Genome wide association studies for identification of stripe rust resistance loci in diverse wheat genotypes

Vikesh Tanwar¹Satish Kumar^1*Chuni Lal¹Rajesh Aggarwal¹Rajitha Nair¹Disha Kamboj¹Prem Lal Kashyap¹Dr Viktam Singh²Johar Singh Saini³Sunil Kashyap³Shabir Hussain Wani⁴Rajender Singh¹Ratan Tiwari¹

• ¹Indian Council of Agricultural Research (ICAR), New Delhi, India
• ²Chaudhary Charan Singh Haryana Agricultural University, Hisar, India
• ³Punjab Agricultural University, Ludhiana, India
• ⁴Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India

Rust, a significant foliar disease affecting wheat crops, poses a major concern for wheat breeders and farmers. Under North Indian conditions, one of the biggest threats to wheat productivity is stripe rust caused by the fungus Puccinia striiformis f.sp. triticii (Pst), and the best way to manage it is by growing resistant varieties. However, continuous mutations observed in Pst have evolved new and more virulent strains, making existing resistance genes less effective. To tackle this challenge, a critical necessity exists to continuously identify and incorporate new resistance genes for developing wheat varieties capable of effectively maintaining resistance against the continuously evolving pathogen strains. This proactive approach is essential for ensuring the resilience of wheat production in the face of changing challenges. For this, using 1938 DArT SNPs markers, a genome-wide association study (GWAS) was carried out on 652 elite diverse wheat genotypes to find out genomic regions associated with Pst. The data collected from the adult plant stage at four locations, i.e., Hisar, Karnal, Gurdaspur, and Khudwani. Through comprehensive analysis, twenty-seven genomic regions were identified that are significantly associated with stripe rust resistance, as indicated by a –log 10 p-value ≥3. This identification utilized three distinct models, i.e., general linear model (GLM), mixed linear model (MLM), and FarmCPU, across all examined locations. Out of these identified genomic regions, four were associated with chromosome 2B, 6B, and three with 6A. Several of these regions got annotated with resistance-associated genes viz. NBLRR, F-box, LRR, Protein kinase, Ser/Thr_kinase, Znf_RING-CH, E3-ubiquitin protein ligase, ABC transporter protein, etc. The results of this study lay a foundation for the identification of novel and effective loci associated with Pst. These resistance loci will be deployed in wheat breeding programs more quickly after transforming these loci into user-friendly markers.