Genome-Wide Association Mapping for Stripe Rust Resistance in Pakistani Spring Wheat Genotypes

Abstract

Stripe rust caused by the pathogen Puccinia striiformis f. sp. tritici (Pst) is a major threat for wheat, resulting in low yield and grain quality loss in many countries. Genetic resistance is a prevalent method to combat the disease. Mapping the resistant loci and their association with traits is highly exploited in this era. A panel of 465 Pakistani spring wheat genotypes were evaluated for their phenotypic response to stripe rust at the seedling and adult plant stages. A total of 765 single nucleotide polymorphism (SNP) markers were applied on 465 wheat genotypes to evaluate their stripe rust response against nine races during the seedling test and in three locations for the field test. Currently, twenty SNPs dispersed on twelve chromosomal regions (1A, 1B, 1D, 2A, 2B, 4A, 4B, 5B, 6A, 6B, 6D and 7B) have been identified that were associated with rust race-specific resistance at the seedling stage. Thirty SNPs dispersed on eighteen chromosomal regions (1A, 1B, 1D, 2A, 2B, 2D, 3A, 3B, 3D, 4B, 5A, 5B, 6A, 6B, 6D, 7A, 7B and 7D) are associated with adult plant resistance. SNP loci IWB3662 was linked with all three Pakistani races, and likewise IWA2344 and IWA4096 were found to be linked with three different USA races. The present research findings can be applied by wheat breeders to increase their resistant capability and yield potential of their cultivars, through marker-assisted selection.

Keywords: SNP; association mapping; genome-wide association studies; stripe rust; wheat.

Figure 1

Infection distribution of the 465 spring wheat genotypes at the seedling stage based on their infection type (IT) score, tested with six stripe rust races from the USA.

Figure 2

Infection distribution of the 465 spring wheat genotypes at the seedling stage based on their infection type (IT) score, tested with three stripe rust races from Pakistan.

Figure 3

Infection distribution of 465 spring wheat genotypes at the adult plant stage and the stripe rust infection type (IT) score across three environments. Scoring for the adult plant response performed in three different environments (two years in Pakistan considered as one location and two locations in the USA).

Figure 4

Infection distribution of 465 spring wheat genotypes at the adult plant stage and the stripe rust disease severity (SEV) score across three environments. Scoring for the adult plant response performed in three different environments (two years in Pakistan considered as one location and two locations in the USA).

Figure 5

Estimated population structure of the 465 spring wheat genotypes (K = 3) based on the Q matrix using the single nucleotide polymorphism (SNP) markers. Q: three (K = 3) different subpopulations as Q1, Q2 and Q3.

Figure 6

Scatter plot of the linkage disequilibrium (LD) decay with the critical r² value and the genetic chromosome distance (cm) for the whole genome. The red line shows the critical r² value i.e., 0.12.