Karnal bunt (KB) disease is one of the most important challenges posed on of wheat (Triticum aestivum L.) industry of Pakistan because of itsinclusionin quarantine list around the globe. This disease is caused by the fungus Tilletia indica M. (Neovossia indica). It affects the grain quality of wheat and hampers its movement in international market resulting in economic losses. Presence of >3% infected grains in wheat lot makes it unsuitable for human consumption. Eradication of this disease is very difficult as no resistant cultivar has been found against KB in Pakistan so far. Genome wide association study (GWAS) was conducted on a set of 199 wheat germplasm collected from Pakistan. In this study 31,000 single nucleotide polymorphism markers were developed by 90K SNP array technology. A linear mixed model in GWAS, accounting for population structure, was fitted to identify significant genomic regions [-log(P) ≥ 4.0] on 6 different chromosomes i.e. 1A, 1D, 2D, 3B, 4A, 5A with novel loci. Candidate genes, through wheat genome assembly, were identified as putative genes related to KB resistance including kinase like protein family. The results of this study can be useful in wheat breeding through marker assisted selection for KB resistant varieties.
