Genome-Wide Association Mapping for Seedling and Adult Plant Resistance to Stripe Rust in Synthetic Hexaploid Wheat

Abstract

Use of genetic diversity from related wild and domesticated species has made a significant contribution to improving wheat productivity. Synthetic hexaploid wheats (SHWs) exhibit natural genetic variation for resistance and/or tolerance to biotic and abiotic stresses. Stripe rust caused by (Puccinia striiformis f. sp. tritici; Pst), is an important disease of wheat worldwide. To characterise loci conferring resistance to stripe rust in SHWs, we conducted a genome-wide association study (GWAS) with a panel of 181 SHWs using the wheat 9K SNP iSelect array. The SHWs were evaluated for their response to the prevailing races of Pst at the seedling and adult plant stages, the latter in replicated field trials at two sites in Ethiopia in 2011. About 28% of the SHWs exhibited immunity at the seedling stage while 56% and 83% were resistant to Pst at the adult plant stage at Meraro and Arsi Robe, respectively. A total of 27 SNPs in nine genomic regions (1BS, 2AS, 2BL, 3BL, 3DL, 5A, 5BL, 6DS and 7A) were linked with resistance to Pst at the seedling stage, while 38 SNPs on 18 genomic regions were associated with resistance at the adult plant stage. Six genomic regions were commonly detected at both locations using a mixed linear model corrected for population structure, kinship relatedness and adjusted for false discovery rate (FDR). The loci on chromosome regions 1AS, 3DL, 6DS and 7AL appeared to be novel QTL; our results confirm that resynthesized wheat involving its progenitor species is a rich source of new stripe (yellow) rust resistance that may be useful in choosing SHWs and incorporating diverse yellow rust (YR) resistance loci into locally adapted wheat cultivars.

Novel QTL for Stripe Rust Resistance on Chromosomes 4A and 6B in Soft White Winter Wheat Cultivars

“…In the FinchˆEltan RIL population, we have presented two QTL which can be selected via molecular markers to incorporate resistance into wheat varieties. The lack of polymorphisms in the D genome in this population, which is not uncommon [46,47], did not allow us to analyze much of the D genome for resistance loci. Therefore, there may be additional QTL from these cultivars that we were not able to identify with the SNP system used.…”

Mining Centuries Old In situ Conserved Turkish Wheat Landraces for Grain Yield and Stripe Rust Resistance Genes

“…Therefore, to avoid potential risk of type II error, a threshold was determined by obtaining p -values within the bottom 0.1 percentile of the distribution. This approach has been used in a few recent GWA studies in wheat (Zegeye et al, 2014; Gao et al, 2016). Based on this approach, a threshold p -value of 0.001 and 0.0001 corresponded to the bottom 0.1 percentile of the distribution for grain yield and yield components and for stripe rust resistance, respectively.…”

A MAGIC population-based genome-wide association study reveals functional association of GhRBB1_A07 gene with superior fiber quality in cotton

“…GWAS has several advantages over traditional QTL analysis, such as higher diversity, better utility of the identified QTL across diverse germplasm, and reduced time required for population development [10–12]. GWAS has been successfully employed in many plants, such as Arabidopsis [13], maize [10, 14], barley [15, 16], wheat [17, 18], rice [19], oat [20], sorghum [21] and soybean [11, 22]. In cotton, a few genetic studies using GWAS have been reported [2, 4, 23, 24].…”