Novel genomic regions associated with seedling and adult plant stage leaf rust resistance in bread wheat (Triticum aestivum L.) identified through multi-locus genome-wide association studies (ML-GWAS) Rust diseases continue to pose threat to wheat production and productivity. Leaf rust is one of the most important rust diseases caused by the fungal pathogen, Puccinia triticina. Imparting host resistance and deploying resistant cultivars are the most economic, reliable and sustainable way to manage the leaf rust of wheat. To identify the genomic regions or quantitative trait nucleotides (QTNs) associated with seedling and adult plant leaf rust resistance, multilocus genome-wide association studies (ML-GWAS) were performed on the association mapping (AM) panel of 400 diverse wheat genotypes using 35K single-nucleotide polymorphism (SNP) genotyping assays. AM panel was also subjected to phenotypic evaluation of leaf rust resistance at seedling and adult plant stage. Six multi-locus GWAS models revealed a set of 201 significantly associated QTNs for seedling and 65 QTNs for adult plant resistance (APR), explaining 1.98-31.72% of the phenotypic variation for leaf rust. Among these QTNs, 51 QTNs for seedling and 15 QTNs for APR were consistently detected in at least two GWAS models and were considered reliable QTNs. Three genomic regions were pleiotropic, each controlling two pathotype-specific seedling resistances to leaf rust. Candidate genes, such as leucine-rich repeat receptor-like (LRR) protein kinases, P-loop containing nucleoside triphosphate hydrolase and serine-threonine/tyrosine-protein kinases (STPK), which have a role in pathogen recognition and
disease resistance were identified with the significantly associated genomic regions. The QTNs identified in this study can used in the wheat improvement programs aimed at enhancing resistance to leaf rust and developing next-generation leaf rust-resistant cultivars.