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 co-locate 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.

Importance of Landraces in Cereal Breeding for Stress Tolerance

“…Many studies that have focused on landraces as a good reservoir of resistance genes against rusts are available for wheat [ 109 , 110 , 111 , 112 , 113 , 114 , 115 , 116 , 117 , 118 , 119 , 120 , 121 ]. The Portuguese durum wheat landrace PI 192051 has been used to map leaf and stem rust resistance QTLs on chromosomes 4A and 7A, respectively, and to develop SNP markers tightly linked to the identified loci [ 122 ].…”

Meta-QTLs and candidate genes for stripe rust resistance in wheat

“…tritici (Pst) is the most devastating and widely occurring disease in major wheat growing regions of the world. The yield losses due to stripe rust can be upto 70% under severe epidemic conditions, adversely affecting grain-filling duration, leading to poor grain yield and quality 3 . Under severe conditions, the yield losses may approach 100%, when the infection occurs at the seedling stage and environmental conditions are conducive for the pathogen to persist until maturity 4 , 5 .…”

“…Several LD-based genome wide association studies (GWAS) for stripe rust resistance have also been conducted, leading to identification of a large number of marker trait associations (MTAs). The activity involving quantitative genetics studies for this trait increased in recent years, with at least five studies reported in 2021 3 , 29 – 32 .…”

Assessment of Genetic Diversity for Stem Rust and Stripe Rust Resistance in an International Wheat Nursery Using Phenotypic and Molecular Technologies

“…Frequent emergence and rapid spread of more virulent and aggressive pathotypes of Pgt (Pretorius et al, 2000;Nazari et al, 2009) and Pst (Ali et al, 2017, Chen, 2020Chen et al, 2014;Wellings, 2011;FAO, 2014) continue to pose a serious threat to global food security (Singh et al, 2011a, Chen, 2020. The emergence of highly virulent pathotypes of Pgt in the East African highlands combines unique and complex virulence defeating many resistance genes previously effective against local Pgt pathotypes in individual geographies (Vikram et al, 2021). The detection of highly aggressive Pgt pathotypes in Uganda in 1999 (Ug99) rendered more than 80% of global wheat varieties susceptible (Singh et al, 2011a).…”

“…Over the past decade 14 variants within the Ug99 race group have emerged and spread across East African countries (Singh et al, 2011a, Bhavani et al, 2019. The rapid evolution, spread and aggressive nature of new Pst pathotypes in major wheat growing countries around the world has made it the most significant disease (Ali et al, 2017, Vikram et al, 2021. Stripe rust has historically been endemic to areas with humid and cool summers or in warm high-altitude areas with cool nights but in recent years, stripe rust has shown greater adaptation in warmer areas, where the disease was previously less important (Ali et al, 2017, Vikram et al, 2021.…”