Prediction and analysis of three gene families related to leaf rust (Puccinia triticina) resistance in wheat (Triticum aestivum L.)

Abstract

BackgroundThe resistance to leaf rust (Lr) caused by Puccinia triticina in wheat (Triticum aestivum L.) has been well studied over the past decades with over 70 Lr genes being mapped on different chromosomes and numerous QTLs (quantitative trait loci) being detected or mapped using DNA markers. Such resistance is often divided into race-specific and race-nonspecific resistance. The race-nonspecific resistance can be further divided into resistance to most or all races of the same pathogen and resistance to multiple pathogens. At the molecular level, these three types of resistance may cover across the whole spectrum of pathogen specificities that are controlled by genes encoding different protein families in wheat. The objective of this study is to predict and analyze genes in three such families: NBS-LRR (nucleotide-binding sites and leucine-rich repeats or NLR), START (Steroidogenic Acute Regulatory protein [STaR] related lipid-transfer) and ABC (ATP-Binding Cassette) transporter. The focus of the analysis is on the patterns of relationships between these protein-coding genes within the gene families and QTLs detected for leaf rust resistance.ResultsWe predicted 526 ABC, 1117 NLR and 144 START genes in the hexaploid wheat genome through a domain analysis of wheat proteome. Of the 1809 SNPs from leaf rust resistance QTLs in seedling and adult stages of wheat, 126 SNPs were found within coding regions of these genes or their neighborhood (5 Kb upstream from transcription start site [TSS] or downstream from transcription termination site [TTS] of the genes). Forty-three of these SNPs for adult resistance and 18 SNPs for seedling resistance reside within coding or neighboring regions of the ABC genes whereas 14 SNPs for adult resistance and 29 SNPs for seedling resistance reside within coding or neighboring regions of the NLR gene. Moreover, we found 17 nonsynonymous SNPs for adult resistance and five SNPs for seedling resistance in the ABC genes, and five nonsynonymous SNPs for adult resistance and six SNPs for seedling resistance in the NLR genes. Most of these coding SNPs were predicted to alter encoded amino acids and such information may serve as a starting point towards more thorough molecular and functional characterization of the designated Lr genes. Using the primer sequences of 99 known non-SNP markers from leaf rust resistance QTLs, we found candidate genes closely linked to these markers, including Lr34 with distances to its two gene-specific markers being 1212 bases (to cssfr1) and 2189 bases (to cssfr2).ConclusionThis study represents a comprehensive analysis of ABC, NLR and START genes in the hexaploid wheat genome and their physical relationships with QTLs for leaf rust resistance at seedling and adult stages. Our analysis suggests that the ABC (and START) genes are more likely to be co-located with QTLs for race-nonspecific, adult resistance whereas the NLR genes are more likely to be co-located with QTLs for race-specific resistance that would be often expressed at the seedling stage. Though our a...

Inferring defense-related gene families in Arabidopsis and wheat

“…There were 11 major families of genes for Arabidopsis defense against biotic stresses (diseases and insects) as uncovered by three approaches (Table 1 ). Three of these families, ABC, NLR and START, are already known to confer race-specific and race-nonspecific resistance to rusts in wheat and other cereal crops [ 4 , 5 ]. The remaining eight families were now found to be associated with Arabidopsis defense against pests.…”

“…This study employed three bioinformatics and genomics approaches to predict up to 1790 defense-related candidate genes within 11 gene families (Table 1 ) in Arabidopsis and their homologs for race-specific and race-nonspecific resistance to leaf, stem and stripe rusts in wheat (Table 4 ). In addition to the three gene families ( ABC , NLR and START ) that are already known to confer race-specific and race-nonspecific resistance to wheat rusts and other pathogens [ 4 , 5 ], eight new gene families for plant defense are now being inferred by the three approaches. It is somewhat surprising that Approach 1 (inference based on sequences of markers for wheat rust resistance) predicted more candidate genes in individual families over the Arabidopsis genome than did Approaches 2 and 3 except for the kinase family where Approach 3 predicted the most genes.…”

“…At the extreme, the predicted SNPs for a rust resistance gene appeared only in one gene family with eight such unique association pairs being Lr21-NLR, Lr34-ABC, Lr37-START, Sr2-Cupin, Yr24-Transcription factor, Yr26-Transporter, Yr36-Kinase and Yr53-Kinase . Two of these pairs, Lr21 - NLR and Lr34 - ABC , are expected because Lr21 and Lr34 are well known to confer race-specific and race-nonspecific resistance to leaf rust and they encode NLR and ABC proteins, respectively [ 4 , 5 ]. Yr36 encodes a protein with a kinase domain fused to a putative START lipid-binding domain [ 49 ] and thus the Yr36 - Kinase pair is expected though Yr36 is sometimes cited as a gene encoding the START protein in the past [ 5 ].…”

“…However, decades of genetic and breeding research have only been able to identify a limited number of genes in crop plants with durable and broad-spectrum resistance to pathogens (particularly rust pathogens in cereal crops). These race-nonspecific genes include those encoding ATP-binding cassette (ABC) transporter and kinase-START (steroidogenic acute regulatory [StAR] protein-related lipid transfer) proteins [ 4 , 5 ].…”

“…There is little information about the proteins and their families beyond these few well-characterized rust resistance genes. For this reason, Peng and Yang [ 5 ] recently used primer sequences of non-SNP markers and flanking sequences of SNP markers for known Lr genes or QTLs for leaf rust resistance to predict candidate genes located at the same or adjacent genomic regions of wheat, but their prediction was only able to identify the candidate genes in the three gene families ( ABC, NLR and START ), likely due to the limited annotations of rust resistance genes across the large, complex wheat genome.…”