Genome-wide association study and genomic prediction of resistance to stripe rust in current Central and Northern European winter wheat germplasm

Abstract

Key message We found two loci on chromosomes 2BS and 6AL that significantly contribute to stripe rust resistance in current European winter wheat germplasm. Abstract Stripe or yellow rust, caused by the fungus Puccinia striiformis Westend f. sp. tritici, is one of the most destructive wheat diseases. Sustainable management of wheat stripe rust can be achieved through the deployment of rust resistant cultivars. To detect effective resistance loci for use in breeding programs, an association mapping panel of 230 winter wheat cultivars and breeding lines from Northern and Central Europe was employed. Genotyping with the Illumina® iSelect® 25 K Infinium® single nucleotide polymorphism (SNP) genotyping array yielded 8812 polymorphic markers. Structure analysis revealed two subpopulations with 92 Austrian breeding lines and cultivars, which were separated from the other 138 genotypes from Germany, Norway, Sweden, Denmark, Poland, and Switzerland. Genome-wide association study for adult plant stripe rust resistance identified 12 SNP markers on six wheat chromosomes which showed consistent effects over several testing environments. Among these, two marker loci on chromosomes 2BS (RAC875_c1226_652) and 6AL (Tdurum_contig29607_413) were highly predictive in three independent validation populations of 1065, 1001, and 175 breeding lines. Lines with the resistant haplotype at both loci were nearly free of stipe rust symptoms. By using mixed linear models with those markers as fixed effects, we could increase predictive ability in the three populations by 0.13–0.46 compared to a standard genomic best linear unbiased prediction approach. The obtained results facilitate an efficient selection for stripe rust resistance against the current pathogen population in the Northern and Central European winter wheat gene pool.

Genome-Wide Association Mapping of Resistance to Warrior (-) Yellow Rust Race at the Seedling Stage in Current Central and Northern European Winter Wheat Germplasm

“…This divergence may be because many other loci contribute more to resistance in the fields in response to a population of pathotypes, while in seedling tests there is only a limited response to a few races. However, the combination of the QTL identified in this study on chromosome 1B at the seedling stage and the QTL on chromosome 7DS at the adult stage [16] in the genomic region of Yr29/Lr46 and Yr18/Lr34, respectively, which are likely to have epistatic effects, could be suggested for the development of durable resistance to yellow and leaf rust diseases in future research.…”

“…We compared the results of our previous study [16], using the same association panel at the adult plant stage in the field, with the results of the present study, which were obtained from seedling stage evaluation in the greenhouse. The correlation coefficients between the seedling and adult plant stages were low (-0.01 to 0.25) because most lines were susceptible at the seedling stage but resistant in the field trials.…”

“…We selected a population of 229 winter wheat cultivars and breeding lines for GWAS to capture broad genetic variability in Europe (Table S1). Using breeder knowledge and the coefficient of determination algorithm [41], we collected genotypes from Germany, Austria, Norway, Sweden, Denmark, Poland, and Switzerland comprising 157, 50, 14, 4, 3, 1, and 1 genotype(s), respectively [16].…”

“…Genomic DNA extraction, SNP genotyping, population structure, and LD analyses were performed as described in Shahinnia et al [16]. Briefly, genotyping was performed using the 25 K Infinium iSelect array (TraitGenetics, Seeland OT Gatersleben, Germany), and the physical location of markers was determined by BLAST using the published Chinese Spring genome sequence (IWGSC RefSeq v1.0).…”

“…Despite the enormous impact of the Warrior (-) race on wheat production in Europe, little is known about the genetic control of resistance to this race, which provides the basis for knowledge-based resistance breeding [11]. Quantitative trait loci (QTL) analysis using classical bi-parental linkage mapping and genome-wide association studies using large diversity panels have successfully identified genomic regions associated with yellow rust resistance and contributed to a better understanding of the genetic basis of disease resistance in both seedling and adult stage wheat [8,[11][12][13][14][15][16]. In addition, the identification of diagnostic molecular markers associated with yellow rust genes improves the ability to rapidly incorporate resistance into breeding material through marker-assisted selection (MAS).…”