Genetic Dissection of Snow Mold Tolerance in US Pacific Northwest Winter Wheat Through Genome-Wide Association Study and Genomic Selection

Abstract

Snow mold is a yield-limiting disease of wheat in the Pacific Northwest (PNW) region of the US, where there is prolonged snow cover. The objectives of this study were to identify genomic regions associated with snow mold tolerance in a diverse panel of PNW winter wheat lines in a genome-wide association study (GWAS) and to evaluate the usefulness of genomic selection (GS) for snow mold tolerance. An association mapping panel (AMP; N = 458 lines) was planted in Mansfield and Waterville, WA in 2017 and 2018 and genotyped using the Illumina® 90K single nucleotide polymorphism (SNP) array. GWAS identified 100 significant markers across 17 chromosomes, where SNPs on chromosomes 5A and 5B coincided with major freezing tolerance and vernalization loci. Increased number of favorable alleles was related to improved snow mold tolerance. Independent predictions using the AMP as a training population (TP) to predict snow mold tolerance of breeding lines evaluated between 2015 and 2018 resulted in a mean accuracy of 0.36 across models and marker sets. Modeling nonadditive effects improved accuracy even in the absence of a close genetic relatedness between the TP and selection candidates. Selecting lines based on genomic estimated breeding values and tolerance scores resulted in a 24% increase in tolerance. The identified genomic regions associated with snow mold tolerance demonstrated the genetic complexity of this trait and the difficulty in selecting tolerant lines using markers. GS was validated and showed potential for use in PNW winter wheat for selecting on complex traits such tolerance to snow mold.

Insights into the Genetic Architecture of Phenotypic Stability Traits in Winter Wheat

“…The majority of these lines were common wheat (284; 62%), whereas the remaining lines were club wheat (172; 38%). This population has been characterized previously for different traits such as grain yield [35], snow mold tolerance [11], eyespot resistance [36], and end-use quality traits [37].…”

“…Our results demonstrate the complex genetic architecture of trait stability and show the potential for improving stability in winter wheat using genomic-assisted approaches.Agronomy 2020, 10, 368 2 of 15 the strength of linkage disequilibrium (i.e., the non-random association of alleles at multiple loci) between markers and functional polymorphism across diverse germplasm [10]. In wheat, GWAS has been conducted in different traits such as grain yield, yield components (thousand kernel weight and kernel number), Fusarium head blight resistance, snow mold tolerance, plant height, and heading date [11][12][13][14][15][16]. Compared with biparental mapping, GWAS results in a higher mapping resolution as it exploits the majority of the recombination histories of the individuals belonging to the diverse population used [17,18].…”

Genomic Selection in Winter Wheat Breeding Using a Recommender Approach

“…An association mapping panel consisting of 456 winter wheat lines adapted to the Pacific Northwest region of the US was evaluated for different grain yield, agronomic, spectral reflectance, and disease resistance traits between the 2015 and 2019 growing seasons across various locations in the state of Washington, US, namely, Lind (LND), Pullman (PUL), Waterville (WAT), and Mansfield (MAN), as described previously [ 17 , 18 , 19 ]. Grain yield (GY), plant height (PH), and heading date (HD) data collection and analyses for an augmented design were previously described in Lozada and Carter [ 20 ].…”

“…Snow mold tolerance (SMT) scores were evaluated in WAT and MAN, based on rating each entry for the disease using a 0-9 scale, where 0 is completely dead, with no green plant tissue visible, and 9 is thriving with no snow mold visible [18]. For these trials, the association mapping panel was planted in paired rows, so that each plot contained two lines-one in the right-side two rows, and one in the left-side two rows [18]. BLUP values for each entry were calculated by combining SMT scores for all environments (ALL) and across years (BLUP17 and BLUP18).…”

Snow mold of winter cereals: a complex disease and a challenge for resistance breeding

“…The association of both traits may have resulted from pleiotropic effects or from the fact, that higher tolerance to low temperatures enabled the plants to better defend themselves against snow mold. Lozada et al (2019) reported the first major study on the genomics of SMR by using genome-wide association study (GWAS) and genomic selection (GS) approaches in winter wheat. This research identified genomic regions in diverse populations of US winter wheat lines from the Pacific Northwest region (PNW).…”