The rice variety Ce253, widely planted in Guangxi Province, China, was selected for this study and was obtained from the Rice Research Institute, Guangxi Academy of Agricultural Sciences. Rice was planted under natural field conditions at the Rice Research Institute of Guangxi Academy of Agricultural Sciences, Nanning, China in 2020. The distance between plants within rows was 16 cm, and the distance between plants in separate rows was 20 cm. Field management, including irrigation, fertilizer application, and pest control, were performed according to normal agricultural practices. Fully filled grains were subjected to grain width, length, and weight measurement with a Wanshen SC-G automatic seed test system. All trait measurements were repeated at least three times.

Genome-wide identification of NB-ARC genes from three species of monocotyledonous and dicotyledonous plants was performed. Hidden Markov Model (HMM) (Punta et al., 2012) (version 3.0) analysis was used for the search. HMM profiles of NB-ARC genes (PF00931.2) were obtained from the Pfam database (http://pfam.xfam.org/) with an e-value≤1e-3. The results of the HMMER sequence alignment were screened to remove protein sequences that were at least 45% longer than the length of the HMM model domain, while retaining the longest protein sequence in the variable shear. Simple Modular Architecture Research Tool (SMART) (version 8.0) (http://smart.embl-heidelberg.de) was used for further analysis with all non-redundant protein sequences (Schultz et al., 1998). Finally, 258 NB-ARC genes models were identified in the rice genome for further analysis. The basic information of the identified NB-ARC proteins was obtained using the tools at the ExPasy website (http://web.expasy.org/protparam/). CDS coordinate information is listed in Supplementary Table S1. Gene family data were analyzed by Gene Denovo Biotechnology Co., Ltd. (Guangzhou, China). A BLASTP search of the NCBI nonredundant protein database was used to assign the NB-ARC domains. Multiple alignments of NB-ARC domains with 11 different plant NB-ARC domains of 11 subgroups were performed using MEME. The submotifs were analyzed through http://weblogo.berkeley.edu/logo.cgi. The 3D model of the NB-ARC genes was predicted by Jpred and SWISS-MODEL. We used the intersection results of Pfam (pfoo31, - e 1e-20) + smart (- e 0.1 -- dome 0.01) and blast (- e 1e-14 and identity >28%) as the identified homologous genes.

The exon-intron structural information for the collected rice NB-ARC genes was acquired from reference genome annotation files (Os-Nipponbare-Reference-IRGSP-1.0 pseudomolecules) to compare genomic and coding sequences (http://rice.uga.edu/). The cDNAs were aligned with their corresponding genomic DNA sequences. To map all NB-ARC genes, the chromosome distribution and conserved regions were confirmed by analysis of reference genome annotation files. A chromosome distribution diagram was drawn using the SVG package in Perl. Gene duplication in rice was identified using the replicate gene classifier program of MCScanX software (Wang et al., 2012). All protein-coding sequences were aligned using blastp, and the alignment results were used as input files for MCScanX software to predict gene replication. A gene was identified as a replication gene according to e-value<1e-5 or e-value<1e-10. Five replication events were identified: segmental, tandem, proximal, and decentralized (dispersed).

Conserved motifs in the gene family sequences were identified using the MEME program (http://alternate.meme-suite.org/tools/meme) with statistical significance (Bailey et al., 2015). The MEME program was run with default settings, maximum motif search value of 15, and an optimum motif width of 10–100 amino acid residues. A phylogenetic tree was constructed with the neighbor-joining algorithm in MEGA (version 7.0) with bootstrap test of 1,000 times and drawn with iTOL (https://itol.embl.de/) (Kumar et al., 2016). ML (maximum likelihood method) evolutionary tree was showed in Supplementary Figure S1. Genome annotations and corresponding protein sequences were downloaded from EnsemblPlants (Brassica_rapa. IVFCAAS v1.36, Brassica_oleracea.v2.1.36, Arabidopsis_thaliana.TAIR10) and GenoScope (Brassica_napus.annotation_v5). The gene structure and motifs were analyzed by systematic evolutionary relationships. Synteny detection was performed by McScanX and drawn with Circos software.

We compared the Ka/Ks ratios as a proxy of the selective pressures acting on gene pairs for reciprocal best match gene pairs from Arabidopsis, rice, and wheat. Ka/Ks was calculated as the ratio of the number of nonsynonymous substitutions per non-synonymous site (Ka) in a period to the number of synonymous substitutions per synonymous site (Ks) in the same period. Ka, Ks, and Ka/Ks values are based on coding sequence alignment and calculated using the KaKs_calculator software package based on the Nei and Gojobori model (Nei and Gojobori, 1986). Positively or negatively selected sites were identified based on Ka/Ks ratios with a confidence interval for each ratio given by a p value and an adjusted p value (Adj.Pval) from multiple comparisons (Massingham and Goldman, 2005). Homologous genes with a Ka/Ks ratio above 1 were under strong positive selection, between 0.5 and 1 were considered to be under weak positive selection, and below 0.1 were considered to be under negative selection (purifying selection).

To assess subcellular localization, sgRNA-Cas9 plant expression vectors were constructed as described previously (Mao et al., 2013). The targeting sequence (5′- TAG​TCG​ACG​ACA​ATG​CTG​CCA​GG-3′), corresponded to +400 to +422 within the third exon encoding the C-terminal end of GNP12 (starting at amino acid residue 134). To construct the GFP plasmids, the cDNAs of LOC_Os101g458510 were amplified from Nipponbare and the cDNA for LOC_Os12g36720 was amplified from Ce253. The cDNAs were cloned into the pBWA(V)HS-ccdb-GLos-GFP vector to generate the insertion. Plasmids CaMV35S:GFP, CaMV35S:LOC_Os101g458510-GFP and CaMV35S:GNP12-GFP were transformed into rice leaf protoplasts for subcellular localization. GFP was excited with a 488 nm laser and imaging was performed.

Panicles of Ce253 of different lengths (3, 5, 10, 15, 20, and 25 cm) at the booting stage were flash-frozen in liquid nitrogen. Total RNA was extracted from these tissues using a EasyPure^® Plant RNA Kit (Trans, Catalog no. ER301-01). RNA purity was determined by assaying 1 µl of total RNA extract on a NanoDrop 1,000. We measured the optical density (OD) ratio between 260 and 280 nm from samples, where pure RNA eluted in H20 (pH 7.0–8.5) or TE (pH 8.0) is expected to exhibit a ratio of 2.0–2.1. Total RNA (2.0 μg) was used for cDNA synthesis with a PrimeScript^™ RT Reagent Kit with gDNA Eraser (TransScript^® II One-Step RT-PCR SuperMix, Tran, Catalog no. AH411-02). The resulting cDNA samples were diluted five-fold and used as templates for qRT-PCR using a TransStart^® Green qPCR SuperMix and a CFX96 RealTime system (Bio-RAD, Hercules, CA, United States) following the manufacturer’s instructions. The qRT-PCR reactions were performed as 10 µl mixtures containing 5 µl of 2× Green qPCR MasterMix, 1 µl of cDNA, 0.25 µl of each primer (10 µM), and 3.5 µl of ddH₂O. Amplification steps were 95°C for 30 s, 40 cycles of 95°C for 5 s, and 60°C for 30 s, followed by 65°C for 5 s, 95°C for 15 s, 60°C for 30 s, and 95°C for 15 s. Each experiment was repeated at least three times. The qRT-PCR analysis was performed using the ΔΔCt method. Details on gene-specific primers used for real-time PCR are provided in Supplementary Table S1. The ubiquitin gene (LOC_Os03g13170) (Chen et al., 2019) was used as a control (^* p < 0.05; ^** p < 0.01; Student’s t-test). RNA samples used for RNA-seq analysis were prepared from different panicles of Ce253 grown under normal field conditions with three biological replicates. RNA library sequencing was performed on an Illumina Hiseq™ 2,500/4,000 platform by Majorbio. Sequence analysis was performed using the method provided by Majorbio (http://www.majorbio.com/). RNA-Seq data for NB-ARC genes in different tissues were obtained from http://expression.ic4r.org/.

The single-nucleotide polymorphisms (SNPs) of 827 accessions used for haplotype analysis were acquired from the 3K rice genomes (3K-RG) dataset. The grain length data for 827 accessions were downloaded from the Rice SNP-Seek Database. One-way ANOVA followed by Duncan’s new multiple-range test were performed using SPSS 21.0 software. The genomic sequences of 1,400 cultivated and 58 wild accessions were obtained from the 3K rice genomes (3K-RG) dataset and OryzaGenome (http://viewer.shigen.info/oryzagenome/), respectively, and were used to construct a minimum spanning tree for RGH1A. Arlequin version 3.5 software was used to calculate a haplotype network and the distance matrix output was used in Hapstar-0.6 to draw a minimum spanning tree. The average nucleotide diversity (π) and Tajima’s D for each subpopulation in RGH1A and 40-kb flanking regions were calculated using DnaSP 5.10 software (Librado and Rozas, 2009). The nucleotide diversity curves were generated using 60 bp window and 15 bp step length.

A total of 258 rice NB-ARC genes were identified in the Nipponbare genome (Supplementary Table S2). The lengths of the CDS for these genes range from 624 (LOC_Os02g27680) to 7,773 (LOC_Os06g41690) bp. Analysis revealed that 49.22% of these NB-ARC genes contain 2–6 introns and 86.04% NB-ARC genes contain 1–4 exons (Supplementary Table S2). Most of the NB-ARC genes have a long CDS and show a highly conserved structure (Figure 1). To explore the expansion of NB-ARC family members in rice, these sequences were used to generate an unrooted phylogenetic tree. The NB-ARC family members were divided into three major groups. Group I contained 29 genes, Group II contained 226 genes, and group III contained only three genes. The NB-ARC genes in group II were further classified into nine subgroups (groups IIa, IIb, IIc, IId, IIe, IIf, IIg, IIh, and IIi). Of these, the two groups with the most members were IIf with 35 genes and IIi with 37 genes. Group IIc contained the fewest number of genes, 13. A total of 15 motifs were identified by MEME, and two of these, M2 and M6, were present in 98.83 and 97.28%, respectively, of the NB-ARC genes. Genes on a single branch contained similar numbers of introns and similar distribution and number of motifs. In a given subtribe of genes, the positions of motifs were highly conserved. In group IIf, the genes contained 1-4 introns and 2–12 exons. Most genes in this group share 10 similar motifs (motifs 1, 2, 3, 4, 6, 8, 9, 10, 11, and 12) (Figure 1). Group IIf was representative in motifs and numbers of NB-ARC genes. Overall, NB-ARC genes were unevenly distributed across all 12 chromosomes, with 29 (11.24%), 61 (23.64%), and 34 (13.18%) genes located on Chr 8, 11, and 12, respectively. (Figure 2A). Gene analysis revealed duplication events including segmental, tandem, proximal, and dispersed, but not singleton duplications. Dispersed (110) and proximal replication 82) most frequently occurred in NB-ARC genes across all chromosomes (Figure 2B). Segmental replication was detected only on Chr2, Chr4, Chr7, and Chr11 (Figure 2B). Pairwise replication of genes was also detected in NB-ARC genes (Figure 2C). The genes in Group IIf, mapped to eight chromosomes, with dispersed, tandem, and proximal replication. In general, genes in subgroup IIf of group II showed typical structure with main motif and contain more genes, and analysis suggested that replication events were the main driving force of NB-ARC evolution.

To study the relationships between the NB-ARC genes of rice and other model plant species, including gramineous plants, we performed cluster analysis (Figure 3A). The NB-ARC genes of a dicotyledon plant, Arabidopsis, and two monocotyledonous plants, rice and wheat, were compared. Pfam was used to compare 1,052 and 50 NB-ARC genes in wheat and Arabidopsis, respectively. Next, based on the highly conserved NB-ARC domains of rice, wheat, and Arabidopsis, a phylogenetic tree was built. The 50 genes of Arabidopsis belonged to a single subgroup, and every subgroup contained rice and wheat genes (Figure 3A). Within each subgroup, genes from the homologous chromosome group generally clustered into a clade (Figure 3A); for example, LocOs12g36690, LocOs12g36720, and LocOs12g33160 were clustered in a subgroup. To further study the relationships between the NB-ARC genes of rice and other plants, we next performed whole genome synteny analysis (Figure 3B). A total of 65 homologous genome segments were distributed on 12 chromosomes in wheat (Supplementary Table S3). The highest number of homologous genome segments, 19, mapped to the syntenic locus in chromosome 4 and wheat chromosomes 2A, 2B, 2D. Two homologous genome segments mapped to chromosome 5 in Arabidopsis (Figure 3B) For further evolutionary analysis, the Ka, Ks, and Ka/Ks values of homologous gene pairs were calculated based on the comparative synteny map (Figure 3C). Ka/Ks ratios of 2,571 gene pairs were evaluated in rice and wheat in protein coding genes. Fifty-two gene pairs had Ka/Ks > 1, 2,412 gene pairs had 0.5 < Ka/Ks < 1, and no gene pairs had <0.1. Ka/Ks ratios were similarly evaluated for 70 gene pairs in rice and Arabidopsis thaliana to examine in protein coding genes. Five gene pairs had Ka/Ks > 1, 59 gene pairs had 0.5 < Ka/Ks < 1, no gene pairs had <0.1, and the remaining had no data so could not be calculated. In rice, 15 gene pairs had Ka/Ks > 1, 431 gene pairs had 0.5 < Ka/Ks < 1, no gene pairs had <0.1, and five gene pairs had 0.1 < Ka/Ks < 0.5 (Supplementary Table S4). Because the majority of homologous NB-ARC gene pairs had 0.5 < Ka/Ks < 1, this suggests that the NB-ARC gene family in these three plant species experienced weak positive selective pressure during evolution. Evolution of the few NB-ARC genes in rice was governed by strong constraints that may have contributed to their structural and functional stability (Figure 2C and Supplementary Table S5). Interestingly, some homologous genome segments mapped between rice and wheat were not observed between rice and Arabidopsis, which may indicate that these homologous pairs formed after the divergence of dicotyledonous and monocotyledonous plants. Overall, the analysis shows that the NB-ARC gene family is highly conserved in monocotyledons and homologous genome segments suggest that segmental duplications may be the main cause of the extension of this gene family. Multiple copies of genes have arisen during the evolution of dicotyledons and monocotyledons.

To study the spatial and temporal expression patterns of NB-ARC genes, transcriptomic profiling was profiled across eight different tissues (anther, callus, leaf, panicle, pistil, root, seed, and shoot) to analyze the role of these genes in rice organ development according to the Rice Expression Database (Supplementary Table S6 and Figure 4A). In our findings, 23 genes exhibited no expression in any tissues, five genes showed expression in eight tissues, and the remaining 88 genes showed FPKM values higher than 1 in more than three tissues. LOC_Os02g25900 and LOC_Os12g36720 exhibited FPKM values higher than 1 in anther, callus, leaf, panicle, pistil, root, seed, and shoot. Expression of these genes varied for different tissues, with expression of 141 genes in root, 94 genes in panicle, and only nine genes in anther.

For the IIf subgroup, one gene was most expressed in callus and 14 genes were most expressed in panicle. Six genes of IIf were most expressed in pistil and 23 genes of IIf were most expressed in root. IIf, a typical subgroup in the NB-ARC gene family, includes genes such as LOC_Os12g36720 that was expressed in eight different tissues (Figure 4A). To confirm the expression patterns, expression levels of 11 genes of different subgroups were detected by qRT-PCR. The results showed that six of these genes exhibited similar expression patterns to the transcriptomic data (Figure 4B). Most of these genes showed high expression in root. LOC_Os12g36720 in IIf was most highly expressed in anther and panicle.

Few studies have explored the roles of NB-ARC genes in normal plant growth and development. To investigate a possible function of these genes to regulate plant panicle development, the expression of selected NB-ARC genes was analyzed at the panicle development stage of cultivated rice (Figure 4B, c). In rice Ce253, 40, 34,32, 46, and 64 genes exhibited FPKM values higher than 1 at 5, 10, 15, 20, and 25 cm panicle length stages, respectively, and 215, 221, 223, 209, and 191 genes had FPKM values lower than 1 in 5, 10, 15, 20, and 25 cm panicle length stages, respectively. Most genes of the first subgroup of IIf had FPKM values lower than 1 at the early stage of young panicle differentiation (5, 10 cm), 12 and 11 genes exhibited FPKM values higher than 1 at 20 and 25 cm panicle length stages, respectively, and two, four, and four genes at 5, 10, and 15 cm panicle length stages, respectively (Figure 4B). The observed expressional activation in panicle development for LOC_Os12g36690, LOC_Os11g45970, and LOC_Os12g36720 suggests these genes play a crucial role in panicle development of rice.

To test the ability of NB-ARC genes to regulate plant panicle development, LOC_Os12g36720 was selected as a representative IIf gene. Expression of this gene was detected in anther, callus, leaf, panicle, pistil, root, seed, and shoot, and exhibited a remarkably high level of expression in Ce253 during panicle development. Interestingly, LOC_Os12g36720 encodes GNP12, a Resistance Gene Homologs (RGH1A) gene (Supplementary Table S7). Therefore, LOC_Os12g36720, GNP12, was selected for further characterization (Supplementary Table S6). To further characterize the function of this gene, we used a CRISPR-Cas9 system for targeted gene mutation of GNP12 in Ce253 (Cr line) (Figure 5A). The resulting deletions lead to frameshifting mutations that result in incomplete peptides of GNP12 that exhibit a loss of NB-ARC domain function. Compared to Ce253, the three Cr lines Cr-1, Cr-2, and Cr-3, were reduced 13.68, 3.71, and 9.39%, respectively, in panicle length (Figure 5B); 23.80, 8.50, and 24%, respectively, in panicle grain number; 2.76, 0.7, and 2.51%, respectively, in grain length; and 26.58, 8.79, and 10.98% in setting percentage, respectively. The three Cr lines showed significant reductions in panicle length, grain number of panicle, grain length, and setting percentage (Figure 5A, b, e, f, h, j). To investigate the tissue structures affected by GNP12, microstructures of grain chaff were observed by scanning electron microscopy (Figure 5D). The chaff of Cr was shorter than that of Ce253 (Figure 5D), but the Cr lines did not differ in length-width grain ratio or grain width (Figure 5C, i, k).

Cytokinin (CTK) is a primary determinant of plant architecture (Tameling et al., 2002). To investigate whether GNP12 influences CTK levels, we compared the CTK content in wild-type and Cr lines. The CTK content in Cr lines was reduced to 30.28% of that in the wild-type (Figure 5l). The results suggest that GNP12 may affect panicle development and grain production in rice through changes in CTK content.

To investigate natural variation in GNP12, we analyzed the polymorphism of GNP12 in the 3K rice genomes (3K-RG) dataset (Wang et al., 2018). We identified eight major haplotypes of GNP12 with 32 single-nucleotide polymorphisms (SNPs) in the coding sequence region in 827 accessions of the 3K-RG dataset (Figure 5m and Table 1). Except for Hap2, the frequencies of the major haplotypes differed significantly among different subgroups. Hap1, Hap5, Hap6, and Hap7 were specifically found in indica rice cultivars, with Hap1 being the most prevalent. Hap2 was mainly identified in indica, temperate japonica, tropical japonica, and Bas rice cultivars. Hap3 was mainly present in tropical japonica and indica rice cultivars. Hap4 and Hap8 were mainly found in Aus rice cultivars (Figure 5n). Phenotypic evaluation showed that Hap1, Hap3, Hap5, and Hap6 in the indica subgroup and Hap3 in the japonica subgroup showed longer grain length than other haplotypes. Haplotype network analysis showed that favorable haplotypes of GNP12 may have different origins. Favorable indica haplotypes Hap3 and Hap6 may have come directly from O. rufipogon I and favorable indica haplotypes Hap1 and Hap5 may have come from novel favorable mutations during indica domestication. Favorable haplotype Hap3 in japonica may have arisen during the differentiation of temperate and tropical japonica (Figure 5o).

To determine whether selection acted on GNP12, we analyzed the nucleotide diversity of GNP12 among different rice subgroups. On average, the nucleotide diversities of GNP12 in tropical japonica and indica subgroups were respectively much lower and higher than those in other haplotypes. To assess whether the DNA sequence evolved randomly or under a non-random process, Tajima’s D values were calculated for GNP12 in tropical japonica and indica and were negative and positive, respectively. Both values deviated significantly from zero, implying potential positive selection and balancing selection acting on GNP12 in tropical japonica and indica, respectively (Figure 5p). To further test whether the observed reduction in nucleotide diversity in tropical japonica was due to positive selection or a bottleneck effect, we calculated the nucleotide diversity of 40-kb flanking regions of GNP12. We found that the average nucleotide diversity of the GNP12 flanking regions in tropical japonica was significantly lower than that in other regions, suggesting that the decrease of nucleotide diversity of GNP12 in tropical japonica may be largely caused by positive selection (Table 2).

To further investigate the subdomains and functions of NB-ARC genes, 11 predicted proteins from group I, group II, and group III were selected for further analysis. Strong conservation was identified for several subdomains: αC, αM, αS, β3, β2-β5, and P-loop (Figure 6A, b). The most conserved residues in the putative NB-ARC domains were found in the P-loop (G193 and S223) and αS (L468) subdomains (Figure 6A). Analysis of the gene structure and conserved motifs revealed high conservation of rice NB ARC genes with no obvious variation in the amino acid residues of the P-loop region among homologous genes (Figure 6C). We observed few variants of the 11 amino acids in the P-loop core, with substantial variation in genic frequency of these variants in rice. These results indicate the significant conservation of the P-loop in most rice NB-ARC proteins. The predicted 3D structures of the identified rice NB-ARC proteins were conserved, which was consistent with the phylogenetic, gene structure, and conserved domain analysis. LOC_Os02g02670, LOC_Os06g41670, LOC_Os06g22460, LOC_Os012g36720, LOC_Os12g17490.1, and LOC_Os10g10360 were predicted to share similar structures (Figure 6C). Predicted models were constructed to heuristically maximize alignment coverage, identity percentage, and confidence score for the tested sequences. For the 11 predicted NB-ARC proteins, α-helix was most highly predicted as secondary structure (37.41–63.56%), followed by random coil (20.03–35.64%), extended strands (7.3–20.84%) and β-strands (0–5.29%) (Figure 6C and Supplementary Table S8). The 3D modeling results revealed similarity of predicted tertiary structures, implying that NB-ARC proteins may have evolved from a shared ancestor and/or under purification selection force for stabilization during long-term acclimation after initial divergence.

To further characterize the function of the NB-ARC genes, subcellular localization studies were performed. We randomly selected two NB-ARC genes, LOC_Os12g36720 (IIf), LOC_Os101g458510 (IIi), for subcellular localization in rice protoplast cells. LOC_Os12g36720-GFP and LOC_Os101g458510-GFP expression vectors were constructed and transformed into rice protoplasts for transient expression. Control GFP expression was observed throughout the membrane, cytoplasm and nucleus, and the GNP12 and LOC_Os101g458510 proteins were mainly expressed in the nucleus and membrane, respectively. This result indicated that these proteins are widely present in various organelles.

NB-ARC proteins play central roles in recognizing pathogens, initiating defense cascades, and maintaining cell development. The NB-ARC conserved domain maintains stable similar structures in different species, likely due to convergent evolution, suggesting these proteins may perform similar recognition and activation mechanisms (Slootweg et al., 2009). In the Fabaceae family, eight conserved motifs of NB-ARC domains have been identified (Pal et al., 2007). Plant NOD-like receptor (NLR) proteins contain NB-ARC domains with structural similarities to their mammalian homologues (Steele et al., 2019). However, there is high polymorphism in some NB-ARC genes in some species. The combination of conserved motifs and the evolution of rich polymorphisms may allow response to environmental signal stimulation to achieve coevolution by replication events. In Arabidopsis, analysis of the NLR family revealed that positive selection and recombination occurred frequently in the leucine-rich repeat (LRR) domain but there was negative selection in the nucleotide-binding (NB-ARC) domain (Mondragón-Palomino et al., 2017). In peanut, AhRAF4 of NB-ARC proteins evolved by recombination with duplications and point mutations from Arachis duranensis (Deng et al., 2018). Among O. sativa (Slootweg et al., 2009), O. glaberrima (Slootweg et al., 2009), and O. brachyantha (FF), a high number of paralogs suggests that the NB-ARC family experienced highly dynamic evolution, with a large number of tandem arrays and duplicated genes observed in the O. sativa subspecies (Jacquemin et al., 2014). NB-ARC genes diversified through duplication to encode receptors adapted to external signals (Andersen et al., 2020). IPm21 encodes a coiled-coil, nucleotide-binding site, leucine-rich repeat (CC-NBS-LRR) protein, and evolutionary analysis of 38 non-redundant Pm21 alleles indicated that the nucleotide diversity of the LRR domain was significantly higher than those of the CC and NB-ARC domains (He et al., 2020). NB-ARC genes can form genomic clusters adjacent to LRR-RLK-XIIs by mechanisms other than genomic clustering (Ngou et al., 2022). Overall, the evolution of NB-ARC genes allows these genes to maintain key function through conservation of the NB-ARC domain while the C-terminal regions of these proteins exhibit polymorphisms to allow these genes to co-evolve with the environment through replication events.

Panicle grain number and length of panicle are important agronomic characteristics, but the genetic determinants of these traits remain unclear. Many genes regulate grain number per panicle, length of panicle, and grain length by influencing hormone activity. ERECTA1 (OsER1) is a cytokinin oxidase/dehydrogenase that negatively regulates grain number per panicle (Ashikari et al., 2005). ERECTA1 acts upstream of the OsMKKK10-OsMKK4-OsMPK6 cascade, and the OsER1-OsMKKK10-OsMKK4-OsMPK6 pathway is required to maintain cytokinin homeostasis (Guo et al., 2020). OsASP1 encodes a TOPLESS-related transcriptional co-repressor, is closely associated with auxin action, and regulates spikelet development (Yoshida et al., 2012). TGW6 encodes a protein with indole-3-acetic acid (IAA)-glucose hydrolase activity that can control IAA supply at the transition from the syncytial to the cellular phase to limit cell number and grain length (Ishimaru et al., 2013). GW6 encodes a GA-regulated GAST family protein and positively regulates grain width and weight (Shi et al., 2020).

NB-ARC genes regulate plant development by catalyzing ADP through ARC structure. NB-ARC proteins carry a central nucleotide-binding-ARC domain that binds ADP/ATP rather than GDP/GTP (Chattopadhyaya and Pal, 2008). The NB-ARC domain may be a molecular switch between ADP (repressed) and ATP (active) binding forms (Steele et al., 2019). A tomato (Lycopersicon esculentum) R protein I-2 with NB-ARC domain is impaired in ATP hydrolysis, but not in ATP binding, suggesting a molecular switch whose state (on/off) depends on nucleotide binding (ATP/ADP) (Tameling et al., 2006). NRTP1 encodes a CC-NB-LRR type protein, and semi-dominant mutant nrtp1-D contains an amino acid substitution in the NB-ARC domain that causes constitutive auto-activation of the NRTP1 protein for a short-root phenotype in rice (Yu et al., 2018). ATP/ADP opentenyltransferases are likely responsible for most isopentenyladenine- and tZ-type cytokinin synthesis (Miyawaki et al., 2006) and catalyze prenylation of adenosine diphosphate (ADP) or triphosphate (ATP) biosynthesis (Kieber and Schaller, 2014). The hydrolysis of adenosine triphosphate (ATP) is directly coupled to the primary active transport of CTK (Nedvěd et al., 2021). In peach, ATP/ADP PpIPT genes are key genes for cytokinin biosynthesis in nodal stems (Li et al., 2018).

The NB-ARC domain of GNP12 protein may act in panicle development by influencing hormone activity to control grain number of panicle, length of panicle, and grain length. Future work is required to test this hypothesis and investigate the regulation of these important genes to better develop molecular tools for improved genetic breeding.