Genome-wide mapping of NBS-LRR genes and their association with disease resistance in soybean

Abstract

BackgroundR genes are a key component of genetic interactions between plants and biotrophic bacteria and are known to regulate resistance against bacterial invasion. The most common R proteins contain a nucleotide-binding site and a leucine-rich repeat (NBS-LRR) domain. Some NBS-LRR genes in the soybean genome have also been reported to function in disease resistance. In this study, the number of NBS-LRR genes was found to correlate with the number of disease resistance quantitative trait loci (QTL) that flank these genes in each chromosome. NBS-LRR genes co-localized with disease resistance QTL. The study also addressed the functional redundancy of disease resistance on recently duplicated regions that harbor NBS-LRR genes and NBS-LRR gene expression in the bacterial leaf pustule (BLP)-induced soybean transcriptome.ResultsA total of 319 genes were determined to be putative NBS-LRR genes in the soybean genome. The number of NBS-LRR genes on each chromosome was highly correlated with the number of disease resistance QTL in the 2-Mb flanking regions of NBS-LRR genes. In addition, the recently duplicated regions contained duplicated NBS-LRR genes and duplicated disease resistance QTL, and possessed either an uneven or even number of NBS-LRR genes on each side. The significant difference in NBS-LRR gene expression between a resistant near-isogenic line (NIL) and a susceptible NIL after inoculation of Xanthomonas axonopodis pv. glycines supports the conjecture that NBS-LRR genes have disease resistance functions in the soybean genome.ConclusionsThe number of NBS-LRR genes and disease resistance QTL in the 2-Mb flanking regions of each chromosome was significantly correlated, and several recently duplicated regions that contain NBS-LRR genes harbored disease resistance QTL for both sides. In addition, NBS-LRR gene expression was significantly different between the BLP-resistant NIL and the BLP-susceptible NIL in response to bacterial infection. From these observations, NBS-LRR genes are suggested to contribute to disease resistance in soybean. Moreover, we propose models for how NBS-LRR genes were duplicated, and apply Ks values for each NBS-LRR gene cluster.

De novo assembly of soybean wild relatives for pan-genome analysis of diversity and agronomic traits

“…TIRonly and TIR-X sequences were not included in this study. For R-genes with CNV, the expression analysis result and related traits reported in previous studies [25][26][27][28][77][78][79] were listed in Supplementary Table 23. …”

Gene Duplication to Reveal Adaptation Clue of Plant to Environmental Stress: A Case Study of NBS-LRR Genes in Soybean

“…glycinea, sudden death syndrome and rust diseases, and nodulation in soybean (Ashfield et al, 2003;Zhu et al, 2010). We described an example of correlation between the NBS-LRR and disease resistance QTL, functional redundancy of disease resistance in soybean on recently duplicated regions harboring these genes as reported by Kang et al (2012).…”

“…Reports showed that some stress-responsive genes in plants were as tandem array, which might have been duplicated (Hanada et al, 2008;Zhang, 2003). Also, genes related to biotic stress response in A. thaliana (Maere et al, 2005) and disease resistance genes containing domain of a nucleotide-binding site and a leucine-rich repeat in soybean (Glycine max) (Kang et al, 2012;Shin et al, 2008) were well retained after the SSD and large scale duplication (LSD), suggesting their roles of adaptive evolution against environmental conditions. We highlighted an overview based on genome resources focusing on plant genome duplication which impacted to gene duplication with their related aspects to environmental changes.…”

“…possibly conferring an adaptation in certain or various environments based on the functional repertoire of the gene duplication in genome (Kang et al, 2012;Kondrashov, 2012). Current accumulated studies demonstrated that new gene copy number may affect function.…”

“…Of the total NBS-LRR genes detected based on their N-terminal domains using homology analyses to the A. thaliana NBS-LRR genes, 116 TIR-NBS-LRRs, 20 CC-NBS-LRRs, and 183 other NBS-LRR were classified (Kang et al, 2012). A significant correlation was shown between the numbers of NBS-LRR genes and the disease resistance QTLs within the NBS-LRR-flanked 2 Mb region supporting the common feature of association between the NBS-LRRs and the loci/QTL for biotic stress in plants.…”