Genome-wide association study reveals favorable alleles associated with common bunt resistance in synthetic hexaploid wheat

Genetic resistance to common bunt is a cost-effective, environmentally friendly, and sustainable approach to controlling the disease. To date, 16 race specific common bunt resistance genes (Bt1-Bt15 and Btp) have been reported in wheat. However, a limited number have been mapped and few markers have been identified, which limits the usage of molecular markers in a marker-assisted breeding program. A total of 125 synthetic hexaploid wheats (SHWs) were evaluated for reactions to a mixture of common bunt races under field conditions in Turkey in 2016 and 2017. The objectives of this study were to identify common bunt resistant genotypes, identify genomic regions conferring resistance to common bunt using 35,798 genotyping-by-sequencing derived single nucleotide polymorphisms (SNPs), and investigate the significant SNPs present within genes using the functional annotations of the underlying genes. We found 29 resistant SHWs that can be used in wheat breeding. The genome-wide association study identified 15 SNPs associated with common bunt resistance and a haplotype block comprising three SNPs in perfect linkage disequilibrium. Five of them were novel and were located on chromosomes 2A, 3D, and 4A. Furthermore, seven of the 15 SNPs were found within genes and had annotations suggesting potential role in disease resistance. This study identified several favorable alleles that decreased common bunt incidence up to 26% in SHWs. These resistant SHWs and candidate genomic regions controlling common bunt resistance will be useful for wheat genetic improvement and could assist in further understanding of the genetic architecture of common bunt resistance.