Identification of Candidate Avirulence and Virulence Genes Corresponding to Stem Rust (<i>Puccinia graminis</i> f. sp. <i>tritici</i>) Resistance Genes in Wheat

Abstract

Stem rust, caused by the biotrophic fungal pathogen <i>Puccinia graminis</i> f. sp. <i>tritici</i> (<i>Pgt</i>), is an important disease of wheat. However, the majority of <i>Pgt</i> virulence/avirulence loci and underlying genes remain uncharacterized due to the constraints of developing bi-parental populations with this obligate biotroph. Genome-wide association studies (GWAS) using a sexual <i>Pgt</i> population mainly collected from the Pacific Northwestern United States were used to identify candidate virulence/avirulence effector genes corresponding to the six wheat <i>Sr</i> genes: <i>Sr5</i>, <i>Sr21</i>, <i>Sr8a</i>, <i>Sr17</i>, <i>Sr9a</i>, and <i>Sr9d</i>. The <i>Pgt</i> isolates were genotyped using whole-genome shotgun sequencing that identified approximately 1.2 million single nucleotide polymorphisms (SNPs) and were phenotyped at the seedling stage on six <i>Sr</i> gene differential lines. Association mapping analyses identified 17 <i>Pgt</i> loci associated with virulence or avirulence phenotypes on six <i>Pgt</i> resistance genes. Among these loci, 16 interacted with a specific <i>Sr</i> gene, indicating <i>Sr</i>-gene specific interactions. However, one avirulence locus interacted with two separate <i>Sr</i> genes (<i>Sr9a</i> and <i>Sr17</i>), suggesting two distinct <i>Sr</i> genes identifying a single avirulence effector. A total of 24 unique effector gene candidates were identified, and haplotype analysis suggests that within this population, <i>AvrSr5</i>, <i>AvrSr21</i>, <i>AvrSr8a</i>, <i>AvrSr17</i>, and <i>AvrSr9a</i> are dominant avirulence genes, while <i>avrSr9d</i> is a dominant virulence gene. The putative effector genes will be fundamental for future effector gene cloning efforts, allowing for further understanding of rust effector biology and the mechanisms underlying virulence evolution in <i>Pgt</i> with respect to race-specific <i>R</i>-genes. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.