathway association study tool (<xref ref-type="bibr" rid="B54">Thrash et&#xa0;al., 2020</xref>) to identify metabolic pathways associated with resistance. We confirmed the role of ethylene in the <italic>E. turcicum-</italic>maize pathosystem in the greenhouse by evaluating resistance responses of plants after treatment with AgNO<sub>3</sub>, a chemical which limits <italic>in planta</italic> ethylene action (<xref ref-type="bibr" rid="B4">Beyer, 1976</xref>; <xref ref-type="bibr" rid="B27">Kumar et&#xa0;al., 2009</xref>). Our results provide additional insight into the role of phytohormones and resistance to NCLB.</p>
</sec>
<sec id="s2" sec-type="materials|methods">
<label>2</label>
<title>Materials and methods</title>
<sec id="s2_1">
<label>2.1</label>
<title>Germplasm</title>
<p>The BGEM population is a BC<sub>1</sub>F<sub>1</sub> exotic-derived DH population. The population was developed at Iowa State University in collaboration with the USDA-ARS Germplasm Enhancement of Maize project (<xref ref-type="bibr" rid="B40">Pollak and Salhuana, 2001</xref>). Briefly, BC<sub>1</sub>F<sub>1</sub> lines were created by crossing exotic accessions to one of two expired Plant Variety Protection (PVP) lines, namely PHZ51 or PHB47, backcrossing the resulting F<sub>1</sub> accessions were backcrossed to their respective ex-PVP parent, and then DH lines were created and self-pollinated (<xref ref-type="bibr" rid="B6">Brenner et&#xa0;al., 2012</xref>). Any lines that were infertile, lacked uniformity, or with poor agronomic traits were discarded. Genetically, the BGEM population is comprised of roughly 25% donor parent and 75% recurrent parent (<xref ref-type="bibr" rid="B47">Sanchez et&#xa0;al., 2018</xref>). The BGEM population represents a broad diversity of exotic derived maize. In total 67 landraces from 13 different countries are represented (<xref ref-type="bibr" rid="B47">Sanchez et&#xa0;al., 2018</xref>).</p>
</sec>
<sec id="s2_2">
<label>2.2</label>
<title>Experimental design</title>
<p>The BGEM population was screened for resistance to <italic>E. turcicum</italic> in three environments from 2019 to 2021. In total, all lines were evaluated four times in the field between 2019 and 2021 and twice in the greenhouse in 2020. All experiments were designed as augmented randomized incomplete block designs using the <italic>agricolae</italic> package (<xref ref-type="bibr" rid="B9">de Mendiburu, 2021</xref>) in the statistical software R, version 3.6.0 (<xref ref-type="bibr" rid="B41">R Core Team, 2021</xref>). Lines from BGEM population were screened at the Crop Sciences Research and Education Centers in Urbana, IL in 2019 (n = 252) and 2021 (n = 240). Differences in the number of lines used in 2019 and the other years were due to seed availability. Field plots were planted in rows that were 3.65 m long with 0.91 m alleys. The 2019 field was irrigated to encourage disease development. Lines were replicated twice in 2019 and 2021. In 2019, incomplete blocks (n = 14) were augmented with Oh7B and NC344 as susceptible and resistant checks, respectively. In 2021, Oh7B, NC344, PHB47, and PHZ51 served as check lines in each incomplete block (n = 16). In 2021 the following NCLB differential lines were included in each replication: A619-<italic>Ht1</italic>, A619-<italic>Ht2</italic>, A619-<italic>Ht3</italic>, A619, B37-<italic>HtN1</italic>, and B37.</p>
<p>In 2020, BGEM lines (n=240) were screened at the Plant Care Facility in Urbana, IL. The 2020 greenhouse experiment was replicated twice with 13 incomplete blocks in each replication. Due to space constraints, replications had to be run separately. One plant per line was grown in a one-gallon pot filled with 1:1:1 general purpose potting mix. Greenhouse conditions were set to 12/12 hr. light-dark cycle. Ambient temperatures were set to 24-28&#xb0;C during the day and 20-22&#xb0;C during the night. Lines were organized in an augmented randomized incomplete block design. Oh7B and NC344 were susceptible and resistant check lines in each block. PHB47 and PHZ51 were randomized once in each replication. The same qualitative check lines used in 2021 were also used in the greenhouse in each replication.</p>
</sec>
<sec id="s2_3">
<label>2.3</label>
<title>Inoculation and phenotyping</title>
<p>In 2019 natural inoculum was relied upon for infection, as the growing season was conducive for disease development and evaluation. For all other experiments, inoculum was prepared using five fungal isolates (19StM06, 19StM07, 19StM09, 19StM11, 19StM12) that were isolated from diseased maize tissue collected from the 2019 field experiment at Crop Science Research and Education Center in Urbana, IL. A mixture of isolates was used to best reproduce disease pressure observed in 2019. For the 2020 greenhouse experiment, plants were inoculated with a spore suspension at the V3 stage (<xref ref-type="bibr" rid="B1">Adhikari et&#xa0;al., 2021</xref>). Fungal isolates were grown on lactose-casein hydrolysate agar (LCA) media for 14 days under 12/12 hr light/dark photoperiod at room temperature. Spores were harvested from 14-day old plates and the concentration adjusted to 4 &#xd7; 10<sup>3</sup> spores/mL in a 0.02% Tween 20 solution. For inoculations, 0.5 mL of the spore suspension was pipetted into the whorl of the plants. Following inoculation, plants were maintained in high humidity conditions for 24 hours to facilitate disease development. In 2021 plants were inoculated at the V4 to V5 stage using infested sorghum grains (<xref ref-type="bibr" rid="B77">Zhang et&#xa0;al., 2020</xref>). Fungal isolates were cultured on LCA for 14 days as described above. After 14 days of culturing, agar pieces cut directly from the plates were added to mushroom bags containing 1000 mL of soaked, autoclaved sorghum grains. The mushroom bags were cultured for two to three weeks at room temperature under 12/12 hr light/dark photoperiod. The infested grains were examined under a dissecting microscope to confirm the presence of conidia then dried and stored at room temperature. Each plant was inoculated with 1.3 g of the prepared inoculum in the whorl at the V3 growth stage.</p>
<p>Disease ratings for the 2019 and 2021 field experiments were taken on a whole plot basis using a 0-100% scale in 5% increments (<xref ref-type="bibr" rid="B39">Poland and Nelson, 2011</xref>) where no disease present was represented by 0%, and a rating of 100% indicated that the total leaf area of the plants was necrotic due to disease. In 2019 two field ratings were taken after lines had started flowering, and ratings were taken 7 days apart. In 2021 a total of four field ratings were taken. Ratings were conducted every 7-14 days starting two weeks before the onset of flowering in the earliest maturing plants.</p>
<p>Lines in the 2020 greenhouse experiment were evaluated for incubation period and disease severity. Incubation period is defined as the number of days after inoculation (DAI) that the first lesions were visible. Lines were evaluated for incubation period every 48 hours until all plants showed lesions. In the greenhouse experiment, a total of four diseased leaf area ratings were taken. Disease leaf area ratings were taken every 7-14 days starting the day when all plants had lesions present. Lines were rated on a single leaf per plant basis using the same 0-100% rating scale mentioned above.</p>
</sec>
<sec id="s2_4">
<label>2.4</label>
<title>Statistical analyses</title>
<p>Disease severity data was examined using the standardized area under the disease progress curve (sAUDPC). sAUDPC is used to compare disease progression between environments or experiments (<xref ref-type="bibr" rid="B50">Simko and Piepho, 2012</xref>). sAUDPC is calculated by first measuring the area under the disease progress curve (AUDPC), which is the area of a trapezoid between two or more time points on a progression curve and accounts for disease severity over time (<xref ref-type="bibr" rid="B24">Jeger and Viljanen-Rollinson, 2001</xref>; <xref ref-type="bibr" rid="B29">Madden et&#xa0;al., 2007</xref>). The sAUDPC value is then obtained by dividing AUDPC by the weighted total of the number of days of disease evaluation. sAUDPC was calculated using the R package <italic>agricolae</italic> (<xref ref-type="bibr" rid="B9">de Mendiburu, 2021</xref>). Both days to anthesis (DTA) and days to silking (DTS) were recorded for the 2019 field experiment. DTA is defined as the number of days after planting when 50% or more of the plot had visible anthers on the tassel. DTS is defined as the number of days after planting when 50% or more of the plot had visible silks emerging from the ears. Pearson correlation coefficients for sAUDPC across all environments were calculated using the <italic>rcorr()</italic> function in the R package <italic>Hmisc</italic> v4.5-0 (<xref ref-type="bibr" rid="B18">Harrell, 2021</xref>). Flowering data was only collected in 2019. Using AUDPC, DTS, and DTA data from 2019, Pearson correlation coefficients were calculated between each trait.</p>
<p>Both sAUDPC and incubation period values were used to fit mixed models and estimate least squared means (LS Means). The following model was fit to estimate LS Means for sAUDPC in the 2019 + 2021 dataset:</p>
<disp-formula>
<mml:math display="block" id="M1">
<mml:mrow>
<mml:msub>
<mml:mtext mathvariant="bold-italic">Y</mml:mtext>
<mml:mrow>
<mml:mtext mathvariant="bold-italic">ijkl</mml:mtext>
</mml:mrow>
</mml:msub>
<mml:mo>=</mml:mo>
<mml:mo>&#xa0;</mml:mo>
<mml:mo>&#xb5;</mml:mo>
<mml:mo>+</mml:mo>
<mml:mtext>&#xa0;</mml:mtext>
<mml:msub>
<mml:mrow>
<mml:mtext>&#xa0;</mml:mtext>
</mml:mrow>
<mml:mtext mathvariant="bold-italic">Gi</mml:mtext>
</mml:msub>
<mml:mo>+</mml:mo>
<mml:mtext>&#xa0;</mml:mtext>
<mml:msub>
<mml:mrow>
<mml:mtext>&#xa0;</mml:mtext>
</mml:mrow>
<mml:mtext mathvariant="bold-italic">Rj</mml:mtext>
</mml:msub>
<mml:mo>+</mml:mo>
<mml:mo>&#xa0;</mml:mo>
<mml:msub>
<mml:mtext mathvariant="bold-italic">B</mml:mtext>
<mml:mrow>
<mml:mtext mathvariant="bold-italic">l</mml:mtext>
<mml:mrow>
<mml:mo stretchy="false" mathvariant="bold">(</mml:mo>
<mml:mrow>
<mml:mtext mathvariant="bold-italic">j</mml:mtext>
<mml:mrow>
<mml:mo stretchy="false" mathvariant="bold">(</mml:mo>
<mml:mtext mathvariant="bold-italic">k</mml:mtext>
<mml:mo stretchy="false" mathvariant="bold">)</mml:mo>
</mml:mrow>
</mml:mrow>
<mml:mo stretchy="false" mathvariant="bold">)</mml:mo>
</mml:mrow>
</mml:mrow>
</mml:msub>
<mml:mo>+</mml:mo>
<mml:mo>&#xa0;</mml:mo>
<mml:msub>
<mml:mtext mathvariant="bold-italic">E</mml:mtext>
<mml:mtext mathvariant="bold-italic">l</mml:mtext>
</mml:msub>
<mml:mo>+</mml:mo>
<mml:mtext mathvariant="bold-italic">G</mml:mtext>
<mml:msub>
<mml:mtext mathvariant="bold-italic">E</mml:mtext>
<mml:mrow>
<mml:mtext mathvariant="bold-italic">il</mml:mtext>
</mml:mrow>
</mml:msub>
<mml:mo>+</mml:mo>
<mml:msub>
<mml:mtext mathvariant="bold-italic">&#x3b5;</mml:mtext>
<mml:mrow>
<mml:mtext mathvariant="bold-italic">ijkl</mml:mtext>
</mml:mrow>
</mml:msub>
</mml:mrow>
</mml:math>
</disp-formula>
<p>The factors are defined as follows: <italic>Y<sub>ijkl</sub>
</italic> is the sAUDPC value from genotype <italic>i</italic> in replicate <italic>j</italic> in block <italic>k</italic> and environment <italic>l</italic>; <italic>G<sub>i</sub>
</italic> is the fixed effect of genotype <italic>I</italic>; <italic>R<sub>j</sub>
</italic> is the random effect of replicate <italic>j</italic>; <italic>B<sub>k(j)</sub>
</italic> is the random effect of block <italic>k</italic> nested in replicate <italic>j</italic> nested in environment <italic>l</italic>; <italic>E<sub>l</sub>
</italic> the random effect of the environment <italic>l; GE<sub>il</sub>
</italic> the random effect of the interaction between genotype <italic>i</italic> and environment <italic>l</italic>; and <italic>&#x3b5;<sub>ijkl</sub>
</italic> the error term. From this model, LS Means were calculated from the estimates of G<sub>i</sub> from the fitted model. For the 2020 incubation period dataset the following mixed model was fit:</p>
<disp-formula>
<mml:math display="block" id="M2">
<mml:mrow>
<mml:msub>
<mml:mtext mathvariant="bold-italic">Y</mml:mtext>
<mml:mrow>
<mml:mtext mathvariant="bold-italic">ij</mml:mtext>
</mml:mrow>
</mml:msub>
<mml:mo>=</mml:mo>
<mml:mo>&#xa0;</mml:mo>
<mml:mo>&#xb5;</mml:mo>
<mml:mo>+</mml:mo>
<mml:mo>&#xa0;</mml:mo>
<mml:msub>
<mml:mtext mathvariant="bold-italic">G</mml:mtext>
<mml:mtext mathvariant="bold-italic">i</mml:mtext>
</mml:msub>
<mml:mo>+</mml:mo>
<mml:mo>&#xa0;</mml:mo>
<mml:msub>
<mml:mtext mathvariant="bold-italic">B</mml:mtext>
<mml:mtext mathvariant="bold-italic">j</mml:mtext>
</mml:msub>
<mml:mo>+</mml:mo>
<mml:mo>&#xa0;</mml:mo>
<mml:msub>
<mml:mtext mathvariant="bold-italic">&#x3b5;</mml:mtext>
<mml:mrow>
<mml:mtext mathvariant="bold-italic">ij</mml:mtext>
</mml:mrow>
</mml:msub>
</mml:mrow>
</mml:math>
</disp-formula>
<p>Terms in the model are described as follows <italic>Y<sub>ij</sub>
</italic> is the incubation period value in days of genotype <italic>i</italic> in block <italic>j</italic>; <italic>G<sub>i</sub>
</italic> is the fixed effect of genotype <italic>i</italic>; <italic>B<sub>j</sub>
</italic> is the random effect of block <italic>j</italic>; and &#x3b5;<sub>ij</sub> the error term associated with <italic>Y<sub>ij</sub>.</italic> The fixed effects for genotype in each model were extracted and used for further analysis. As with the previous model, LS Means were calculated from the estimates of G<sub>i</sub> from the fitted model.</p>
</sec>
<sec id="s2_5">
<label>2.5</label>
<title>Genotyping</title>
<p>The BGEM population was previously genotyped (<xref ref-type="bibr" rid="B47">Sanchez et&#xa0;al., 2018</xref>). A dataset consisting of 62,077 single nucleotide polymorphisms (SNPs) was obtained from Sanchez, Liu (<xref ref-type="bibr" rid="B47">Sanchez et&#xa0;al., 2018</xref>). This dataset was generated for the DH BGEM lines via genotyping-by-sequencing (<xref ref-type="bibr" rid="B14">Elshire et&#xa0;al., 2011</xref>) by the Cornell University Genomic Diversity Facility with data analysis by the Buckler Lab for Maize Genetics and Diversity. The 62,077 SNP dataset was generated by filtering SNPs with a large amounts of missing data and low allele frequencies, followed by SNPs in the same genetic position (<xref ref-type="bibr" rid="B47">Sanchez et&#xa0;al., 2018</xref>). Within the BGEM population, the average number of recombination events was higher than expected. A Bayes theorem described by Sanchez, Liu (<xref ref-type="bibr" rid="B47">Sanchez et&#xa0;al., 2018</xref>) was implemented to correct for monomorphic markers that were flanked by markers with donor parent genotypes. After correction, the number of recombination events was reduced, and the donor genome composition was closer to 25%, as expected. All edits to the genotypic dataset were conducted prior to this study.</p>
</sec>
<sec id="s2_6">
<label>2.6</label>
<title>Identification of markers associated with disease resistance</title>
<p>To identify candidate regions associated with resistance to <italic>E. turcicum</italic> two mapping strategies were employed using TASSEL v5.2.81 (<xref ref-type="bibr" rid="B5">Bradbury et&#xa0;al., 2007</xref>). First, we used a generalized linear model (GLM) in TASSEL to identify significant markers, as well as a stepwise regression approach to identify markers that were associated with disease severity and incubation period. The Bayesian corrected genotypic dataset was filtered to remove markers with a minor allele frequency less than 0.05. Two principal components, calculated in TASSEL using the standard PCA plugin, were used to control for population structure. The phenotypic datasets used were the LS Means estimated using the 2019 + 2021 combined disease severity and the 2020 incubation period datasets (<xref ref-type="supplementary-material" rid="SM1">
<bold>File S1</bold>
</xref>). The same genotypic dataset was used for both phenotypes. The GLM model was ran for both phenotypes with 1000 permutations. A significance threshold of &#x3b1; = 0.10 was applied using permutation corrected <italic>p</italic>-values. For the second approach, stepwise regression was implemented in TASSEL independently of the GLM association analysis. The two principal components calculated in TASSEL were included as numeric covariates along with the estimated LS Means value for each line. The stepwise regression analysis was implemented for both the 2019 + 2021 combined disease severity and the 2020 incubation period datasets. The <italic>p</italic>-value model was used with 1000 permutations with entry and exit limits of 1 &#xd7; 10<sup>-5</sup> and 2 &#xd7; 10<sup>-5</sup>, respectively. A significance threshold of &#x3b1; = 0.10 was used to identify significant SNPs.</p>
</sec>
<sec id="s2_7">
<label>2.7</label>
<title>Pathways Association Study Tool</title>
<p>The Pathway Association Study Tool (PAST) approach (<xref ref-type="bibr" rid="B54">Thrash et&#xa0;al., 2020</xref>) was implemented via the MaizeGDB online platform (<xref ref-type="bibr" rid="B68">Woodhouse et&#xa0;al., 2021</xref>). PAST is designed to take outputs generated by TASSEL and provide biological insight into association study results. The software interprets the results from association analysis to identify metabolic pathways associated with genes that are strongly associated with the trait through significant markers or when genes are moderately associated with a trait, but the markers themselves may not have been significant in the original association study. PAST uses the output from association analysis, allelic effects files, and a linkage disequilibrium file to assign SNPs to genes based on LD and genomic distance between SNPs and genes before then identifying significant metabolic pathways. PAST analysis was conducted for the 2019 + 2021 combined disease severity dataset and the 2020 incubation period dataset. The association and effect files generated from the GLM were used as the input for the PAST analysis. A gene assignment window size of 1000 base pairs was used. Pathways with at least five genes were considered and significance was determined based on 1000 permutations. A Type I error rate of &#x3b1; = 0.05 was used to determine statistical significance for each pathway.</p>
</sec>
<sec id="s2_8">
<label>2.8</label>
<title>Differentially expressed genes associated with ethylene</title>
<p>A recent study examined differences in gene expression in maize and sorghum plants inoculated with different strains of <italic>E. turicum</italic> (<xref ref-type="bibr" rid="B1">Adhikari et&#xa0;al., 2021</xref>) (<xref ref-type="supplementary-material" rid="SM1">
<bold>File S2</bold>
</xref>). Our hypothesis was that genes involved in the synthesis of ethylene were differentially expressed in mock-inoculated maize plants versus <italic>E. turcicum</italic> inoculated maize plants. A list of genes associated with ethylene biosynthesis was downloaded from CornCyc7.5 available through the MaizeGDB (<ext-link ext-link-type="uri" xlink:href="corncyc-b73-v3.maizegdb.org">corncyc-b73-v3.maizegdb.org</ext-link>) (<xref ref-type="supplementary-material" rid="SM1">
<bold>File S3</bold>
</xref>).</p>
<p>Transcriptome data were generated by <xref ref-type="bibr" rid="B1">Adhikari et&#xa0;al. (2021)</xref>. Briefly the maize line B73 was grown in the greenhouse and either inoculated with <italic>E. turcicum</italic> or mock inoculated with sterile deionized H<sub>2</sub>O (DI H<sub>2</sub>O). RNA was extracted from plant tissue collected at 24 and 72 hours after inoculation (hai) and sequenced at the Roy J. Carver Biotechnology Center at the University of Illinois at Urbana-Champaign. Quality control, alignment, and normalization were conducted using standard procedures (<xref ref-type="bibr" rid="B1">Adhikari et&#xa0;al., 2021</xref>). We used the final dataset with annotated differentially expressed genes (DEGs) and calculated false discovery rates (FDR) (<xref ref-type="bibr" rid="B1">Adhikari et&#xa0;al., 2021</xref>). (<xref ref-type="supplementary-material" rid="SM1">
<bold>File S2</bold>
</xref>). Global FDR adjusted p-values were calculated based on the Benjamini &amp; Hochberg procedure (<xref ref-type="bibr" rid="B3">Benjamini and Hochberg, 1995</xref>).</p>
<p>Our objective with the RNA data was to examine the expression of genes associated with ethylene biosynthesis in maize during the <italic>E. turcicum</italic> infection stage. Therefore, we are interested in three contrasts: DEG of maize 24 and 72 hai with <italic>E. turcicum</italic>, DEG of maize 24 hai with <italic>E. turcicum</italic> and DI H<sub>2</sub>O, and DEG of maize 72 hai with <italic>E. turcicum</italic> and DI H<sub>2</sub>O. Using a list of known genes involved in ethylene biosynthesis (<xref ref-type="supplementary-material" rid="SM1">
<bold>File S3</bold>
</xref>), we filtered the normalized list of DEGs for those only involved in ethylene biosynthesis. Then, for each contrast we only examined DEGs with an FDR value greater than or equal to 0.05. We hypothesized that ethylene biosynthesis could be involved in maize early defense against <italic>E. turcicum</italic>.</p>
</sec>
<sec id="s2_9">
<label>2.9</label>
<title>Greenhouse ethylene assay</title>
<p>A subset of DH lines was chosen to evaluate the role of ethylene in resistance against <italic>E. turcicum.</italic> In maize, ethylene is inhibited by the foliar application of AgNO<sub>3</sub> (<xref ref-type="bibr" rid="B27">Kumar et&#xa0;al., 2009</xref>). Using LS Means data from the 2021 field experiment, we examined disease phenotypes within exotic donor families. Only the ex-PVP recurrent parents have been genotyped, and there is no genotypic information for the landrace donor parents. We chose a resistant and susceptible line, as we wanted to see if inhibiting ethylene affected phenotypes of resistant or susceptible lines differently (<xref ref-type="table" rid="T1">
<bold>Table&#xa0;1</bold>
</xref>). We selected pairs of lines categorized as resistant or susceptible within five exotic landrace groups. Both ex-PVP recurrent parents, PHB47 and PHZ51, were included in the assay. Our goal was to assess the role of ethylene between resistant and susceptible lines, within different exotic families, and within different recurrent parent backgrounds.</p>
<table-wrap id="T1" position="float">
<label>Table&#xa0;1</label>
<caption>
<p>Lines selected to evaluate the role of ethylene in resistance against <italic>E. turcicum</italic>.</p>
</caption>
<table frame="hsides">
<thead>
<tr>
<th valign="middle" align="center">Line</th>
<th valign="middle" align="left">Landrace</th>
<th valign="middle" align="left">RP<sup>*</sup>
</th>
<th valign="middle" align="left">Pedigree</th>
<th valign="middle" align="left">R/S<sup>^</sup>
</th>
</tr>
</thead>
<tbody>
<tr>
<td valign="middle" align="center">BGEM-0078-S</td>
<td valign="middle" align="left">Cristalino Amarillo</td>
<td valign="middle" align="left">PHB47</td>
<td valign="middle" align="left">(CRISTALINO AMAR AR21004/PHB47 #001-(2n)-002</td>
<td valign="middle" align="center">R</td>
</tr>
<tr>
<td valign="middle" align="center">BGEM-0079-S</td>
<td valign="middle" align="left">Cristalino Amarillo</td>
<td valign="middle" align="left">PHB47</td>
<td valign="middle" align="left">(CRISTALINO AMAR AR21004/PHB47 #005-(2n)-003</td>
<td valign="middle" align="center">S</td>
</tr>
<tr>
<td valign="middle" align="center">BGEM-0087-N</td>
<td valign="middle" align="left">Dulcillo del Noroeste</td>
<td valign="middle" align="left">PHZ51</td>
<td valign="middle" align="left">(DULCILLO DE NO SON57/PHZ51)/PHZ51 #001-(2n)-001-001-B</td>
<td valign="middle" align="center">R</td>
</tr>
<tr>
<td valign="middle" align="center">BGEM-0088-N</td>
<td valign="middle" align="left">Dulcillo del Noroeste</td>
<td valign="middle" align="left">PHZ51</td>
<td valign="middle" align="left">(DULCILLO DE NO SON57/PHZ51)/PHZ51 #002-(2n)-002</td>
<td valign="middle" align="center">S</td>
</tr>
<tr>
<td valign="middle" align="center">BGEM-0108-S</td>
<td valign="middle" align="left">Elotes Occident</td>
<td valign="middle" align="left">PHZ51</td>
<td valign="middle" align="left">(ELOTES OCCIDENT NAY29/PHB47)/PHB47 #002-(2n)-001-001-B</td>
<td valign="middle" align="center">R</td>
</tr>
<tr>
<td valign="middle" align="center">BGEM-0109-N</td>
<td valign="middle" align="left">Elotes Occident</td>
<td valign="middle" align="left">PHZ51</td>
<td valign="middle" align="left">(ELOTES OCCIDENT DGO236/PHZ51)/PHZ51 #004-(2n)-002-002-B</td>
<td valign="middle" align="center">S</td>
</tr>
<tr>
<td valign="middle" align="center">BGEM-0120-N</td>
<td valign="middle" align="left">Jora</td>
<td valign="middle" align="left">PHZ51</td>
<td valign="middle" align="left">((Jora - ANC 1/PHZ61 B)/PHZ51)-(2n)-001-001-B</td>
<td valign="middle" align="center">R</td>
</tr>
<tr>
<td valign="middle" align="center">BGEM-0121-N</td>
<td valign="middle" align="left">Jora</td>
<td valign="middle" align="left">PHZ51</td>
<td valign="middle" align="left">((Jora - ANC 1/PHZ61 B)/PHZ51)-(2n)-002-001-B</td>
<td valign="middle" align="center">S</td>
</tr>
<tr>
<td valign="middle" align="center">BGEM-0162-S</td>
<td valign="middle" align="left">Morado</td>
<td valign="middle" align="left">PHB47</td>
<td valign="middle" align="left">(MORADO BOV567/PHB47)/PHB47 #002-(2n)-001</td>
<td valign="middle" align="center">R</td>
</tr>
<tr>
<td valign="middle" align="center">BGEM-0167-S</td>
<td valign="middle" align="left">Morado</td>
<td valign="middle" align="left">PHB47</td>
<td valign="middle" align="left">(MORADO BOV567/PHB47)/PHB47 #005-(2n)-003</td>
<td valign="middle" align="center">S</td>
</tr>
<tr>
<td valign="middle" align="center">PHB47</td>
<td valign="middle" align="center">-</td>
<td valign="middle" align="center">-</td>
<td valign="middle" align="center">-</td>
<td valign="middle" align="center">R</td>
</tr>
<tr>
<td valign="middle" align="center">PHZ51</td>
<td valign="middle" align="center">-</td>
<td valign="middle" align="center">-</td>
<td valign="middle" align="center">-</td>
<td valign="middle" align="center">R</td>
</tr>
</tbody>
</table>
<table-wrap-foot>
<fn>
<p>
<sup>*</sup>RP, recurrent parent.</p>
</fn>
<fn>
<p>
<sup>^</sup>R/S, Resistant/Susceptible.</p>
</fn>
<fn>
<p>Lines were selected in pairs from five exotic landrace groups based on phenotype to see if exotic landrace background influenced ethylene production and if inhibiting ethylene influenced the phenotypes of resistant and susceptible lines differently. Both recurrent parents, PHZ51 and PHB47, were included in the experiment.</p>
</fn>
</table-wrap-foot>
</table-wrap>
<p>The experiment was arranged in a split-plot design. The whole-plot was a complete block of plants, and the subplot was each BGEM line randomly assigned to each treatment within each complete block. Lines were either treated with AgNO<sub>3</sub> followed by inoculation with <italic>E. turcicum</italic>, or treated with DI H<sub>2</sub>O followed by inoculation with <italic>E. turcicum</italic>. There were three whole-plots (complete blocks) per treatment and each line occurred once in each whole-plot. Greenhouse growing conditions were the same as the conditions described previously. The <italic>E. turcicum</italic> spore suspension was prepared as explained above. At the V3 growth stage, plants were treated with either 20 mM AgNO<sub>3</sub> in 0.001% Tween 20 (<xref ref-type="bibr" rid="B61">Wang et&#xa0;al., 2017</xref>) or with sterile water in 0.001% Tween 20 at a rate of 187 L ha<sup>-1</sup> at 207 kPa using a spray chamber (Technical Machinery Inc., Sacramento, CA). The chamber was equipped with an even flat-fan nozzle 8002E (TeeJet Technologies, Wheaton, IL) and plants were sprayed 45 cm above the tallest leaf. After treatment, plants were allowed to dry completely before inoculation with 4 &#xd7; 10<sup>3</sup> spores/mL in a 0.02% Tween 20 solution prepared as mentioned previously. Plants were inoculated by pipetting 0.5 mL of spore suspension into the whorl. After inoculation, a high-humidity environment was maintained overnight to encourage disease development. All plants were evaluated for incubation period and disease severity on a per plant basis as described previously. AUDPC was calculated using the <italic>agricolae</italic> package (<xref ref-type="bibr" rid="B9">de Mendiburu, 2021</xref>) in the statistical software R, version 3.6.0 (<xref ref-type="bibr" rid="B41">R Core Team, 2021</xref>). We ran an ANOVA to appropriately account for the differences in the whole-plots and the subplot replicates.</p>
</sec>
</sec>
<sec id="s3" sec-type="results">
<label>3</label>
<title>Results</title>
<sec id="s3_1">
<label>3.1</label>
<title>Characterization of the BGEM population</title>
<p>The BGEM population was evaluated for DTA and DTS in 2019 and for resistance to <italic>E. turcicum</italic> in 2019 and 2021 in the field at the Crop Sciences Research and Education Center in Urbana, IL. A field trial of the BGEM population was lost during the 2020 growing season due to poor emergence, followed by a hailstorm, which destroyed the field. Thus, the BGEM population was grown a second time and evaluated for resistance in the greenhouse in 2020 at the Plant Care Facility in Urbana, IL. All checklines performed as expected. In the 2019 and 2021 field environments, Oh7B was more susceptible than NC344. The BGEM recurrent parents, PHB47 and PHZ51, were moderately resistant in the 2021 field season with PHZ51 being the more resistant recurrent parent. The observed range of phenotypes suggest that there was sufficient disease pressure in each experiment to evaluate for disease severity and incubation period, even in the uninoculated field trial (<xref ref-type="table" rid="T2">
<bold>Table&#xa0;2</bold>
</xref>).</p>
<table-wrap id="T2" position="float">
<label>Table&#xa0;2</label>
<caption>
<p>Variation for standardized AUDPC (sAUDPC), incubation period (IP), days to anthesis (DTA) and days to silk (DTS) in each environment the BGEM population was screened in.</p>
</caption>
<table frame="hsides">
<thead>
<tr>
<th valign="top" align="left">Environment</th>
<th valign="top" align="left">Trait</th>
<th valign="top" align="left">Minimum</th>
<th valign="top" align="left">Maximum</th>
<th valign="top" align="left">Mean</th>
</tr>
</thead>
<tbody>
<tr>
<td valign="top" align="left">2019 Field</td>
<td valign="top" align="left">sAUDPC<sup>*</sup>
</td>
<td valign="top" align="left">17.50</td>
<td valign="top" align="left">87.50</td>
<td valign="top" align="left">42.59</td>
</tr>
<tr>
<td valign="top" align="left">2021 Field</td>
<td valign="top" align="left">sAUDPC<sup>*</sup>
</td>
<td valign="top" align="left">8.07</td>
<td valign="top" align="left">49.43</td>
<td valign="top" align="left">27.62</td>
</tr>
<tr>
<td valign="top" align="left">2020 GH</td>
<td valign="top" align="left">IP<sup>^</sup>
</td>
<td valign="top" align="left">5</td>
<td valign="top" align="left">19</td>
<td valign="top" align="left">10</td>
</tr>
<tr>
<td valign="top" align="left">2019 Field</td>
<td valign="top" align="left">DTA<sup>#</sup>
</td>
<td valign="top" align="left">61</td>
<td valign="top" align="left">84</td>
<td valign="top" align="left">69</td>
</tr>
<tr>
<td valign="top" align="left">2019 Field</td>
<td valign="top" align="left">DTS<sup>+</sup>
</td>
<td valign="top" align="left">63</td>
<td valign="top" align="left">84</td>
<td valign="top" align="left">71</td>
</tr>
</tbody>
</table>
<table-wrap-foot>
<fn>
<p>
<sup>*</sup>sAUDPC, standardized area under the disease progress curve.</p>
</fn>
<fn>
<p>
<sup>^</sup>IP, incubation period, the number of days from inoculation to the appearance of first lesions.</p>
</fn>
<fn>
<p>#DTA, days to anthesis, the number of days after planting until 50% of the plot has visible anthers.</p>
</fn>
<fn>
<p>
<sup>+</sup>DTS, days to silking, the number of days after planting until 50% of the plot has visible silks.</p>
</fn>
</table-wrap-foot>
</table-wrap>
<p>Due to the high evolutionary potential of <italic>E. turcicum</italic>, we examined whether isolates collected from Champaign County could overcome major genes associated with resistance. In 2020 and 2021 A619-<italic>Ht1</italic>, A619-<italic>Ht2</italic>, A619-<italic>Ht3</italic>, A619, B37-<italic>HtN1</italic>, and B37 were included to evaluate whether the mixture of 19StM06, 19StM07, 19StM09, 19StM11, 19StM12 were able to overcome major genes associated with resistance. In the 2020 greenhouse experiment we did not observe a significant difference in AUDPC or incubation period among lines containing major genes and their respective background based on a Dunnett&#x2019;s test (&#x3b1; <italic>=</italic> 0.05), but we observed typical resistant responses for <italic>Ht2, Ht3</italic>, and <italic>HtN1</italic>. In the 2021 field experiment the AUDPC for A619-<italic>Ht2</italic> and A619-<italic>Ht3</italic> were significantly different from A619 based on a Dunnett&#x2019;s test (<italic>p&lt;</italic> 0.001), indicating that <italic>Ht2</italic> and <italic>Ht3</italic> conferred resistance. Additionally, B37-<italic>HtN1</italic> was significantly different from B37 (&#x3b1; = 0.01), indicating that <italic>HtN</italic> conferred resistance. Discrepancies between genotype performance in the greenhouse and the field environment could be due to other <italic>E. turcicum</italic> genotypes present in the field environment. The effectiveness of qualitative and quantitative under greenhouse conditions differs from the field environment (<xref ref-type="bibr" rid="B43">Raymundo and Hooker, 1981b</xref>; <xref ref-type="bibr" rid="B7">Chung et&#xa0;al., 2010</xref>). Thus, it is possible that the observed discrepancy in phenotypes between the field and greenhouse environments could be attributed to environmental effects on the plants, as well as additional strains present in the field environments.</p>
<p>We observed a difference in resistance responses between the greenhouse and field environments. The 2019 and 2021 field environments were strongly and significantly correlated, (r= 0.64, &#x3b1; = 0.001) while the 2020 greenhouse environment had a weaker correlation with the 2019 field environment (r = -0.21, &#x3b1; = 0.01) and the 2021 field environment (r = -0.29, &#x3b1; = 0.01, <xref ref-type="table" rid="T3">
<bold>Table&#xa0;3</bold>
</xref>). The strong correlation between the 2019 and 2021 field data underscores that similar levels of resistance were observed even though one field was artificially inoculated while the other relied on natural inoculum. In the mixed model for the 2019 + 2021 combined dataset, environment contributed the most variance, followed by the genotype &#xd7; environment interaction (<xref ref-type="table" rid="T4">
<bold>Table&#xa0;4</bold>
</xref>). The model used to estimate LS Means in the 2020 incubation period dataset only included block but not replication. Replication was not included as it had a covariance estimate of zero, indicating that block and replication were redundant. By including the blocking factor in the model, we are still able to account for variation in the greenhouse environment. The 2020 greenhouse diseased leaf area was analyzed in the same manner as the 2020 greenhouse incubation period. The estimated LS Means for the 2019 + 2021 combined dataset and the 2020 incubation period dataset showed a range of phenotypic responses suitable for association mapping (<xref ref-type="fig" rid="f1">
<bold>Figure&#xa0;1</bold>
</xref>, <xref ref-type="table" rid="T1">
<bold>Table&#xa0;1</bold>
</xref>).</p>
<table-wrap id="T3" position="float">
<label>Table&#xa0;3</label>
<caption>
<p>Pearson correlation coefficients between LS Means disease severity among environments.</p>
</caption>
<table frame="hsides">
<thead>
<tr>
<th valign="top" align="left"/>
<th valign="top" align="left">2021 Field</th>
<th valign="top" align="left">2020 GH DLA<sup>+</sup>
</th>
<th valign="top" align="left">2020 GH IP<sup>^</sup>
</th>
</tr>
</thead>
<tbody>
<tr>
<td valign="top" align="left">2019 Field</td>
<td valign="top" align="left">0.64<sup>***</sup>
</td>
<td valign="top" align="left">0.16<sup>**</sup>
</td>
<td valign="top" align="left">-0.21<sup>**</sup>
</td>
</tr>
<tr>
<td valign="top" align="left">2021 Field</td>
<td valign="top" align="left"/>
<td valign="top" align="left">0.34<sup>***</sup>
</td>
<td valign="top" align="left">-0.29<sup>***</sup>
</td>
</tr>
<tr>
<td valign="top" align="left">2020 GH DLA</td>
<td valign="top" align="left"/>
<td valign="top" align="left"/>
<td valign="top" align="left">-0.37<sup>***</sup>
</td>
</tr>
</tbody>
</table>
<table-wrap-foot>
<fn>
<p>Significance <sup>***</sup> p &#x2264; 0.001, <sup>**</sup> p &#x2264; 0.01.</p>
</fn>
<fn>
<p>
<sup>+</sup>DLA, diseased leaf area.</p>
</fn>
<fn>
<p>
<sup>^</sup>IP, incubation period.</p>
</fn>
<fn>
<p>Field environments were evaluated for diseased leaf area (DLA) while greenhouse experiments were evaluated for incubation period (IP) and diseased leaf area.</p>
</fn>
</table-wrap-foot>
</table-wrap>
<table-wrap id="T4" position="float">
<label>Table&#xa0;4</label>
<caption>
<p>Covariance estimates with standard deviation for all fixed factors included in each mixed model used to estimate LS Means for incubation period and the 2019 + 2021 combined disease severity datasets.</p>
</caption>
<table frame="hsides">
<thead>
<tr>
<th valign="middle" align="right">Factor</th>
<th valign="middle" align="center">2019 + 2021 Fields</th>
<th valign="middle" align="center">Incubation Period</th>
<th valign="middle" align="center">2020 GH DLA</th>
</tr>
</thead>
<tbody>
<tr>
<td valign="middle" align="right">Environment</td>
<td valign="middle" align="center">95.65(9.78)</td>
<td valign="middle" align="center">&#x2212;</td>
<td valign="middle" align="center">&#x2212;</td>
</tr>
<tr>
<td valign="middle" align="right">Genotype &#xd7; Environment</td>
<td valign="middle" align="center">17.20(4.15)</td>
<td valign="middle" align="center">&#x2212;</td>
<td valign="middle" align="center">&#x2212;</td>
</tr>
<tr>
<td valign="middle" align="right">Environment/Replication/Block</td>
<td valign="middle" align="center">11.71(3.42)</td>
<td valign="middle" align="center">&#x2212;</td>
<td valign="middle" align="center">&#x2212;</td>
</tr>
<tr>
<td valign="middle" align="right">Environment/Replication</td>
<td valign="middle" align="center">3.62(1.90)</td>
<td valign="middle" align="center">&#x2212;</td>
<td valign="middle" align="center">&#x2212;</td>
</tr>
<tr>
<td valign="middle" align="right">Block</td>
<td valign="middle" align="center">&#x2212;</td>
<td valign="middle" align="center">0.17 (0.41)</td>
<td valign="middle" align="center">5520 (74.29)</td>
</tr>
<tr>
<td valign="middle" align="right">Residuals</td>
<td valign="middle" align="center">31.75(5.6)</td>
<td valign="middle" align="center">2.32 (1.52)</td>
<td valign="middle" align="center">5499 (74.16)</td>
</tr>
</tbody>
</table>
</table-wrap>
<fig id="f1" position="float">
<label>Figure&#xa0;1</label>
<caption>
<p>Histograms showing the distribution of least squared means (LS Means). The x-axis shows LS Means values, and the y-axis shows the frequency. LS Means were estimated for <bold>(A)</bold> incubation period and <bold>(B)</bold> standardized area under the disease progress curve (sAUDPC). Dashed and solid horizontal lines represent recurrent parents PHZ51 and PHB47, respectively. (180 x 100 mm, 300 dpi).</p>
</caption>
<graphic mimetype="image" mime-subtype="tiff" xlink:href="fpls-14-1272951-g001.tif"/>
</fig>
</sec>
<sec id="s3_2">
<label>3.2</label>
<title>Identification of significant markers associated with resistance to NCLB</title>
<p>In order to identify candidate markers associated with resistance to NCLB, we employed genome-wide association analysis using TASSEL (<xref ref-type="bibr" rid="B5">Bradbury et&#xa0;al., 2007</xref>). To control for population structure, two principal components were included in the model, as most of the variation is explained by the first two components (<xref ref-type="fig" rid="f2">
<bold>Figure&#xa0;2</bold>
</xref>). We then employed a GLM model using TASSEL to examine the genetic architecture of resistance to NCLB. For both the 2019 + 2021 field dataset and the 2020 greenhouse incubation period dataset log quantile-quantile plots were constructed to assess the effectiveness of two principal components to control population structure (<xref ref-type="fig" rid="f3">
<bold>Figures&#xa0;3B, D</bold>
</xref>). Given the genetic design of the BGEM population, this approach is appropriate to control for population structure while controlling for any false positives. The same mapping approach was used for the 2019 + 2021 field dataset, the 2020 greenhouse incubation period dataset, and the 2020 greenhouse diseased leaf area dataset. We did not identify any significant markers using the 2020 greenhouse diseased leaf area dataset. In total, four significant markers were identified using the GLM model in TASSEL (<xref ref-type="fig" rid="f3">
<bold>Figure&#xa0;3</bold>
</xref>).</p>
<fig id="f2" position="float">
<label>Figure&#xa0;2</label>
<caption>
<p>Figures illustrating the population structure of the BGEM population. <bold>(A)</bold> Is a scatter plot for principal components 1 and 2 plotted against each other. The shape of the points represents each ex-PVP background. The ex-PVP parents, PHB47 and PHZ51, are highlighted in red. <bold>(B)</bold> Is a scree plot of all principal components. The x-axis is the principal component number, and the y-axis is the proportion of total variation explained by each principal component. (200 x 100 mm, 300 dpi).</p>
</caption>
<graphic mimetype="image" mime-subtype="tiff" xlink:href="fpls-14-1272951-g002.tif"/>
</fig>
<fig id="f3" position="float">
<label>Figure&#xa0;3</label>
<caption>
<p>Results from the generalized linear model (GLM) with two principal components to control for population structure <bold>(A, C)</bold> and qq-plots showing observed versus expected -log<sub>10</sub>(<italic>p</italic>) <bold>(B, D)</bold>. A significance threshold of &#x3b1;=0.1 was established based on 1000 permutations conducted in TASSEL. For incubation period, evaluated in the greenhouse in 2020, <bold>(A, B)</bold> three SNPs were significant. The annotated SNP, S3_8266879, was also significant with a stepwise regression model. For the 2019 + 2021 combined field sAUDPC data, <bold>(C, D)</bold> one SNP was significant. (300 x 180 mm, 300 dpi).</p>
</caption>
<graphic mimetype="image" mime-subtype="tiff" xlink:href="fpls-14-1272951-g003.tif"/>
</fig>
<p>The BGEM-DH lines have a high percentage of recurrent parent genome, and as such, linkage disequilibrium (LD) decays at a much slower rate than expected. In some regions, the LD blocks are large and span 100,000,000 bp or beyond (<xref ref-type="bibr" rid="B47">Sanchez et&#xa0;al., 2018</xref>). Given the LD structure in this population, we considered genes within 1 Mbp of a significant marker when examining candidate genes. Three markers on chromosome 3 were associated with delayed incubation period (<xref ref-type="table" rid="T5">
<bold>Table&#xa0;5</bold>
</xref>, <xref ref-type="fig" rid="f3">
<bold>Figure&#xa0;3A</bold>
</xref>). A stepwise regression approach using the same marker dataset identified a single significant marker for incubation period on chromosome three (S3_8266879; <italic>p =</italic> 5 &#xd7; 10<sup>-5</sup>), which was also significant in the GLM model (<italic>p =</italic> 0.033, <xref ref-type="table" rid="T5">
<bold>Table&#xa0;5</bold>
</xref>, <xref ref-type="fig" rid="f3">
<bold>Figure&#xa0;3A</bold>
</xref>). The marker S3_8266879 is within GRMZ2G108898, plant cysteine oxidase 1 (<italic>PCO1</italic>). <italic>PCO1</italic> spans from 8,263,929 bp to 8,269,675 bp on chromosome 3. The other two significant markers identified in the GLM model for incubation period, S3_15712704 (<italic>p =</italic> 0.53) and S3_18008517 (<italic>p =</italic> 0.55) were proximal to GRMZM2G445261 a probable carboxylesterase 15 and GRMZM2G380195 a pentatricopeptide repeat-containing protein chloroplastic, respectively. While these genes were the closest to the most significant marker, it is important to keep in mind the extensive LD structure in this population.</p>
<table-wrap id="T5" position="float">
<label>Table&#xa0;5</label>
<caption>
<p>SNPs associated with resistance to <italic>E. turcicum</italic> were identified in the BGEM populations using genome-wide association and stepwise regression models.</p>
</caption>
<table frame="hsides">
<thead>
<tr>
<th valign="middle" align="center">Dataset</th>
<th valign="middle" align="center">Chr.<sup>*</sup>
</th>
<th valign="middle" align="center">SNP<sup>^</sup>
</th>
<th valign="middle" align="center">Perm. <italic>p</italic>-value (GWAS)</th>
<th valign="middle" align="center">
<italic>p</italic>-value (Step Reg.)</th>
<th valign="middle" align="center">Nearest gene</th>
<th valign="middle" align="center">Distance from marker (BP)</th>
</tr>
</thead>
<tbody>
<tr>
<td valign="middle" align="center">Incubation Period</td>
<td valign="middle" align="center">3</td>
<td valign="middle" align="center">S3_8266879</td>
<td valign="middle" align="center">0.033</td>
<td valign="middle" align="center">5 &#xd7; 10<sup>-5</sup>
</td>
<td valign="middle" align="center">GRMZM2G108898</td>
<td valign="middle" align="center">Genic</td>
</tr>
<tr>
<td valign="middle" align="center">Incubation Period</td>
<td valign="middle" align="center">3</td>
<td valign="middle" align="center">S3_15712704</td>
<td valign="middle" align="center">0.053</td>
<td valign="middle" align="center">&#x2212;</td>
<td valign="middle" align="center">GRMZM2G445261</td>
<td valign="middle" align="center">10,690</td>
</tr>
<tr>
<td valign="middle" align="center">Incubation Period</td>
<td valign="middle" align="center">3</td>
<td valign="middle" align="center">S3_18008517</td>
<td valign="middle" align="center">0.055</td>
<td valign="middle" align="center">&#x2212;</td>
<td valign="middle" align="center">GRMZM2G380195</td>
<td valign="middle" align="center">1,896</td>
</tr>
<tr>
<td valign="middle" align="center">2019 + 2021 LS Means</td>
<td valign="middle" align="center">2</td>
<td valign="middle" align="center">S2_10777410</td>
<td valign="middle" align="center">0.053</td>
<td valign="middle" align="center">&#x2212;</td>
<td valign="middle" align="center">GRMZM2G068982</td>
<td valign="middle" align="center">5,033</td>
</tr>
</tbody>
</table>
<table-wrap-foot>
<fn>
<p>
<sup>*</sup> Chromosome.</p>
</fn>
<fn>
<p>
<sup>^</sup> Single Nucleotide Polymorphism.</p>
</fn>
<fn>
<p>The significant SNPs identified in the 2019 + 2021 combined dataset and for incubation period are shown.</p>
</fn>
</table-wrap-foot>
</table-wrap>
<p>Resistance to diseased leaf area (DLA) is genetically distinct from incubation period; a single marker was significant on chromosome 2 (<xref ref-type="fig" rid="f3">
<bold>Figure&#xa0;3C</bold>
</xref>). The significant marker, S2_10777410 (<italic>p =</italic> 0.053), is proximal to GRMZM2G068982, a methionine aminopeptidase. Using the same marker dataset, a stepwise regression approach did not reveal any significant markers for the field DLA dataset (<xref ref-type="table" rid="T5">
<bold>Table&#xa0;5</bold>
</xref>). Stepwise regression is more conservative than GLM, and our findings are consistent in that no significant markers were identified using stepwise regression.</p>
<p>There was no overlap in significant markers for incubation period and disease severity. We observed a weak negative correlation between disease severity and incubation period (<xref ref-type="table" rid="T3">
<bold>Table&#xa0;3</bold>
</xref>). Although we observed some chlorotic resistant responses in our 2019 and 2021 field experiments and 2020 greenhouse experiment, we did not identify any significant markers near any of the major genes for NCLB resistance, <italic>Ht1, Ht2, Ht3, HtN1</italic> (<xref ref-type="supplementary-material" rid="SF1">
<bold>Figure S1</bold>
</xref>). If the qualitative resistance genes were present in the population, they may have been at too low of a frequency to detect any significant markers in these regions. It is also possible that these responses were due to novel resistance genes.</p>
</sec>
<sec id="s3_3">
<label>3.3</label>
<title>Metabolic pathways associated with disease resistance</title>
<p>To better understand the molecular mechanisms associated with resistance to NCLB we conducted a metabolic pathway analysis and examined a previously published RNA-seq dataset. We identified metabolic pathways associated with disease severity and incubation period using the results from the GLM model and the PAST software (<xref ref-type="bibr" rid="B54">Thrash et&#xa0;al., 2020</xref>). In total, 24 metabolic pathways (&#x3b1; = 0.05) were associated with resistance to <italic>E. turcicum</italic> (<xref ref-type="table" rid="T6">
<bold>Table&#xa0;6</bold>
</xref>), including nine associated with incubation period and 15 associated with disease severity. Several pathways associated with plant hormones were significant including jasmonic acid biosynthesis (PWY-735, <italic>p</italic> = 0.02) and cytokine-O-glucosides biosynthesis (PWY-2902, <italic>p</italic> = 0.04) in the combined disease severity dataset. Additionally, gibberellin inactivation I (PWY-102, <italic>p =</italic> 0.01) and brassinosteroids inactivation (PWY-6546, <italic>p =</italic> 0.03) were significant in the incubation period dataset. A pathway of particular interest is the ethylene biosynthesis pathway (ETHYL-PWY) which was significant for both incubation period (<italic>p =</italic> 0.006) and disease severity (<italic>p =</italic> 0.01). Ethylene synthesis has previously been associated with disease resistance in plants (<xref ref-type="bibr" rid="B13">Dong, 1987</xref>; <xref ref-type="bibr" rid="B56">van Loon et&#xa0;al., 2006</xref>). Additionally, S-adenosyl-L-methionine cycle II (PWY-5041) was significant for disease severity. S-adenosyl-L-methionine (SAM) is the starting substrate in ethylene synthesis. It is converted to 1-aminocyclopropane-1-carboxylic acid (ACC) by ACC synthase (ACS), which is subsequently converted into ethylene via oxidation by ACC oxidase (ACO) (<xref ref-type="bibr" rid="B69">Xu and Zhang, 2015</xref>).</p>
<table-wrap id="T6" position="float">
<label>Table&#xa0;6</label>
<caption>
<p>Significant metabolic pathways associated with increasing or decreasing incubation period and the 2019 + 2021 combined disease severity datasets.</p>
</caption>
<table frame="hsides">
<thead>
<tr>
<th valign="bottom" align="center">Pathway ID</th>
<th valign="bottom" align="center">Pathway Name</th>
<th valign="bottom" align="center">
<italic>p</italic>-Value</th>
<th valign="top" align="center">Effect</th>
<th valign="top" align="center">Dataset</th>
</tr>
</thead>
<tbody>
<tr>
<td valign="bottom" align="center">ETHYL-PWY</td>
<td valign="bottom" align="center">ethylene biosynthesis I (plants)</td>
<td valign="bottom" align="center">0.0062419</td>
<td valign="top" align="center">Decrease</td>
<td valign="top" align="center">IP<sup>*</sup>
</td>
</tr>
<tr>
<td valign="bottom" align="center">PWY-5667</td>
<td valign="bottom" align="center">CDP-diacylglycerol biosynthesis I</td>
<td valign="bottom" align="center">0.0273528</td>
<td valign="top" align="center">Decrease</td>
<td valign="top" align="center">IP</td>
</tr>
<tr>
<td valign="bottom" align="center">PWY-5138</td>
<td valign="bottom" align="center">unsaturated, even numbered fatty acid-oxidation</td>
<td valign="bottom" align="center">0.0354694</td>
<td valign="top" align="center">Decrease</td>
<td valign="top" align="center">IP</td>
</tr>
<tr>
<td valign="bottom" align="center">PWY-3181</td>
<td valign="bottom" align="center">tryptophan degradation VI (via tryptamine)</td>
<td valign="bottom" align="center">0.0367993</td>
<td valign="top" align="center">Decrease</td>
<td valign="top" align="center">IP</td>
</tr>
<tr>
<td valign="bottom" align="center">PWY-581</td>
<td valign="bottom" align="center">indole-3-acetate biosynthesis II</td>
<td valign="bottom" align="center">0.0459157</td>
<td valign="top" align="center">Decrease</td>
<td valign="top" align="center">IP</td>
</tr>
<tr>
<td valign="bottom" align="center">PWY-5080</td>
<td valign="bottom" align="center">very long chain fatty acid biosynthesis I</td>
<td valign="bottom" align="center">0.0026768</td>
<td valign="top" align="center">Increase</td>
<td valign="top" align="center">IP</td>
</tr>
<tr>
<td valign="bottom" align="center">PWY-102</td>
<td valign="bottom" align="center">gibberellin inactivation I (2-hydroxylation)</td>
<td valign="bottom" align="center">0.0152976</td>
<td valign="top" align="center">Increase</td>
<td valign="top" align="center">IP</td>
</tr>
<tr>
<td valign="bottom" align="center">PWY-5097</td>
<td valign="bottom" align="center">lysine biosynthesis VI</td>
<td valign="bottom" align="center">0.0268191</td>
<td valign="top" align="center">Increase</td>
<td valign="top" align="center">IP</td>
</tr>
<tr>
<td valign="bottom" align="center">PWY-6546</td>
<td valign="bottom" align="center">brassinosteroids inactivation</td>
<td valign="bottom" align="center">0.0334693</td>
<td valign="top" align="center">Increase</td>
<td valign="top" align="center">IP</td>
</tr>
<tr>
<td valign="bottom" align="center">LIPASYN-PWY</td>
<td valign="bottom" align="center">phospholipases</td>
<td valign="bottom" align="center">0.007419</td>
<td valign="top" align="center">Decrease</td>
<td valign="top" align="center">DLA<sup>#</sup>
</td>
</tr>
<tr>
<td valign="bottom" align="center">PWY-6441</td>
<td valign="bottom" align="center">spermine and spermidine degradation III</td>
<td valign="bottom" align="center">0.011873</td>
<td valign="top" align="center">Decrease</td>
<td valign="top" align="center">DLA</td>
</tr>
<tr>
<td valign="bottom" align="center">PWY-735</td>
<td valign="bottom" align="center">jasmonic acid biosynthesis</td>
<td valign="bottom" align="center">0.022039</td>
<td valign="top" align="center">Decrease</td>
<td valign="top" align="center">DLA</td>
</tr>
<tr>
<td valign="bottom" align="center">PWY-5097</td>
<td valign="bottom" align="center">lysine biosynthesis VI</td>
<td valign="bottom" align="center">0.032238</td>
<td valign="top" align="center">Decrease</td>
<td valign="top" align="center">DLA</td>
</tr>
<tr>
<td valign="bottom" align="center">PWY-6959</td>
<td valign="bottom" align="center">L-ascorbate degradation V</td>
<td valign="bottom" align="center">0.032430</td>
<td valign="top" align="center">Decrease</td>
<td valign="top" align="center">DLA</td>
</tr>
<tr>
<td valign="bottom" align="center">PWY-6803</td>
<td valign="bottom" align="center">phosphatidylcholine acyl editing</td>
<td valign="bottom" align="center">0.037275</td>
<td valign="top" align="center">Decrease</td>
<td valign="top" align="center">DLA</td>
</tr>
<tr>
<td valign="bottom" align="center">PWY-2902</td>
<td valign="bottom" align="center">cytokinin-O-glucosides biosynthesis</td>
<td valign="bottom" align="center">0.048633</td>
<td valign="top" align="center">Decrease</td>
<td valign="top" align="center">DLA</td>
</tr>
<tr>
<td valign="bottom" align="center">PWY-5041</td>
<td valign="bottom" align="center">S-adenosyl-L-methionine cycle II</td>
<td valign="bottom" align="center">0.007802</td>
<td valign="top" align="center">Increase</td>
<td valign="top" align="center">DLA</td>
</tr>
<tr>
<td valign="bottom" align="center">ETHYL-PWY</td>
<td valign="bottom" align="center">ethylene biosynthesis I (plants)</td>
<td valign="bottom" align="center">0.014177</td>
<td valign="top" align="center">Increase</td>
<td valign="top" align="center">DLA</td>
</tr>
<tr>
<td valign="bottom" align="center">PWY-5690</td>
<td valign="bottom" align="center">TCA cycle II (plants and fungi)</td>
<td valign="bottom" align="center">0.019701</td>
<td valign="top" align="center">Increase</td>
<td valign="top" align="center">DLA</td>
</tr>
<tr>
<td valign="bottom" align="center">PWY-6363</td>
<td valign="bottom" align="center">D-myo-inositol (1,4,5)-trisphosphate degradation</td>
<td valign="bottom" align="center">0.021242</td>
<td valign="top" align="center">Increase</td>
<td valign="top" align="center">DLA</td>
</tr>
<tr>
<td valign="bottom" align="center">PWY-702</td>
<td valign="bottom" align="center">methionine biosynthesis II</td>
<td valign="bottom" align="center">0.026966</td>
<td valign="top" align="center">Increase</td>
<td valign="top" align="center">DLA</td>
</tr>
<tr>
<td valign="bottom" align="center">PWY-6549</td>
<td valign="bottom" align="center">glutamine biosynthesis III</td>
<td valign="bottom" align="center">0.031528</td>
<td valign="top" align="center">Increase</td>
<td valign="top" align="center">DLA</td>
</tr>
<tr>
<td valign="bottom" align="center">UDPNACETYLGALSYN-PWY</td>
<td valign="bottom" align="center">UDP-N-acetyl-D-glucosamine biosynthesis II</td>
<td valign="bottom" align="center">0.047356</td>
<td valign="top" align="center">Increase</td>
<td valign="top" align="center">DLA</td>
</tr>
<tr>
<td valign="bottom" align="center">PWY-5138</td>
<td valign="bottom" align="center">unsaturated, even numbered fatty acid-oxidation</td>
<td valign="bottom" align="center">0.047695</td>
<td valign="top" align="center">Increase</td>
<td valign="top" align="center">DLA</td>
</tr>
</tbody>
</table>
<table-wrap-foot>
<fn>
<p>
<sup>*</sup>IP, incubation period.</p>
</fn>
<fn>
<p>#DLA, diseased leaf area.</p>
</fn>
<fn>
<p>Only pathways significant at &#x3b1; <italic>=</italic> 0.05 are shown.</p>
</fn>
</table-wrap-foot>
</table-wrap>
<p>Pathogens are known to mimic phytohormones and interfere with signaling (<xref ref-type="bibr" rid="B10">Denance et&#xa0;al., 2013</xref>), as well as to target regulatory components involved with <italic>in planta</italic> hormone production (<xref ref-type="bibr" rid="B45">Robert-Seilaniantz et&#xa0;al., 2011</xref>). Thus, we examined an RNA-seq dataset (<xref ref-type="bibr" rid="B1">Adhikari et&#xa0;al., 2021</xref>) for DEGs associated with ethylene biosynthesis during the early stages of infection. We examined three contrasts: inoculated versus uninoculated maize 24 hai, inoculated versus uninoculated maize 72 hai, and inoculated maize 24 versus 72 hai. Only one gene associated with ethylene biosynthesis, GRMZM2G07529 (FDR = 0.03), was upregulated, with a fold change of 16.87, in maize 24 hai with <italic>E. turcicum</italic> compared to maize 24 hai with DI H<sub>2</sub>O. GRMZM2G07529 is annotated as ACC oxidase <italic>ACO31</italic>. ACO is the final oxidation step in the synthesis of ethylene (<xref ref-type="bibr" rid="B69">Xu and Zhang, 2015</xref>). Thus, during the initial phases of infection ethylene production may be increased, indicating that it may play a role in resistance to NCLB.</p>
</sec>
<sec id="s3_4">
<label>3.4</label>
<title>Investigation of ethylene and resistance to <italic>E. turcicum</italic>
</title>
<p>We hypothesized that inhibiting ethylene would alter NCLB disease severity. We used a foliar treatment of AgNO<sub>3</sub> to examine the effect of ethylene on disease resistance. AgNO<sub>3</sub> inhibits ethylene action <italic>in planta</italic> by reducing the ability of ethylene receptors to bind to ethylene, which results in decreased ethylene sensitivity and the inhibition of continuous ethylene production (<xref ref-type="bibr" rid="B27">Kumar et&#xa0;al., 2009</xref>). We hypothesized that inhibition of ethylene by applying AgNO<sub>3</sub> would decrease disease severity and increase incubation period. Furthermore, we postulated that host resistant level and genetic background might alter the magnitude by which inhibiting ethylene improves resistance and increases incubation period.</p>
<p>To examine the role of ethylene in <italic>E. turcicum</italic> infection, a total of 10 DH lines and both recurrent parents were selected. We selected DH lines in pairs within each exotic family, where the pair had contrasting disease phenotypes. Plants were either treated with AgNO<sub>3</sub> or DI H<sub>2</sub>O prior to a whorl inoculation with <italic>E. turcicum</italic>. From our ethylene inhibition assay, disease severity was significantly impacted by genotype (<xref ref-type="table" rid="T7">
<bold>Table&#xa0;7</bold>
</xref>, <italic>p</italic> = 0.012) and by treatment with AgNO<sub>3</sub> or deionized H<sub>2</sub>O (<xref ref-type="table" rid="T7">
<bold>Table&#xa0;7</bold>
</xref>, <italic>p</italic> = 1.756 &#xd7; 10<sup>-5</sup>). Similarly, incubation period was significantly impacted by genotype (<xref ref-type="table" rid="T8">
<bold>Table&#xa0;8</bold>
</xref>, <italic>p</italic> = 0.004) and by treatment with AgNO<sub>3</sub> or deionized H<sub>2</sub>O <xref ref-type="table" rid="T8">
<bold>Table&#xa0;8</bold>
</xref>, <italic>p</italic> = 4.281 &#xd7; 10<sup>-5</sup>). In plants treated with AgNO<sub>3</sub>, incubation period increased and AUDPC decreased (<xref ref-type="fig" rid="f4">
<bold>Figure&#xa0;4</bold>
</xref>). We did not observe a significant impact of the line&#x2019;s resistance level, exotic family, or recurrent parent on AUDPC or incubation period (&#x3b1; = 0.05). In this experiment, application of AgNO<sub>3</sub> affected all genotypes similarly meaning that, of the lines screened, no line was more or less resistant relative to the other lines after AgNO<sub>3</sub> application; thus, inhibiting ethylene using AgNO<sub>3</sub> decreases disease severity similarly in the lines screened.</p>
<table-wrap id="T7" position="float">
<label>Table&#xa0;7</label>
<caption>
<p>Analysis of variance (ANOVA) output from the model used to evaluate the split-plot ethylene design to assess the effect of whole-plot and subplot on AUDPC.</p>
</caption>
<table frame="hsides">
<thead>
<tr>
<th valign="middle" align="right">Source</th>
<th valign="middle" align="right">DF<sup>*</sup>
</th>
<th valign="middle" align="right">SS<sup>#</sup>
</th>
<th valign="middle" align="right">MS<sup>^</sup>
</th>
<th valign="middle" align="right">F-value</th>
<th valign="middle" align="right">P-value</th>
</tr>
</thead>
<tbody>
<tr>
<td valign="middle" align="right">Whole Plot</td>
<td valign="middle" align="right">2</td>
<td valign="middle" align="right">5524</td>
<td valign="middle" align="right">2762.1</td>
<td valign="middle" align="right">1.6573</td>
<td valign="middle" align="right">0.20764</td>
</tr>
<tr>
<td valign="middle" align="right">Genotype</td>
<td valign="middle" align="right">11</td>
<td valign="middle" align="right">51549</td>
<td valign="middle" align="right">4686.3</td>
<td valign="middle" align="right">2.8117</td>
<td valign="middle" align="right">0.01209</td>
</tr>
<tr>
<td valign="middle" align="right">Whole Plot/Treatment</td>
<td valign="middle" align="right">3</td>
<td valign="middle" align="right">62622</td>
<td valign="middle" align="right">20873.9</td>
<td valign="middle" align="right">12.5241</td>
<td valign="middle" align="right">1.756 &#xd7; 10<sup>-5</sup>
</td>
</tr>
<tr>
<td valign="middle" align="right">Whole Plot &#xd7; Genotype</td>
<td valign="middle" align="right">22</td>
<td valign="middle" align="right">35546</td>
<td valign="middle" align="right">1615.7</td>
<td valign="middle" align="right">0.9694</td>
<td valign="middle" align="right">0.52271</td>
</tr>
<tr>
<td valign="middle" align="right">Error</td>
<td valign="middle" align="right">30</td>
<td valign="middle" align="right">50001</td>
<td valign="middle" align="right">1666.7</td>
<td valign="middle" align="right">&#xa0;</td>
<td valign="middle" align="right">&#xa0;</td>
</tr>
</tbody>
</table>
<table-wrap-foot>
<fn>
<p>
<sup>*</sup>DF, degrees of freedom.</p>
</fn>
<fn>
<p>#SS, sums of squares.</p>
</fn>
<fn>
<p>
<sup>^</sup>MS, mean squares.</p>
</fn>
</table-wrap-foot>
</table-wrap>
<table-wrap id="T8" position="float">
<label>Table&#xa0;8</label>
<caption>
<p>Analysis of variance (ANOVA) output from the model used to evaluate the split-plot ethylene design to assess the effect of whole-plot and subplot on incubation period.</p>
</caption>
<table frame="hsides">
<thead>
<tr>
<th valign="middle" align="right">Source</th>
<th valign="middle" align="right">DF<sup>*</sup>
</th>
<th valign="middle" align="right">SS<sup>#</sup>
</th>
<th valign="middle" align="right">MS<sup>^</sup>
</th>
<th valign="middle" align="right">F-value</th>
<th valign="middle" align="right">P-value</th>
</tr>
</thead>
<tbody>
<tr>
<td valign="middle" align="right">Whole Plot</td>
<td valign="middle" align="right">2</td>
<td valign="middle" align="right">0.75</td>
<td valign="middle" align="right">0.375</td>
<td valign="middle" align="right">0.3123</td>
<td valign="middle" align="right">0.7339</td>
</tr>
<tr>
<td valign="middle" align="right">Genotype</td>
<td valign="middle" align="right">11</td>
<td valign="middle" align="right">43.042</td>
<td valign="middle" align="right">3.9129</td>
<td valign="middle" align="right">3.2587</td>
<td valign="middle" align="right">0.00417</td>
</tr>
<tr>
<td valign="middle" align="right">Whole Plot/Treatment</td>
<td valign="middle" align="right">3</td>
<td valign="middle" align="right">38.875</td>
<td valign="middle" align="right">12.9583</td>
<td valign="middle" align="right">10.7918</td>
<td valign="middle" align="right">4.281 &#xd7; 10<sup>-5</sup>
</td>
</tr>
<tr>
<td valign="middle" align="right">Whole Plot &#xd7; Genotype</td>
<td valign="middle" align="right">22</td>
<td valign="middle" align="right">30.583</td>
<td valign="middle" align="right">1.3902</td>
<td valign="middle" align="right">1.1577</td>
<td valign="middle" align="right">0.34438</td>
</tr>
<tr>
<td valign="middle" align="right">Error</td>
<td valign="middle" align="right">33</td>
<td valign="middle" align="right">39.625</td>
<td valign="middle" align="right">1.2008</td>
<td valign="middle" align="right">&#xa0;</td>
<td valign="middle" align="right">&#xa0;</td>
</tr>
</tbody>
</table>
<table-wrap-foot>
<fn>
<p>
<sup>*</sup>DF, degrees of freedom.</p>
</fn>
<fn>
<p>#SS, sums of squares.</p>
</fn>
<fn>
<p>
<sup>^</sup>MS, mean squares.</p>
</fn>
</table-wrap-foot>
</table-wrap>
<fig id="f4" position="float">
<label>Figure&#xa0;4</label>
<caption>
<p>Boxplots showing distribution of incubation period <bold>(A)</bold> and AUDPC <bold>(B)</bold> when plants were sprayed with AgNO<sub>3,</sub> light blue, and sterile water, dark blue, before inoculation with <italic>E. turcicum.</italic> A total of 12 plants were replicated three times in each treatment. (300 x 115 mm, 300 dpi).</p>
</caption>
<graphic mimetype="image" mime-subtype="tiff" xlink:href="fpls-14-1272951-g004.tif"/>
</fig>
</sec>
</sec>
<sec id="s4" sec-type="discussion">
<label>4</label>
<title>Discussion</title>
<p>We evaluated the exotic-derived BGEM population for resistance to NCLB and examined the role of metabolic pathways in resistance to NCLB, specifically ethylene. We identified several significant markers for diseased leaf area and incubation period. These markers can be used to enrich the repertoire of quantitative resistance genes effective against <italic>E. turcicum</italic>. Additionally, we report that the ethylene synthesis pathway modulates a defense response against <italic>E. turcicum</italic>. Finally, we report variation in the ethylene metabolic pathway as a whole that is associated with resistance to NCLB.</p>
<p>This is the first study to report on disease resistance in the BGEM population. While we did not map any previously identified qualitative genes, several interesting responses were observed during the early stages of infections in some lines (<xref ref-type="supplementary-material" rid="SF1">
<bold>Figure S1</bold>
</xref>). Of note, the lines BGEM-0081-S, BGEM-0027-S, BGEM-0087-S, BGEM-0116-S, and BGEM-0154-S showed defense responses that were the most unique, could be useful in breeding for resistance and are worth examining closer in future experiments (<xref ref-type="supplementary-material" rid="SF1">
<bold>Figure S1</bold>
</xref>). Allelic variation has been reported for the major genes <italic>Ht2/3</italic> (<xref ref-type="bibr" rid="B21">Hurni et&#xa0;al., 2015</xref>; <xref ref-type="bibr" rid="B72">Yang et&#xa0;al., 2021</xref>), and it would be reasonable to expect allelic variation for other qualitative resistance genes.</p>
<p>We identified three markers associated with incubation period and one marker associated with DLA (<xref ref-type="table" rid="T5">
<bold>Table&#xa0;5</bold>
</xref>). We observed no overlap between the significant markers associated with incubation period and the marker associated with diseased leaf area indicating that the genetic architecture underlying disease severity and incubation period are distinct. It was surprising to see no overlap in significant markers for disease severity and incubation period; however, this phenomenon has been reported previously (<xref ref-type="bibr" rid="B2">Balint-Kurti et&#xa0;al., 2010</xref>). Incubation period and disease severity are important measures of resistance to <italic>E. turccium.</italic> Both traits are typically strongly correlated (<xref ref-type="bibr" rid="B51">Smith and Kinsey, 1993</xref>; <xref ref-type="bibr" rid="B64">Welz and Geiger, 2000</xref>). In this study we observed significant, weak negative correlations between disease severity and incubation period (<xref ref-type="table" rid="T3">
<bold>Table&#xa0;3</bold>
</xref>), suggesting that the ability to delay the onset of lesions is a separate component of resistance than restricting the pathogen growth after initial lesion development. Both incubation period and disease severity are believed to be controlled by genetically similar mechanisms (<xref ref-type="bibr" rid="B49">Schechert et&#xa0;al., 1999</xref>; <xref ref-type="bibr" rid="B65">Welz et&#xa0;al., 1999</xref>).</p>
<p>Of the three significant markers associated with incubation period, one marker (S3_8266879) was significant after the stepwise regression approach in TASSEL and is within GRMZM2G108898, a plant cysteine oxidase 1 (PCO1). Plant cysteine oxidases are associated with oxygen sensing and stress response in plants (<xref ref-type="bibr" rid="B63">Weits et&#xa0;al., 2014</xref>). When under hypoxic conditions, such as flooding, PCOs initiate downstream ethylene production by stabilizing ethylene response factors (ERFs) such as ERF-VII (<xref ref-type="bibr" rid="B19">Hartman et&#xa0;al., 2021</xref>). In Arabidopsis, several PCOs were found to be sensitive to <italic>in planta</italic> oxygen levels and necessary for mediating the stability of ERF-VII transcription factors in low oxygen environments (<xref ref-type="bibr" rid="B66">White et&#xa0;al., 2018</xref>). Because ethylene is a stress hormone, it makes sense that ERFs would be important in plant hosts under abiotic and biotic stress factors. In maize two ERFs, <italic>ZmERF061</italic> and <italic>ZmERF105</italic>, have been implicated as important for NCLB resistance (<xref ref-type="bibr" rid="B74">Zang et&#xa0;al., 2020</xref>; <xref ref-type="bibr" rid="B75">Zang et&#xa0;al., 2021</xref>).</p>
<p>We identified a single marker associated with disease severity, S2_10777410. This marker is proximal to a methionine aminopeptidase, GRMZM2G068982. Methionine aminopeptidases function as catalysts in cleaving methionine from synthesized polypeptides. Methionine is involved in many metabolic pathways, including the production of ethylene. The ethylene biosynthesis pathway was significant (&#x3b1; = 0.05) in the post-GWAS PAST analysis. Interestingly, <italic>ACO</italic> was strongly upregulated in maize plants 24 hai with <italic>E. turcicum</italic> compared to mock inoculated control. It is known that ethylene production is upregulated in response to pathogen invasion (<xref ref-type="bibr" rid="B28">Li et&#xa0;al., 2012</xref>; <xref ref-type="bibr" rid="B69">Xu and Zhang, 2015</xref>). The final step in ethylene synthesis is the oxidation of ACC by ACO which yield ethylene. The upregulation of <italic>ACO</italic> during the initial stages of infection supports our hypothesis that ethylene is an important defense-related hormone for resistance against NCLB. In our ethylene experiment, we saw that the inhibition of ethylene significantly increased incubation period and significantly decreased disease severity. This same trend has been observed in other pathosystems, where inhibiting ethylene or decreasing ethylene production improves resistance (<xref ref-type="bibr" rid="B13">Dong, 1987</xref>; <xref ref-type="bibr" rid="B56">van Loon et&#xa0;al., 2006</xref>; <xref ref-type="bibr" rid="B61">Wang et&#xa0;al., 2017</xref>).</p>
<p>The role of ethylene in plant defense against biotic stress factors, such as pests and pathogens, is highly complex, as both the synthesis and response to ethylene can be modulated to confer resistance or susceptibility. In some pathosystems it has also been shown that plant sensitivity to ethylene production is important in mediating resistance. Ethylene insensitive mutants in Arabidopsis had higher disease severity to necrotrophic and hemibiotrophic pathogens, while disease severity was lower for biotrophic pathogens (<xref ref-type="bibr" rid="B56">van Loon et&#xa0;al., 2006</xref>). In rice, increased accumulation of ethylene increased host susceptibility to rice dwarf virus (<xref ref-type="bibr" rid="B78">Zhao et&#xa0;al., 2017</xref>), but decreased ethylene accumulation resulted in decreased resistance to the hemibiotrophic pathogen <italic>Magnaporthe oryzae</italic> (<xref ref-type="bibr" rid="B76">Zhai et&#xa0;al., 2022</xref>). In tomato, plants with antisense mutations for the ERF <italic>LeETR4</italic> were generally more resistant to the bacterial pathogen <italic>Xanthomonas campestris</italic> pv. <italic>vesicatoria</italic>, suggesting expression of ERFs may be important in rapid response to pathogen invasion (<xref ref-type="bibr" rid="B8">Ciardi et&#xa0;al., 2001</xref>). Two ERFs have been identified in maize. Transcription of these ERFs are upregulated during <italic>E. turcicum</italic> infection, suggesting that ethylene sensitivity may be as important as ethylene production in defense response (<xref ref-type="bibr" rid="B74">Zang et&#xa0;al., 2020</xref>; <xref ref-type="bibr" rid="B75">Zang et&#xa0;al., 2021</xref>). Given the complexity of the role of ethylene in stress response, it is likely that there are many pleiotropic effects associated with ethylene synthesis and sensing.</p>
<p>After ethylene is synthesized, there are several downstream effects, including interactions with JA, as well as potential pleiotropic roles. In Arabidopsis it was shown that ethylene biosynthesis is activated due to insect herbivory, with downstream effects, such as increased transcription of ethylene response factors and JA synthesis (<xref ref-type="bibr" rid="B44">Rehrig et&#xa0;al., 2014</xref>). Additionally, in Arabidopsis a calcium elongation factor and a glutathione S-transferase were upregulated when ethylene production was increased (<xref ref-type="bibr" rid="B52">Stotz et&#xa0;al., 2000</xref>). Other downstream effects of ethylene synthesis include increased callose accumulation and increased expression of <italic>Tdy2</italic>, enhancing overall resistance to aphids in maize (<xref ref-type="bibr" rid="B59">Varsani et&#xa0;al., 2019</xref>). In maize, ethylene production is shown to mediate the expression of <italic>mir-1</italic>, an insect defense related gene, and is believed to also interact with JA (<xref ref-type="bibr" rid="B17">Harfouche et&#xa0;al., 2006</xref>). Metabolite abundance has been implicated and ethylene synthesis have been shown to be interconnected in mediating resistance to the necrotrophic pathogen <italic>Fusarium graminearum</italic> (<xref ref-type="bibr" rid="B79">Zhou et&#xa0;al., 2019</xref>).</p>
<p>Most research has investigated the qualitative role of ethylene in plant-pathogen interactions. However, little is known about the effect of allelic variation in ethylene related genes on disease severity. Here we show that there is variation in the ethylene metabolic pathway as a whole that is signiciantly associated with NCLB resistance. Our study is limited in that we did not measure ethylene production or the expression of genes associated with the production or response to ethylene. However, the ethylene inhibition experiment suggests that ethylene is an important part of the maize-<italic>E. turcicum</italic> pathosystem. Other areas of exploration would be to measure quantitative differences in ethylene production in response to pathogen inoculation in lines with allelic diversity in the ethylene pathway, as well as to evaulate mutants and natural alleles of genes related to ethylene biosynthesis and sensing. Additionally, future studies could examine the effect of the exogenous application of ethylene on gene expression and disease resistance. While no individual genotypes were statistically different between treatment with AgNO<sub>3</sub> and sterile water, we observed a range in disease severity in each treatment. Based on our findings, it is plausible that allelic variation in genes associated with ethylene production and ethylene sensitivity could translate to altered defense responses.</p>
</sec>
<sec id="s5" sec-type="conclusions">
<label>5</label>
<title>Conclusion</title>
<p>Northern corn leaf blight is an economically important disease. We screened the BGEM population for resistance to NCLB, identified metabolic pathways associated with resistance to NCLB, and confirmed the role of ethylene in resistance to NCLB. In this study we demonstrate the utility of the BGEM population as a source of novel alleles for resistance, and contribute to the growing body of literature focused on the role of ethylene in plant-microbe interactions, specifically maize-<italic>E. turcicum.</italic> In this study, we contribute to the growing body of literature by examining the role of ethylene in NCLB resistance.</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>SL: Conceptualization, Formal Analysis, Investigation, Methodology, Validation, Visualization, Writing &#x2013; original draft. AL: Methodology, Validation, Writing &#x2013; review and editing. SM: Conceptualization, Methodology, Resources, Writing &#x2013; review and editing. TJ: Conceptualization, Data curation, Funding acquisition, Methodology, Project administration, Resources, Supervision, Writing &#x2013; review and editing.</p>
</sec>
</body>
<back>
<sec id="s8" sec-type="funding-information">
<title>Funding</title>
<p>The authors declare financial support was received for the research, authorship, and/or publication of this article. This research was supported by the Department of Energy (DOE) Office of Science, Office of Biological and Environmental Research (BER), grant no. DE-SC0019189 to TJ and SM.</p>
</sec>
<ack>
<title>Acknowledgments</title>
<p>The authors would like to acknowledge Aislinn Geedey for critical feedback in the manuscript preparation.</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.2023.1272951/full#supplementary-material">https://www.frontiersin.org/articles/10.3389/fpls.2023.1272951/full#supplementary-material</ext-link>
</p>
<supplementary-material xlink:href="DataSheet_1.csv" id="SM1" mimetype="text/csv"/>
<supplementary-material xlink:href="DataSheet_2.csv" id="SM2" mimetype="text/csv"/>
<supplementary-material xlink:href="DataSheet_3.csv" id="SM3" mimetype="text/csv"/>
<supplementary-material xlink:href="Image_1.pdf" id="SF1" mimetype="application/pdf">
<label>Supplementary Figure&#xa0;1</label>
<caption>
<p>Variation in chlorotic responses during the early stages of <italic>E. turcicum</italic> infection and colonization in multiple BGEM lines, <bold>(A)</bold> BGEM-0081-S, <bold>(B)</bold> BGEM-0027-S, <bold>(C)</bold> BGEM-0087-S, <bold>(D)</bold> BGEM-0016-S, <bold>(E)</bold> BGEM-0154-S.</p>
</caption>
</supplementary-material>
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