Genome-wide association mapping for stripe rust (Puccinia striiformis F. sp. tritici) in US Pacific Northwest winter wheat (Triticum aestivum L.).

KEY MESSAGE: Potential novel and known QTL for race-specific all-stage and adult plant resistance to stripe rust were identified by genome-wide association mapping in the US PNW winter wheat accessions. Stripe rust (Puccinia striiformis F. sp. tritici; also known as yellow rust) is a globally devastating disease of wheat (Triticum aestivum L.) and a major threat to wheat production in the US Pacific Northwest (PNW), therefore both adult plant and all-stage resistance have been introduced into the winter wheat breeding programs in the PNW. The goal of this study was to identify quantitative trait loci (QTL) and molecular markers for these resistances through genome-wide association (GWAS) mapping in winter wheat accessions adapted to the PNW. Stripe rust response for adult plants was evaluated in naturally occurring epidemics in a total of nine environments in Washington State, USA. Seedling response was evaluated with three races under artificial inoculation in the greenhouse. The panel was genotyped with the 9K Illumina Wheat single nucleotide polymorphism (SNP) array and additional markers linked to previously reported genes and QTL for stripe rust resistance. The population was grouped into three sub-populations. Markers linked to Yr17 and previously reported QTL for stripe rust resistance were identified on chromosomes 1B, 2A, and 2B. Potentially novel QTL associated with race-specific seedling response were identified on chromosomes 1B and 1D. Potentially novel QTL associated with adult plant response were located on chromosomes 2A, 2B, 3B, 4A, and 4B. Stripe rust was reduced when multiple alleles for resistance were present. The resistant allele frequencies were different among sub-populations in the panel. This information provides breeders with germplasm and closely linked markers for stripe rust resistance to facilitate the transfer of multiple loci for durable stripe rust resistance into wheat breeding lines and cultivars.

Identification of quantitative trait loci (QTL) for resistance to Fusarium crown rot (Fusarium pseudograminearum) in multiple assay environments in the Pacific Northwestern US.

Fusarium crown rot (FCR), caused by Fusarium pseudograminearum and F. culmorum, reduces wheat (Triticum aestivum L.) yields in the Pacific Northwest (PNW) of the US by as much as 35%. Resistance to FCR has not yet been discovered in currently grown PNW wheat cultivars. Several significant quantitative trait loci (QTL) for FCR resistance have been documented on chromosomes 1A, 1D, 2B, 3B, and 4B in resistant Australian cultivars. Our objective was to identify QTL and tightly linked SSR markers for FCR resistance in the partially resistant Australian spring wheat cultivar Sunco using PNW isolates of F. pseudograminerarum in greenhouse and field based screening nurseries. A second objective was to compare heritabilities of FCR resistance in multiple types of disease assaying environments (seedling, terrace, and field) using multiple disease rating methods. Two recombinant inbred line (RIL) mapping populations were derived from crosses between Sunco and PNW spring wheat cultivars Macon and Otis. The Sunco/Macon population comprised 219 F(6):F(7) lines and the Sunco/Otis population comprised 151 F(5):F(6) lines. Plants were inoculated with a single PNW F. pseudograminearum isolate (006-13) in growth room (seedling), outdoor terrace (adult) and field (adult) assays conducted from 2008 through 2010. Crown and lower stem tissues of seedling and adult plants were rated for disease severity on several different scales, but mainly on a numeric scale from 0 to 10 where 0 = no discoloration and 10 = severe disease. Significant QTL were identified on chromosomes 2B, 3B, 4B, 4D, and 7A with LOD scores ranging from 3 to 22. The most significant and consistent QTL across screening environments was located on chromosome 3BL, inherited from the PNW cultivars Macon and Otis, with maximum LOD scores of 22 and 9 explaining 36 and 23% of the variation, respectively for the Sunco/Macon and Sunco/Otis populations. The SSR markers Xgwm247 and Xgwm299 flank these QTL and are being validated for use in marker-assisted selection for FCR resistance. This is the first report of QTL associated with FCR resistance in the US.

Chromosomes 3B and 4D are associated with several milling and baking quality traits in a soft white spring wheat (Triticum aestivum L.) population.

Wheat is marketed based on end-use quality characteristics and better knowledge of the underlying genetics of specific quality parameters is essential to enhance the breeding process. A set of 188 recombinant inbred lines from a 'Louise' by 'Penawawa' mapping population was grown in two crop years at two locations in the Pacific Northwest region of the United States and data were collected on 17 end-use quality traits using established quality analysis protocols. Using an established genetic linkage map, composite interval mapping was used to identify QTL associated with 16 of the 17 quality traits. QTL were found on 13 of the 21 wheat chromosomes. A large number of QTL were located on chromosomes 3B and 4D and coincided with traits for milling quality and starch functionality. Chromosome 3B contained 10 QTL, which were localized to a 26.2 cM region. Chromosome 4D contained 7 QTL, all of which were located on an 18.8 cM region of this chromosome. The majority of the alleles for superior end-use quality were associated with the cultivar Louise. The identified QTL detected remained highly significant independent of grain yield and protein quantity. The identification of these QTL for end-use quality gives key insight into the relationship and complexity of end-use quality traits. It also improves our understanding of these relationships, thereby allowing plant breeders to make valuable gains from selection for these important traits.

Identifying QTL for high-temperature adult-plant resistance to stripe rust (Puccinia striiformis f. sp. tritici) in the spring wheat (Triticum aestivum L.) cultivar 'Louise'.

Over time, many single, all-stage resistance genes to stripe rust (Puccinia striiformis f. sp. tritici) in wheat (Triticum aestivum L.) are circumvented by race changes in the pathogen. In contrast, high-temperature, adult-plant resistance (HTAP), which only is expressed during the adult-plant stage and when air temperatures are warm, provides durable protection against stripe rust. Our objective was to identify major quantitative trait loci (QTL) for HTAP resistance to stripe rust in the spring wheat cultivar 'Louise'. The mapping population consisted of 188 recombinant inbred lines (RIL) from a Louise (resistant) by 'Penawawa' (susceptible) cross. F(5:6) lines were evaluated for stripe rust reaction under natural infection in replicated field trials at five locations in the US Pacific Northwest in 2007 and 2008. Infection type (IT) and disease severity were recorded for each RIL 2-4 times per location. In all environments, Penawawa, the susceptible parent, was rated with an IT ranging from 6 to 8 at all growth stages evaluated. In contrast, Louise, the resistant parent, was rated with an IT of 2 or 3 across growth stages. Distribution of IT values was bimodal, indicating a single major gene was affecting the trait. The parents and RIL population were evaluated with 295 polymorphic simple sequence repeat and one single nucleotide polymorphism markers. One major QTL, designated QYrlo.wpg-2BS, associated with HTAP resistance in Louise, was detected on chromosome 2BS (LOD scores ranging from 5.5 to 62.3 across locations and years) within a 16.9 cM region flanked by Xwmc474 and Xgwm148. SSR markers associated with QYrlo.wpg-2BS are currently being used in marker-based forward breeding strategies to transfer the target region into adapted germplasm to improve the durability of resistance in resulting cultivars.