Identification of New Leaf Rust Resistance Loci in Wheat and Wild Relatives by Array-Based SNP Genotyping and Association Genetics

Abstract

Leaf rust caused by Puccinia triticina is the most widespread rust disease of wheat. As pathogen populations are constantly evolving, identification of novel sources of resistance is necessary to maintain disease resistance and stay ahead of this plant-pathogen evolutionary arms race. The wild genepool of wheat is a rich source of genetic diversity, accounting for 44% of the Lr genes identified. Here we performed a genome-wide association study (GWAS) on a diverse germplasm of 385 accessions, including 27 different Triticum and Aegilops species. Genetic characterization using the wheat 90 K array and subsequent filtering identified a set of 20,501 single nucleotide polymorphic (SNP) markers. Of those, 9,570 were validated using exome capture and mapped onto the Chinese Spring reference sequence v1.0. Phylogenetic analyses illustrated four major clades, clearly separating the wild species from the T. aestivum and T. turgidum species. GWAS was conducted using eight statistical models for infection types against six leaf rust isolates and leaf rust severity rated in field trials for 3–4 years at 2–3 locations in Canada. Functional annotation of genes containing significant quantitative trait nucleotides (QTNs) identified 96 disease-related loci associated with leaf rust resistance. A total of 21 QTNs were in haplotype blocks or within flanking markers of at least 16 known Lr genes. The remaining significant QTNs were considered loci that putatively harbor new Lr resistance genes. Isolation of these candidate genes will contribute to the elucidation of their role in leaf rust resistance and promote their usefulness in marker-assisted selection and introgression.

Unravelling consensus genomic regions conferring leaf rust resistance in wheat via meta‐QTL analysis

“…Gu et al (2020), in a recent study, uncovered an RLK gene that plays an important role in resistance to P. triticina infection and has a positive regulatory effect on the hypersensitive reaction cell death process induced by P. triticina. TraesCS6A02G073300, encoding a 3-ketoacyl-CoA synthase, has been reported to harbor quantitative trait nucleotides in close proximity to leaf rust resistance genes in wheat (Fatima et al, 2020). The 50S ribosomal protein L28 encoded by TraesCS1D02G003700 belongs to the ribosomal protein family, and members of this family have been shown to confer tolerance against fungal pathogens in plants (Yang et al, 2013).…”

Unravelling consensus genomic regions conferring leaf rust resistance in wheat via meta-QTL analysis

“…Gu et al (2020), in a recent study, uncovered an RLK gene that plays an important role in resistance to P. triticina infection and has a positive regulatory effect on the hypersensitive reaction (HR) cell death process induced by P. triticina. TraesCS6A02G073300, encoding a 3-ketoacyl-CoA synthase, has been reported to harbour quantitative trait nucleotides (QTNs) in close proximity to leaf rust genes in wheat (Fatima et al 2020). The 50S ribosomal protein L28 encoded by TraesCS1D02G003700 belongs to the ribosomal protein family, and members of this family have been shown to confer tolerance against fungal pathogens in plants (Yang et al 2013).…”

Mining of Leaf Rust Resistance Genes Content in Egyptian Bread Wheat Collection

“…Rusts are caused by Puccinia spp., considered to be the most significant wheat disease and representing a big concern for wheat breeders and farmers [ 8 ]. It leads to tremendous strike yield losses annually to wheat crops worldwide [ 9 , 10 ].…”