Genome wide association studies and expression analyses identify candidate genes for spot blotch resistance in bread wheat.

GWAS of 1,273 wheat lines identified a stable MTA 3B_6127880 on 3BS chromosome arm for spot blotch resistance, and the associated candidate genes were differentially expressed in resistant vs. susceptible genotypes. Spot blotch (SB), caused by Bipolaris sorokiniana, poses a threat to global wheat production. We evaluated 1,500 elite wheat lines for SB across two environments to identify genomic regions and candidate genes (CGs) conferring resistance. Disease severity, measured as area under the disease progress curve (AUDPC), was negatively correlated with days to heading (DH) and stay-green traits (SGTs). Genome-wide association studies (GWAS) using three different models (MLM, FarmCPU, BLINK) identified seven and eleven stable MTAs for AUDPC and SGTs, respectively, with three (3B_6127880, 5B_546704556, 5B_546132836) common to both traits. To reduce the confounding effects of DH, a separate GWAS was conducted on a subset of genotypes with similar heading dates, confirming 3B_6127880 as a consistent locus for AUDPC, located near to previously known SB QTLs on 3BS chromosome arm. Several other putative MTAs and haplotypes associated with AUDPC and SGTs were identified. A time-course analysis of CGs associated with the important MTAs revealed differential expression in the resistant (Chirya 3) and susceptible (Sonalika) genotypes under SB infection. The identified SNPs, alleles, haplotypes, and CGs may be used in marker-assisted selection and breeding programs to develop wheat varieties with enhanced resistance to SB.