Genome-wide association mapping for eyespot disease in US Pacific Northwest winter wheat

Abstract

Eyespot, caused by the soil-borne necrotrophic fungi Oculimacula yallundae and O. acuformis, is a disease of major economic significance for wheat, barley and rye. Pacific Northwest (PNW) winter wheat (Triticum aestivum L.) grown in areas of high rainfall and moderate winters is most vulnerable to infection. The objective of this research was to identify novel genomic regions associated with eyespot resistance in winter wheat adapted to the PNW. Two winter wheat panels of 469 and 399 lines were compiled for one of the first genome-wide association studies (GWAS) of eyespot resistance in US winter wheat germplasm. These panels were genotyped with the Infinium 9K and 90K iSelect SNP arrays. Both panels were phenotyped for disease resistance in a two-year field study and in replicated growth chamber trials. Growth chamber trials were used to evaluate the genetic resistance of O. acuformis and O. yallundae species separately. Best linear unbiased predictors (BLUPs) were calculated across all field and growth chamber environments. A total of 73 marker-trait associations (MTAs) were detected on nine different chromosomes (1A, 2A, 2B, 4A, 5A, 5B, 7A, 7B and 7D) that were significantly associated (p-value <0.001) with eyespot resistance in Panel A, and 19 MTAs on nine different chromosomes (1A, 1B, 2A, 2D, 3B, 5A, 5B, 7A, and 7B) in Panel B. The most significant SNPs were associated with Pch1 and Pch2 resistance genes on the long arms of chromosome 7D and 7A. Most of the novel MTAs appeared to have a minor effect on reducing eyespot disease. Nevertheless, eyespot disease scores decreased as the number of resistance alleles increased. Seven SNP markers, significantly associated with reducing eyespot disease across environments and in the absence and presence of Pch1 were identified. These markers were located on chromosomes 2A (IWB8331), 5A (IWB73709), 5B (IWB47298), 7AS (IWB47160), 7B (IWB45005) and two SNPs (Ex_c44379_2509 and IAAV4340) had unknown map positions. The additive effect of the MTAs explained most of the remaining phenotypic variation not accounted for by Pch1 or Pch2. This study provides breeders with adapted germplasm and novel sources of eyespot resistance to be used in the development of superior cultivars with increased eyespot resistance.

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

“…Regression analyses showed the direct relationship between increasing number of favorable alleles and increased snow mold tolerance demonstrating an additive response. Previously, pyramiding favorable alleles was observed to increase resistance for stripe rust (Naruoka et al, 2015) and eyespot disease (Lewien et al, 2018) for the same population of US PNW winter wheat lines. Lines differing at a single locus (e.g., lines with eight favorable alleles vs. lines having nine) had similar levels of tolerance, suggesting that additive effects for these alleles might not be enough for significant differences to occur.…”

“…This population consisted of club (172 lines; 37.6%) and common (286; 62.4%) wheat. The AMP was previously characterized for different traits including stripe rust resistance (Naruoka et al, 2015; Liu et al, 2018), eyespot resistance (Lewien et al, 2018), end-use quality traits (Jernigan et al, 2018), preharvest sprouting tolerance, and low falling number (Martinez et al, 2018). Additionally, 295 winter wheat breeding lines from the Washington State University (WSU) Winter Wheat Breeding and Genetics Program evaluated for snow mold tolerance between 2015 and 2018 were used as selection candidates (TST lines) for independent validations.…”

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].…”

Genomic regions and candidate genes linked with Phytophthora capsici root rot resistance in chile pepper (Capsicum annuum L.)

“…Interaction of QTL for P. capsici resistance have been well established in previous studies in chile pepper [ 45 , 51 – 53 ], and indicates the potential of combining favorable alleles to improve disease resistance. In other crops such as winter wheat ( Triticum aestivum L.), pyramiding resistant alleles has been demonstrated to increase resistance or tolerance to various diseases such as stripe rust (causative agent: Puccinia striiformis [ 54 ], eyespot disease ( Oculimacula yallundae and Oculicmacula acuformisi ) [ 55 ]; and snow mold ( Microdochium [ Fusarium ] nivale ) [ 56 ]. The QTL interactions identified in the current study have not been reported elsewhere, and hence could represent novel genomic regions showing additive effects that could be targeted for future breeding and selection for improved P. capsici resistance.…”