Genome-wide association mapping reveals a rich genetic architecture of stripe rust resistance loci in emmer wheat (Triticum turgidum ssp. dicoccum)

Abstract

Key message SNP-based genome scanning in worldwide domesticated emmer germplasm showed high genetic diversity, rapid linkage disequilibrium decay and 51 loci for stripe rust resistance, a large proportion of which were novel. AbstractCultivated emmer wheat (Triticum turgidum ssp. dicoccum), one of the oldest domesticated crops in the world, is a potentially rich reservoir of variation for improvement of resistance/tolerance to biotic and abiotic stresses in wheat. Resistance to stripe rust (Puccinia striiformis f. sp. tritici) in emmer wheat has been under-investigated. Here, we employed genome-wide association (GWAS) mapping with a mixed linear model to dissect effective stripe rust resistance loci in a worldwide collection of 176 cultivated emmer wheat accessions. Adult plants were tested in six environments and seedlings were evaluated with five races from the United States and one from Italy under greenhouse conditions. Five accessions were resistant across all experiments. The panel was genotyped with the wheat 90,000 Illumina iSelect single nucleotide polymorphism (SNP) array and 5106 polymorphic SNP markers with mapped positions were obtained. A high level of genetic diversity and fast linkage disequilibrium decay were observed. In total, we identified 14 loci associated with field resistance in multiple environments. Thirty-seven loci were significantly associated with all-stage (seedling) resistance and six of them were effective against multiple races. Of the 51 total loci, 29 were mapped distantly from previously reported stripe rust resistance genes or quantitative trait loci and represent newly discovered resistance loci. Our results suggest that GWAS is an effective method for characterizing genes in cultivated emmer wheat and confirm that emmer wheat is a rich source of stripe rust resistance loci that can be used for wheat improvement.Electronic supplementary materialThe online version of this article (doi:10.1007/s00122-017-2957-6) contains supplementary material, which is available to authorized users.

Genome-Wide Association Studies for Pasmo Resistance in Flax (<em>Linum Usitatissimum L.</em>)

“…GWAS have been successfully applied to the identification of MTAs for many important flax agronomic traits (Soto-Cerda et al, 2014b;a;Xie et al, 2017;You et al, 2018c). The effectiveness of GWAS in identifying MTAs for disease resistance traits is exemplified in wheat for fungal diseases such as Fusarium head blight (FHB) (Buerstmayr et al, 2009), leaf and stem rusts (Liu et al, 2017).…”

Genome-Wide Association Mapping for Stripe Rust Resistance in Pakistani Spring Wheat Genotypes

“…Moreover, a high level of resistance (IT score = 0–3) response appeared at the adult plant stage and a low level of resistance phenotype appeared at the seedling stage. Similarly, a more susceptible response appeared at the seedling stage than at the adult plant stage [ 16 , 27 , 28 , 29 ]. Wheat genotypes were more susceptible to USA stripe rust races compared to Pakistani stripe rust races, where the resistant phenotype response was dominant.…”

“…Population structure, based on the Bayesian model, divides the 465 genotypes into three subpopulations (K = 3). Based on the genotype diversity, a different number of subpopulations were reported, as two subpopulations [ 16 ], three subpopulations [ 29 ], six subpopulations [ 32 ], seven subpopulation [ 31 ] and eight subpopulations [ 27 ]. Critical r 2 was used to estimate the extent of the LD decay with the line intersecting the smooth curve [ 19 ].…”

“…The major factors that influenced the association mapping were the population size, the germplasm choice and the marker density over whole genome [ 32 ]. Several association mapping studies were reported for stripe rust using different molecular markers as diversity arrays technology (DArT) [ 26 , 33 , 34 ], simple sequence repeats (SSR) [ 35 , 36 ] and SNP [ 19 , 27 , 29 , 37 , 38 ].…”

Genomics-assisted breeding in minor and pseudo-cereals

“…Recently, GWAS of minor cereals have focused on practical traits, whereas earlier studies tended to focus on the evaluation and potential of using GWAS in each target species. Disease resistance is one of the most commonly targeted traits for GWAS of oat (Montilla-Bascón et al 2015), emmer wheat (Liu et al 2017), and sorghum (Prom et al 2019). To utilize the rich nutrients of minor cereals (e.g., reviewed by Muthamilarasan et al (2016)), several GWAS results for grain ingredients have been reported in sorghum (Rhodes et al 2014), oat (Newell et al 2012), and foxtail millet (Jaiswal et al 2019).…”