The size and shape of wheat seeds are important characteristics that are monitored in breeding programs due to the impact they may have on the two largest economic factors determining the success of a cultivar, quality and yield. Despite this importance, there are mixed reports on the ability of plant breeders to accurately phenotype as unique a characteristic as 'shape' or to effectively implement selection procedures based on the morphology of wheat seeds. Furthermore, the complex physiological and genetic relationships between individual components of seed morphology complicate the matter of effectively improving yield or quality via seed shape. Due to recent developments in both phenotyping procedures and methods of genetic analysis, plant breeders can now understand seed shape at the genotypic level and translate that knowledge into meaningful improvements to wheat breeding programs. In this dissertation, a thorough review of the literature surrounding seed shape in hexaploid wheat is provided, as well as results of experiments comparing different phenotyping methods, clarification of QTL underlying seed shape in both adapted and 'exotic' mapping populations, as well as preliminary work in phenotypic characterization of unique genetic resources for future mapping work using association mapping. This work adds to the current body of scientific knowledge by improving upon seed phenotyping methods, suggesting differential modes of action of QTL on specific dimensions of seeds, validating previously reported seed shape QTL, and showing the impact of divergent selection for seed fill period on kernel morphology. It is hoped this work will facilitate the further improvement of not only wheat, but all plant organs of economic importance.

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.

Kernel hardness (KHA) is a major factor determining break flour yield (BFY) and end-use quality of common wheat (Triticum aestivum L.). Within the soft wheat class, genotypes with consistently softer grains than common soft wheat are considered to be 'extra-soft'. In addition, 'extra-soft' wheats have greater BFY than common soft wheat lines. In order to better understand this interrelationship, a set of 164 F6-recombinant inbred lines (RILs) developed from a soft x 'extra-soft' wheat cross was evaluated for KHA, BFY, and other related traits in six field environments. The estimates of broad-sense heritability for KHA and BFY ranged from 0.84 to 0.96 and 0.56 to 0.76, respectively. Significant environmental effects and genotype by environment interactions were detected for all traits evaluated. A comprehensive genetic linkage map was created with 650 molecular markers based on this mapping population. Three chromosome translocations, 1BL. 1RS, 2N^S-2AS. 2AL and 5B:7B, were identified during linkage analysis. A total of 47 quantitative trait loci (QTL) were identified for nine traits including KHA, BFY, bran yield (BRN), unground middling yield (MID), plant height (PHT), days to heading (HDD), thousand-kernel weight (TKW), grain protein content (GPC), and test weight (TWT). The number of QTL per trait ranged from three for MID to nine for GPC. The phenotypic variance explained by individual QTL ranged from 5.8 to 47.6%. Among five QTL identified for KHA, the two most important QTL were located on chromosomes 4DS (Xbarc1118-Rht-D1 interval) and 4BS (Xwmc617-Rht-B1 interval), indicating that the 'extra-soft' characteristic was not controlled by the 5DS Hardness (Ha) locus which encodes the two puroindoline genes pinA and pinB. The co-location of QTL for KHA, BFY, BRN, and MID on 4DS suggested that genetic factors affecting KHA may have a pleiotropic effect on BFY. Two co-located QTL for TWT, TKW and PHT were detected on 4DS and 4BS, and a QTL for HDD was detected on 4DS, indicating that these QTL may represent the consequence of the semi-dwarfing green-revolution genes Rht-D1 and Rht-B1 located on 4DS and 4BS, respectively. Additional analysis suggested that the QTL for KHA on 4DS and 4BS are the effects of genes linked to Rht-D1 and Rht-B1, rather than pleiotropic effects of these genes. Some coincident QTL for the traits that were evaluated represent the interrelationships of phenotypic traits, where both KHA and BFY were associated with HDD and TWT based on path coefficient analysis. Association mapping can be an effective means for identifying, validating, and fine mapping genes and QTL in crop plants. To test this approach, a set of 94 diverse elite wheat lines was phenotyped for five important traits and genotyped with 487 molecular markers. In this study, the marker-trait association analysis showed that the gene pinB (Ha locus) was significantly associated with KHA as it is known to define the difference between soft and hard wheat classes. Additionally, the significant associations of marker XwPt-7187 with KHA, XwPt-1250 and XwPt-4628 with TWT, and Xgwm512 with PHT mark the first report of such associations in these genomic regions. This study, aiming at the genetic dissection of wheat kernel extra-softness and related traits, enhanced our understanding of both genetic control of and environmental effects on these important traits. Path coefficient analysis showed the promise of an alternative phenotypic selection approach that is more cost effective than direct measurement of kernel quality. Three chromosome translocations were discovered and their approximate chromosome break points were located. Numerous QTL were identified for these important traits. The major QTL can serve as a start point for fine mapping that eventually lead to the cloning of the QTL through map-based or candidate gene approach. Association mapping, as an alternate approach and complementary tool to QTL mapping, was demonstrated feasible in wheat for identification of marker-trait associations and cross validation of QTL or genes identified from bi-parent mapping populations.

This work is a comprehensive history of wheat across all its main areas of production. New techniques such as in vitro culture now enable the development of a greater level of understanding of the genetics of wheat.