Wheat grain quality has a complex genetic architecture heavily influenced by the growing environment. Consistency in wheat quality not only affects the efficiency of milling and baking but also the quality of end-use products. The objectives of this study were to 1) analyze the different wheat quality parameters in Recombinant Inbred Lines (RILs) grown under different environments, and 2) to identify Quantitative Trait Loci (QTLs) associated with quality stability in RILs grown under different environments. A set of 180 RILs derived from two spring wheat lines "Halberd" and "Len" were grown at Uvalde and College Station TX, in the 2009/2010 growing season and at Chillicothe and College Station TX, in 2010/2011 growing seasons. The experiment was laid out in Randomized Complete Block Design (RCBD) with four replications within each location. Each line was tested for multiple quality traits that included grain hardness, protein content, dough mixing properties and bread baking quality using Single Kernel Characterization System (SKCS), Near-Infrared Reflectance Spectrometry (NIRS) analysis, mixograph and the Sodium Dodecyl Sulfate Sedimentation (SDSS) test. Genetic linkage map construction was carried out with 116 single nucleotide polymorphism (SNP) markers in the RILs. Then composite interval mapping was carried out to identify QTLs associated with quality traits. The SDSS column height was positively correlated across four environments. Similarly, it was found to have significant positive correlation with mixing tolerance and peak time within and also across locations. However, the SDSS was negatively correlated with the hardness index. The protein percent was not significant with any of the quality traits within and across environments. We were able to detect many QTLs for different quality traits but most of them were site specific. Only a few QTLs were consistent across environments. Most of the QTLs for quality traits i.e., SDSS, peak time, mixing tolerance and hardness index were identified on chromosome 1B. We were able to detect overlapped QTLs for SDSS column height and mixing tolerance on chromosome 1B. Furthermore, overlapping QTLs for mixing tolerance and peak time were detected on an unknown chromosome. We also detected overlapping QTLs for hardness index on chromosome 1B. We identified one stable QTL for SDSS column height on chromosome 4B. This QTL was detected based on the coefficient of variation (CV) for SDSS in four different environments.

Four agronomically and genetically diverse winter wheat parents were utilized as the experimental organisms. Atlas 66 and NB 68513 were selected as cultivars with a high and stable protein content when grown under different environmental condidtions. They are intermediate for grain yield when grown in the Pacific Northwest. Yamhill and Hyslop represented low protein, high yielding cultivars adapted to the Pacific Northwest. Data were obtained from crosses between the two high protein cultivars and the two low protein cultivars based on the performance of the parents and the F1 and F2 generations. These experimental populations were grown in 1971 at the Pendleton Experiment Station and the Central Oregon Experimental site at Madras, Oregon. Measurements were made on an individual plant basis for protein content, grain yield, 50 kernel weight, kernels per spike, tillers per plant and plant height. Differences among and within crosses were determined by the analysis of variance. Information concerning the nature of inheritance was obtained by comparing the F1 and F2 means in relation to performance of the parents; the frequency distribution of the generations for protein content; and by determining broad and narrow sense heritability estimates for the six characters studied. The existence of possible phenotypic associations among the six characters studied was determined by using correlation coefficients. In order to evaluate the possible direct and indirect effects of grain yield and the components of yield on protein content, path coefficient analyses were employed. Significant differences were observed among and within crosses at both the Pendleton and Madras sites for most characters measured. The F1 and F2 mean values were found to be near the mid-parent of the two parents in all four crosses for plant height, 50 kernel weight and kernels per spike. There were several exceptions depending on the particular cross and specific character. Protein content mean values were also intermediate between the two parents for the F1 and F2 generations. In crosses involving Hyslop, the mean values tended to be near the highest parent. Little or no transgressive segregation was noted in the F2 generation. Evidence of non additive gene action was noted both for grain yield and tiller number in the F1 and F2 generations with the mean values exceeding the highest parent in all crosses for grain yield at the Pendleton site. Tillers per plant at Pendleton and both tillers per plant and grain yield at Madras also showed some degree of hybrid vigor, but the magnitude depended on the particular cross. The high broad and narrow sense heritability estimates obtained both at Pendleton and Madras for all traits suggested that there was a large amount of genetic variation present for the characters studied. The narrow sense estimates further suggested that a high percentage of the total genetic variation was due to genes which function in an additive manner. Significant negative correlations were noted between protein content and grain yield including some of the components of yield. In evaluating the direct and indirect effects with path coefficient analysis, these negative associations resulted from the large negative indirect effects of 50 kernel weight and kernels per spike on protein content via grain yield at the Madras site. At the Pendleton site, where moisture became a limiting factor, the negative association resulted largely as the indirect effect of 50 kernel weight on protein content through grain yield. The large environmental influence on protein content was particularly striking at the Pendleton site. With the spring application of nitrogen, a delay in maturity for Hyslop and Yamhill was noted and with the subsequent loss of moisture, shriveled grain resulted and hence a higher protein content with lower grain yield. This resulted in the grain protein of Hyslop and Yamhill being higher than that of Atlas 66 and NB 68513. The results of this study suggest that it may be necessary to compromise in attempting to develop high protein lines with maximum yield. However, it should be possible to increase the protein content two to three percent and still maintain the yielding ability of Hyslop and Yamhill.

Wheat (Triticum aestivum L.) is used in diverse baked products that require specific end use quality traits. Kernel texture, flour water absorption capacity, gluten strength, starch composition, and other flour constituents all influence overall flour functionality and dough rheology, specifying both wheat market class and intended end product. Wheat breeders need to develop cultivars with superior end-use quality traits, while also optimizing important agronomic traits. Our first objective was to use a genetic linkage map and 207 recombinant inbred lines (RIL) from a soft white 'Coda' by 'Brundage' cross to identify quantitative trait loci (QTL) for grain, milling, and baking traits. The linkage map was developed using 570 single nucleotide polymorphisms (SNP) and 136 simple sequence repeat markers. The RILs were grown in five locations in Idaho and Washington from 2006 to 2013. We detected three QTL on chromosomes 2D, 4B, and 6B that were consistently associated with multiple end-use quality traits. Our second objective was to use a genetic linkage map and 131 RILs from a soft white 'Louise' by 'Alpowa' cross to identify QTL associated with arabinoxylan content and milling traits. The linkage map consisted of 924 SNPs and 41 linkage groups. This population was grown in three Washington locations from 2011 to 2012. We detected 28 QTL associated with seven arabinoxylan content and milling traits. Our third objective was to use 480 advanced breeding lines and Pacific Northwest cultivars to identify molecular markers associated with 21 end-use quality traits. Genotypic data from the iSelect 90K SNP chip was combined with best linear unbiased predictions of historic phenotypic data from the USDA-ARS Western Wheat Quality Laboratory. Genome-wide association mapping in the R package, genome association and prediction integrated tool (GAPIT), detected significant markers for multiple end-use quality traits on chromosomes1B, 1D, 2D, 5A, 5B, and 7A. An improved understanding of the genetic architecture underlying end-use quality traits in wheat may assist breeders with cultivar development for superior end-use quality, particularly by increasing frequencies of favorable alleles in breeding populations. Cultivars with superior end-use quality will allow US wheat producers to maintain domestic and international markets.

Grain yield and grain protein are often negatively associated in wheat. When yield increases and grain protein decreases, there can be an adverse effect on the milling and baking quality if the desired end product is bread flour. It has been suggested that this inverse association is the result of selecting for a higher harvest index (ratio of grain yield to total biomass), to enhance grain yield. Parents, Fl, F2, and F3 generations of three crosses and reciprocal backcrosses of one cross were space-planted to study the association of grain protein content with grain and biological yields, harvest index, and related traits. Selection P5221, a high protein selection, was a common parent in crosses with three different genotypes. Differences were observed among generations within crosses for biological yield, grain yield, harvest index, grain protein content, grain hardness, and protein yield. The coefficients of variation for the measured traits were low for the three crosses. No associations between grain protein content and grain yield were observed in the populations studied. The largest association detected was between harvest index and grain protein. The r values ranged from -0.39 to -0.46, and rho was not different from -0.50 in two of the crosses. Path coefficient analyses revealed that this association was mostly due to the direct effect of harvest index on grain protein content, with little direct or indirect effect via other plant traits. In the cross P5221/ORCR 8313, biological yield exhibited a moderately large (0.64) direct effect on grain protein content; however this was offset by the negative indirect effect of tiller number. The R2 of the path analyses were relatively small for the three crosses, indicating that most of the variation in grain protein content was not explained by the variables included in the analyses. A possible negative association between grain protein content and harvest index, although moderate, suggests that selection for high yield should not be based on further increases of harvest index because grain protein could decrease.