Soft white wheat is used in domestic and foreign markets for various end products requiring specific quality profiles. Phenotyping for end-use quality traits can be costly, time-consuming and destructive in nature, so it is advantageous to use molecular markers to select experimental lines with superior traits. An association mapping panel of 469 soft white winter wheat cultivars and advanced generation breeding lines was developed from regional breeding programs in the U.S. Pacific Northwest. This panel was genotyped on a wheat-specific 90 K iSelect single nucleotide polymorphism (SNP) chip. A total of 15,229 high quality SNPs were selected and combined with best linear unbiased predictions (BLUPs) from historical phenotypic data of the genotypes in the panel. Genome-wide association mapping was conducted using the Fixed and random model Circulating Probability Unification (FarmCPU). A total of 105 significant marker-trait associations were detected across 19 chromosomes. Potentially new loci for total flour yield, lactic acid solvent retention capacity, flour sodium dodecyl sulfate sedimentation and flour swelling volume were also detected. Better understanding of the genetic factors impacting end-use quality enable breeders to more effectively discard poor quality germplasm and increase frequencies of favorable end-use quality alleles in their breeding populations.

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1347ReseaRch C otton fiber is a highly variable natural product. Depending on growing conditions and genotypes, fiber yield and quality can differ significantly across locations. There are, however, several fiber properties that govern the farm gate value of upland cotton: high volume instrument (HVI) upper-half mean length (UHML), fiber bundle strength (strength), micronaire, color, and trash content. Other fiber quality traits, for example, fiber maturity, that is, the secondary cell wall thickness relative to its perimeter, also impact end product quality but are not a part of the U.S. marketing system. Plant breeders working to improve upland cotton quality usually concentrate on UHML and strength while holding micronaire, uniformity of fiber length, and elongation of fiber before breakage within market or predetermined limits. In plant breeding, regardless of the crop species, breeding efforts tend to focus on genetic gain, primarily for yield, within their target environment or environments and yield and trait stability across their target environments, generally referred to as genotype ABSTRACT Cotton (Gossypium hirsutum L.) is a high value cash crop for the southern United States with an annual production of over 3.2 million t. For breeders to fully maximize yield potential and to improve fiber properties of new cotton cultivars, it is important to use representative test locations to evaluate genotype × environment (G×E) effects and trait repeatability. In this study, G×E analysis was performed on 31 upland cotton genotypes developed by the Texas A&M AgriLife research Cotton Improvement Lab along with three commercial check cultivars. Seven distinct test locations across Texas representing major cotton growing regions were selected for the 2-yr study. All experimental plots were managed with standard field practices and were machine harvested to determine yield. Hand-harvested boll samples were ginned on a 10-saw laboratory gin and high volume instrument (HVI) fiber properties determined. Yield and lint percent along with HVI fiber bundle strength (strength) and upper-half mean length (UHML) were analyzed. optimum test locations were identified for lint yield, lint percent, strength, and UHML. Combined correlation analysis of all traits indicated a high association between fiber yield and lint percent but highly negative association of yield traits and UHML. repeatability of UHML and strength were 0.85 and 0.75, respectively, across all test locations in Texas over 2 yr suggesting a large genotypic component governing those traits.

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.

Cotton (Gossypium hirsutum L.) fiber color is influenced by biotic and abiotic factors as well as genetics. After boll opening, exposure to the elements modifies fiber color; fibers may become grayer (excessive moisture leading to biotic activity) and lose luster (lower reflectance). Excessive weathering will lead to poorer processing efficiency and lower dye uptake. Genetically whiter cotton fibers could result in reduced use of bleaching agents before dyeing, thus lowering production costs and providing a more environmentally‐friendly product. Cotton cultivars TAM B182–33 ELS (Extra Long Staple) and Tamcot CAMD‐E were crossed with 12 cultivars from China, 7 from northern Africa, 10 from southern Africa, and 7 from the United States and grown in a line x tester design at College Station, TX during 2010 and 2011. Seedcotton was harvested by hand on the day of maturity, deburred, and allowed to dry in limited light. Lint was separated into 2‐g subsamples, and color measurements were taken using a Konica‐Minolta CR‐310 reflectance colorimeter. Absolute color measurements were obtained in the CIE L*a*b* color system. General and specific combining abilities for all the variables were determined. Genetic variation existed for all color parameters measured. The cultivars A 7215 (southern Africa), Tejas (United States), PAN 575 (northern Africa), Lintsing Sze Tze 4B (China), F 280 (northern Africa), and Nanging #12 (China) and their F1 progenies demonstrated superior whiteness. PAN 575 was the best general combiner for whiteness with the two testers in the study.