Genome wide association studies (GWAS) analysis of karnal bunt resistance in Wheat (Triticum aestivum L.) germplasm collection from Pakistan

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.

小麦印度腥黑穗病（Karnal bunt, KB）是巴基斯坦普通小麦（Triticum aestivum L.）产业面临的最严峻挑战之一，因其被全球纳入检疫名录。该病害由印度腥黑穗病菌（Tilletia indica M.，即Neovossia indica）引起，会降低小麦籽粒品质并阻碍其进入国际市场，进而造成经济损失。当小麦批次中染病籽粒占比超过3%时，该批次小麦即不适于人类食用。由于迄今为止巴基斯坦尚未发现抗KB的小麦品种，因此根除该病害极为困难。本研究对从巴基斯坦收集的199份小麦种质资源开展全基因组关联分析（Genome-Wide Association Study, GWAS），通过90K SNP芯片技术开发了31000个单核苷酸多态性（Single Nucleotide Polymorphism, SNP）标记。采用考虑群体结构的线性混合模型进行GWAS分析，在1A、1D、2D、3B、4A、5A共6条不同染色体上鉴定到显著性基因组区域[-log(P) ≥ 4.0]，且包含新的抗性位点。通过小麦基因组组装鉴定到候选基因，这些基因被认定为与KB抗性相关的推定基因，包括激酶样蛋白家族。本研究结果可通过标记辅助选择技术，用于抗KB小麦品种的育种工作。