Genomic regions associated with stripe rust resistance against the Egyptian race revealed by genome-wide association study

Abstract

Background: Wheat stripe rust (caused by Puccinia striiformis f. sp. Tritici), is a major disease that causes huge yield damage. New pathogen races appeared in the last few years and caused a broke down in the resistant genotypes. In Egypt, some of the resistant genotypes began to be susceptible to stripe rust in recent years. This situation increases the need to produce new genotypes with durable resistance. Besides, looking for a new resistant source from the available wheat genotypes all over the world help in enhancing the breeding programs.

Results: In the recent study, a set of 103-spring wheat genotypes from different fourteen countries were evaluated to their field resistant to stripe rust for two years. These genotypes included 17 Egyptian genotypes from the old and new cultivars. The 103-spring wheat genotypes were reported to be well adapted to the Egyptian environmental conditions. Out of the tested genotypes, eight genotypes from four different countries were found to be resistant in both years. Genotyping was carried out using genotyping-by-sequencing and a set of 26,703 SNPs were used in the genome-wide association study. Five SNP markers, located on chromosomes 2A and 4A, were found to be significantly associated with the resistance in both years. Three gene models associated with disease resistance and underlying these significant SNPs were identified. One immune Iranian genotype, with the highest number of different alleles from the most resistant Egyptian genotypes, was detected.

Conclusion: the high variation among the tested genotypes in their resistance to the Egyptian stripe rust race confirming the possible improvement of stripe rust resistance in the Egyptian wheat genotypes. The identified five SNP markers are stable and could be used in marker-assisted selection after validation in different genetic backgrounds. Crossing between the immune Iranian genotype and the Egyptian genotypes will improve stripe rust resistance in Egypt.

Keywords: Coefficient of Infection; Disease severity; Genome-wide association study; Linkage disequilibrium; Single marker analysis; gene expression.

Fig. 1

The response of the 103-tested spring wheat genotypes to stripe rust resistance at the adult stage under the Egyptian conditions at 2019 and 2020

Fig. 2

Number of resistant genotypes with coefficient of infection (CI) ranging from 0-4% in 2019 and 2020 experiments

Fig. 3

Quantile-Quantile (QQ) plot comparing the performance of the mixed linear model (MLM) used for of GWAS for stripe rust resistance at 2019 a and 2020 b with the performance of generalized linear model + principle coordinate (GLM +PC) for stripe rust at 2019 c and 2020 d

Fig. 4

Number of markers significantly associated with the resistance to the Egyptian race of stripe rust at adult growth stage in 2019 and 2020 and the common markers between both years: a. significant SNP markers based on the GWAS using GLM+PC model, b. significant DArT markers based on single marker analysis (SMA)

Fig. 5

Phenogram represents the chromosomal location of DArT and SNP markers significantly associated with stripe rust resistance at 2019 and 2020 and the common markers between both the two years

Fig. 6

Linkage disequilibrium (LD) analysis in the tested genotypes: a. heatmap of LD between the significant SNPs on chromosome 2A and b. heatmap of LD between the significant SNPs on chromosome 4A and the significant DArT marker on the same chromosome

Fig. 7

The expression of the three gene models harboring significant SNPs in transcripts per million (TPM). Blue, red and grey column represent the expression under control conditions at reproductive, seedling and vegetative growth stages, respectively. While, light blue, black and green column represent the expression under disease conditions at the same growth stages

Fig. 8

Histogram represents the number of targeted alleles of DArT markers (red columns) and SNP markers (black columns) which were found to be associated with stripe rust resistance in the eight resistant genotypes