Genome-Wide Association Studies Reveal All-Stage Rust Resistance Loci in Elite Durum Wheat Genotypes

Abstract

Leaf rust, caused by Puccinia triticina (Pt), stripe rust caused by Puccinia striiformis f. sp. tritici (Pst), and stem rust caused by Puccinia graminis f. sp. tritici (Pgt) are major diseases to wheat production globally. Host resistance is the most suitable approach to manage these fungal pathogens. We investigated the phenotypic and genotypic structure of resistance to leaf rust, stem rust, and stripe rust pathogen races at the seedling stage in a collection of advanced durum wheat breeding lines and cultivars adapted to Upper Mid-West region of the United States. Phenotypic evaluation showed that the majority of the durum wheat genotypes were susceptible to Pt isolates adapted to durum wheat, whereas all the genotypes were resistant to common wheat type-Pt isolate. The majority of genotypes were resistant to stripe rust and stem rust pathogen races. The durum panel genotyped using Illumina iSelect 90 K wheat SNP assay was used for genome-wide association mapping (GWAS). The GWAS revealed 64 marker-trait associations (MTAs) representing six leaf rust resistance loci located on chromosome arms 2AS, 2AL, 5BS, 6AL, and 6BL. Two of these loci were identified at the positions of Lr52 and Lr64 genes, whereas the remaining loci are most likely novel. A total of 46 MTAs corresponding to four loci located on chromosome arms 1BS, 5BL, and 7BL were associated with stripe rust response. None of these loci correspond to designated stripe rust resistance genes. For stem rust, a total of 260 MTAs, representing 22 loci were identified on chromosome arms 1BL, 2BL, 3AL, 3BL, 4AL, 5AL, 5BL, 6AS, 6AL, 6BL, and 7BL. Four of these loci were located at the positions of known genes/alleles (Sr7b, Sr8155B1, Sr13a, and Sr13b). The discovery of known and novel rust resistance genes and their linked SNPs will help diversify rust resistance in durum wheat.

Keywords: association mapping; durum wheat; leaf rust; molecular markers; resistance; stem rust; stripe rust.

FIGURE 1

Distributions of the seedling responses of the durum wheat genotypes to Puccinia triticina isolates BBBSJ_TUN 20-1, EEEEE_ETH 13D17-1, EEEEE_ETH 63-1, BBBSJ_MOR 33-1, BBBQJ_MEX10, and MBDSS_ALK-ND. X-axis corresponds to linearized Stakman scale (0-to-9).

FIGURE 2

Distributions of the seedling responses of the durum wheat genotypes to Puccinia striiformis f. sp. tritici races PSTv-37, PSTv-41, and PSTv-52.

FIGURE 3

Distributions of the seedling responses of the durum wheat genotypes to Puccinia graminis f. sp. tritici races TTKSK, TTKST, TTKTT, TKTTF, TRTTF, and JRCQC. X- axis corresponds to the linearized Stakman scale (0-to-9).

FIGURE 4

Correlation between durum wheat line infection types to leaf rust, stem rust, and stripe rust pathogen races. Cells with significant correlations at P-value < 0.05 were in blue color.

FIGURE 5

Scatter plot demonstrating linkage disequilibrium (LD) decay across the 14 durum wheat chromosomes for the 248 durum wheat genotypes. The LD estimate (R²) for pairs of SNPs was plotted against the corresponding genetic distance in centimorgan (cM) based on the tetraploid consensus map of Maccaferri et al. (2015). The dashed lines represent the LD decay that dropped by half at around 2.5 cM in average.

FIGURE 6

Manhattan plots showing P-values for single-nucleotide polymorphism (SNP) markers associated with response to leaf rust in durum wheat genotypes to the three durum wheat type isolates BBBSJ_TUN 20-1, EEEEE_ETH 13D14-1, and EEEEE_ETH 63-1. The horizontal dashed red line indicates significance level at P-value ≤ 0.001. The horizontal dotted black line indicates significance level at FDR ≤ 0.05.

FIGURE 7

Manhattan plots showing P-values for single-nucleotide polymorphism (SNP) markers associated with response to stripe rust in durum wheat genotypes to the three Pst isolates PSTv-37, PSTv-52, and PSTv-41. The horizontal dashed red line indicates significance level at P-value ≤ 0.001. The horizontal dotted black line indicates significance level at FDR ≤ 0.05.

FIGURE 8

Manhattan plots showing P-values for single-nucleotide polymorphism (SNP) markers associated with response to stem rust in durum wheat genotypes to the three Pgt races TTKSK, TTKST, TTKTT, TKTTF, TRTTF, and JRCQC. The horizontal dashed red line indicates significance level at P-value ≤ 0.001. The horizontal dotted black line indicates significance level at FDR ≤ 0.05.