Genome-Wide Identification of Wheat Gene Resources Conferring Resistance to Stripe Rust

Abstract

Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), threatens global wheat production. Breeding resistant varieties is a key to disease control. In this study, 198 modern wheat varieties were phenotyped with the prevalent Pst races CYR33 and CYR34 at the seedling stage and with mixed Pst races at the adult-plant stage. Seven stable resistance varieties with infection type (IT) ≤ 2 and disease severity (DS) ≤ 20% were found, including five Chinese accessions (Zhengpinmai8, Zhengmai1860, Zhoumai36, Lantian36, and Chuanmai32), one USA accession (GA081628-13E16), and one Pakistani accession (Pa12). The genotyping applied a 55K wheat single-nucleotide polymorphism (SNP) array. A genome-wide association study (GWAS) identified 14 QTL using a significance threshold of p ≤ 0.001, which distributed on chromosomes 1B (4), 1D (2), 2B (4), 6B, 6D, 7B, and 7D (4 for CYR33, 7 for CYR34, 3 for mixed Pst races), explaining 6.04% to 18.32% of the phenotypic variance. Nine of these QTL were potentially novel, as they did not overlap with the previously reported Yr or QTL loci within a ±5.0 Mb interval (consistent with genome-wide LD decay). The haplotypes and resistance effects were evaluated to identify the favorable haplotype for each QTL. Candidate genes within the QTL regions were inferred based on their transcription levels following the stripe rust inoculation. These resistant varieties, QTL haplotypes, and favorable alleles will aid in wheat breeding for stripe rust resistance.

Keywords: GWAS; QTL; SNP array; haplotype; stripe rust; wheat.

Figure 1

The distribution and correlation of the stripe rust responses at the seedling and adult-plant stages. (a) Violin plots illustrating the distribution of stripe rust resistance phenotypes for the CYR33 and CYR34 races at the seedling stage, and mixed Pst races at the adult-plant stage across three field environments (Pst18/19/20 represent the DS values scored at the CD18, CD19, and CD20 environments, respectively). (b) Heatmap of Pearson correlation coefficients quantifying the relationships among the stripe rust responses across the different races and developmental stages. The color intensity reflects the strength of the correlation, with positive (blue) and negative (red) values indicating direct or inverse associations, respectively. The phenotypic data consist of infection type (IT) and/or disease severity (DS) values, as defined in Section 4. “CYR33/34–DS/IT–I/II” represents the DS or IT values obtained after the inoculation with CYR33 or CYR34, which were scored during the first or second replicate in the greenhouse at the seedling stage.

Figure 2

The phylogenetic relationships and linkage disequilibrium (LD) decay in 198 wheat accessions. (a) The neighbor-joining phylogenetic tree, constructed from the genome-wide single-nucleotide polymorphism (SNP) data, depicting the genetic relationships among the accessions. The branch colors correspond to the predefined groups (Table S1). (b) A linkage disequilibrium decay plot based on 44,759 high-quality SNP markers. The LD is measured as the squared correlation coefficient (r²) between pairs of SNPs, plotted against the genomic distance (kilobase, Kb).

Figure 3

The effects of the QYr.baafs-2B.1 haplotypes and candidate genes on the stripe rust resistance to the CYR33 race. (a) A Manhattan plot from a GWAS analyzing the seedling-stage responses to the CYR33 race. The genome-wide significance threshold is set at a –log10 (p) value of 3.0, with each dot representing an SNP marker. The red dots represent SNP markers significantly associated with Pst resistance. (b) The phenotypic effects of the QYr.baafs-2B.1 haplotypes in the seedling-stage trials with the CYR33 race. The disease severity (DS) and infection type (IT) are shown as means ± standard deviation (SD). (c) A local Manhattan plot and haplotype block around QYr.baafs-2B.1. The zoomed region highlights the peak-associated SNPs (–log10 (p) ≥ 4.0) and their LD structure.