Identification of Disease Resistance Parents and Genome-Wide Association Mapping of Resistance in Spring Wheat

Abstract

The likelihood of success in developing modern cultivars depend on multiple factors, including the identification of suitable parents to initiate new crosses, and characterizations of genomic regions associated with target traits. The objectives of the present study were to (a) determine the best economic weights of four major wheat diseases (leaf spot, common bunt, leaf rust, and stripe rust) and grain yield for multi-trait restrictive linear phenotypic selection index (RLPSI), (b) select the top 10% cultivars and lines (hereafter referred as genotypes) with better resistance to combinations of the four diseases and acceptable grain yield as potential parents, and (c) map genomic regions associated with resistance to each disease using genome-wide association study (GWAS). A diversity panel of 196 spring wheat genotypes was evaluated for their reaction to stripe rust at eight environments, leaf rust at four environments, leaf spot at three environments, common bunt at two environments, and grain yield at five environments. The panel was genotyped with the Wheat 90K SNP array and a few KASP SNPs of which we used 23,342 markers for statistical analyses. The RLPSI analysis performed by restricting the expected genetic gain for yield displayed significant (p < 0.05) differences among the 3125 economic weights. Using the best four economic weights, a subset of 22 of the 196 genotypes were selected as potential parents with resistance to the four diseases and acceptable grain yield. GWAS identified 37 genomic regions, which included 12 for common bunt, 13 for leaf rust, 5 for stripe rust, and 7 for leaf spot. Each genomic region explained from 6.6 to 16.9% and together accounted for 39.4% of the stripe rust, 49.1% of the leaf spot, 94.0% of the leaf rust, and 97.9% of the common bunt phenotypic variance combined across all environments. Results from this study provide valuable information for wheat breeders selecting parental combinations for new crosses to develop improved germplasm with enhanced resistance to the four diseases as well as the physical positions of genomic regions that confer resistance, which facilitates direct comparisons for independent mapping studies in the future.

Keywords: association mapping; disease resistance; prairie provinces; priority 1 diseases; restrictive linear phenotypic selection index; selection index; trait donor; western Canada.

Figure 1

Frequency distribution of the best linear unbiased estimators (BLUEs) of disease severity and grain yield computed from all environments for (a) all 196 genotypes, and (b) the 22 selected genotypes. For all four diseases, we considered genotypes with a mean disease severity score of 1–2, 2.1–3.0, 3.1–5.0, 5.1–7.0, and 7.1–9.0 as resistant, moderately resistant, intermediate, moderately susceptible, and susceptible, respectively.

Figure 2

Partitioning of total variance into genotypes (G), environments (E), G × E interactions, and residual (error) variance components.

Figure 3

Bar graphs of best unbiased estimators (BLUEs) computed from all environments and the four selection parameters: the expected genetic gain (EGG) per trait, response to selection (RS), index, and the correlations between the index and genetic merit (CGM). The plots were made only for the top 20 of 3215 economic weights of which the four selected economic weights have * as a prefix. Trait acronyms—Cb (common bunt), Lr (leaf rust), Ls (leaf spot), Yld (grain yield), and Yr (stripe rust). See Table S5 for details.

Figure 4

Bar graph of the overall disease scores (BLUE) of the 22 lines and cultivars chosen using 4 out of the 3125 economic weights. Of the 22 genotypes, 17 were selected using all four economic weights, Kane and AAC Connery were selected using one and two weights, respectively, and the remaining three genotypes (5701PR, AAC Bailey, and AAC Brandon) were selected using three weights. See Table S5E for details.

Figure 5

Manhattan plots of Log₁₀(1/p) values computed using weighted mixed linear model, PC1 to PC3 from principal component analysis to account for population structure, best linear unbiased estimators (BLUEs) of disease scores computed from all environments, and genotype data of 23,342 polymorphic SNPs. The horizontal line shows the threshold p-value of 3.1 × 10⁻⁴ (3.51). The A, B, and D genomes are in green, orange, and purple colors, respectively. Chromosomes and physical positions are shown on the x-axis. See Table S6 for detailed results.

Figure 6

Comparisons of the overall disease severity recorded in all combined environments between selected and unselected genotypes at each genomic region identified using genome-wide association analysis. Disease resistant donor genotypes were selected based on a restricted linear phenotypic selection index. The dots indicate outlier scores.