Genome-Wide Association Study for Spot Blotch Resistance in Hard Winter Wheat

Abstract

Spot blotch (SB) caused by Cochliobolus sativus (anamorph: Bipolaris sorokiniana) is an economically important disease of wheat worldwide. Under a severe epidemic condition, the disease can cause yield losses up to 70%. Previous approaches like bi-parental mapping for identifying SB resistant genes/QTLs exploited only a limited portion of the available genetic diversity with a lower capacity to detect polygenic traits, and had a lower marker density. In this study, we performed genome-wide association study (GWAS) for SB resistance in hard winter wheat association mapping panel (HWWAMP) of 294 genotypes. The HWWAMP was evaluated for response to B. sorokiniana (isolate SD40), and a range of reactions was observed with 10 resistant, 38 moderately resistant, 120 moderately resistant- moderately susceptible, 111 moderately susceptible, and 15 susceptible genotypes. GWAS using 15,590 high-quality SNPs and 294 genotypes we identified six QTLs (p = <0.001) on chromosomes 2D, 3A, 4A, 4B, 5A, and 7B that collectively explained 30% of the total variation for SB resistance. Highly associated SNPs were identified for all six QTLs, QSb.sdsu-2D.1 (SNP: Kukri_c31121_1460, R² = 4%), QSb.sdsu-3A.1 (SNP: Excalibur_c46082_440, R² = 4%), QSb.sdsu-4A.1 (SNP: IWA8475, R² = 5.5%), QSb.sdsu-4B.1 (SNP: Excalibur_rep_c79414_306, R² = 4%), QSb.sdsu-5A.1 (SNP: Kukri_rep_c104877_2166, R² = 6%), and QSb.sdsu-7B.1 (SNP: TA005844-0160, R² = 6%). Our study not only validates three (2D, 5A, and 7B) genomic regions identified in previous studies but also provides highly associated SNP markers for marker assisted selection. In addition, we identified three novel QTLs (QSb.sdsu-3A.1, QSb.sdsu-4A.1, and QSb.sdsu-4B.1) for SB resistance in wheat. Gene annotation analysis of the candidate regions identified nine NBS-LRR and 38 other plant defense-related protein families across multiple QTLs, and these could be used for fine mapping and further characterization of SB resistance in wheat. Comparative analysis with barley indicated the SB resistance locus on wheat chromosomes 2D, 3A, 5A, and 7B identified in our study are syntenic to the previously identified SB resistance locus on chromosomes 2H, 3H, 5H, and 7H in barley. The 10 highly resistant genotypes and SNP markers identified in our study could be very useful resources for breeding of SB resistance in wheat.

Keywords: GWAS; QTLs; SNPs; Triticum aestivum; hard winter wheat; marker-assisted selection; spot blotch.

FIGURE 1

Frequency distribution of the mean spot blotch infection response of 294 HWWAMP genotypes. The x-axis exhibits 1–5 scores of mean infection response of each genotype. The y-axis represents the number of genotypes (also numbered on the bar) that exhibited the infection response. Salamouni and Glenlea were the resistant and susceptible checks of the experiment, respectively.

FIGURE 2

Genome wide association scan for SB resistance in hard winter wheat association mapping panel (HWWAMP). Manhattan plot developed using mixed linear model (MLM) (A) and general linear model (GLM) (B) in TASSEL v.5. The -log₁₀ (P) values from a genome-wide scan are plotted against positions on each of the 21 wheat chromosomes. Horizontal lines indicate genome-wide significance thresholds.

FIGURE 3

Gene annotation of QTLs identified on chromosome 7B (A) and 2D (B) for spot blotch resistance in hard winter wheat. The far left image is a Manhattan plot indicating the level of marker association with the trait (I). Next is a visualization of linkage disequilibrium (black is a D’ value of 100%, another color is a D’ value of less than 100%), significant haplotype blocks are outlined in black (II). Names of the markers in the region of interest along with their cM position (III), and physical position (IV). Most significant marker is highlighted in red. The far right image is a physical map of candidate genes on 7B and 2D chromosome segments spanning from 608.7 to 611.7 Mb and 606.9 to 608.8 Mb, respectively (IV and V). Genes in bold code Pathogenesis-related (PR) proteins. The cM position is based on Wang S. et al. (2014) and the physical position is based on IWGSC 2018.

FIGURE 4

Comparative analysis showing synteny in spot blotch resistance QTLs mapped on wheat (TGACv1 2014) and barley (Mascher et al., 2017) chromosomes. The map was made using CIRCOS (Circular Genome Data Visualization). Each color indicates a different chromosome. Arcs in bold shows the corresponding marker related to the respective QTL.