Genome-wide association analysis of Mexican bread wheat landraces for resistance to yellow and stem rust

Abstract

Deploying under-utilized landraces in wheat breeding has been advocated to accelerate genetic gains in current era of genomics assisted breeding. Mexican bread wheat landraces (Creole wheats) represent an important resource for the discovery of novel alleles including disease resistance. A core set of 1,098 Mexican landraces was subjected to multi-location testing for rust diseases in India, Mexico and Kenya. The landrace core set showed a continuous variation for yellow (YR) and stem rust (SR) disease severity. Principal component analysis differentiated Mexican landraces into three groups based on their respective collection sites. Linkage disequilibrium (LD) decay varied from 10 to 32 Mb across chromosomes with an averge of 23Mb across whole genome. Genome-wide association analysis revealed marker-trait associations for YR resistance in India and Mexico as well as for SR resistance in Kenya. In addition, significant additive-additive interaction effects were observed for both YR and SR resistance including genomic regions on chromosomes 1BL and 3BS, which colocate with pleiotropic genes Yr29/Lr46/Sr58/Pm39/Ltn2 and Sr2/Yr30/Lr27, respectively. Study reports novel genomic associations for YR (chromosomes 1AL, 2BS, and 3BL) and SR (chromosomes 2AL, 4DS, and 5DS). The novel findings in Creole wheat landraces can be efficiently utilized for the wheat genetic improvement.