Wheat (Triticum aestivum, L) and barley (Hordeum vulgare) are widely grown as winter annual grains in a double crop rotation with soybean (Glycine max, L. Merr.) in much of the U.S. Improved management strategies and the development cultivars that meet the quality requirements of higher value end-use markets is important to increase production and profitability of winter annual grains and the double crop rotation in the Eastern U.S. In Chapter I, fifteen commercially relevant winter wheat genotypes ranging in maturity were sown in a split-plot design (sowing date=main plot, genotype=subplot) at three different sowing dates (considered to be 'very early' (20-28 days before recommended), 'early (6-11 days before recommended)', or 'recommended') and replicated three times at eight environments (site-year) from 2015-2018 in VA and KY. Grain yield, tiller estimation, heading date, protein, and 1000-kernel weight were assessed for each yield plot. At all environments, sowing earlier in the fall achieved an earlier (P<0.05) heading date, while grain yields varied depending on environment and genotype. Genotype by sowing date interactions were non-significant (P<0.05) at five site-years and significant (P<0.05) at three site-years. Molecular markers can be associated with phenotypic traits via quantitative trait loci (QTL) mapping, these markers can be used by breeders in marker assisted selection (MAS) to indirectly select phenotypic traits that are difficult or expensive to measure. In Chapter II, the genetic architecture of end-use quality is investigated in two soft red winter wheat bi-parental (Pioneer '25R47' / 'Jamestown' and Pioneer '26R46' / 'Tribute'). Both populations were genotyped with a public 90,000 wheat iSelect SNP-Array, grown over two crop seasons at two Virginia sites, evaluated for quality traits at the USDA-ARS Soft Wheat Quality Lab (SWQL), and analyzed with QTL mapping. This chapter describes a total of 24 putative QTL that were identified on 13 different chromosomes and associated with grain characteristics, milling, and/or baking performance along with phenotypic data for both populations, other putative QTL, and transgressive progeny with exceptional flour yield and cookie diameters. A region on 3A (Qfy.vt.3A.Jtwn) is a strong candidate to be utilized for MAS in soft red winter wheat breeding programs as it explained 6.9-10.3% (Pioneer 25R47 / Jamestown) and 4.6-17.0% (Pioneer 26R46 / Tribute) of the phenotypic variation for flour yield. In Chapter III, malt quality genetic structure was investigated in two winter 'malt x feed' doubled haploid barley breeding populations. Both populations were genotyped with the iSelect InfiniumTM SNP assay consisting of 50,000 barley SNPs, grown in two to three Virginia environments (Blacksburg and Warsaw) during 2017 - 2019, and characterized for 11 phenotypic traits associated with malting quality. QTL mapping validated six previously reported regions (Mohammadi, et al., 2015, GrainGenes 3.0, 2019) that are strongly associated (LOD > 3.0) with relevant malt quality traits. Phenotypic variation for malt quality was largely and consistently explained by QTL on chromosomes 1H, 5H, and 7H in the Endeavor / VA09B-34 population and by two separate QTL on 1H in the Violetta / VA09B-34 population. A region on 4H corresponding with QDp.DiMo-4H, explained between 12.1 - 42.2% (Endeavor / VA09B-34) and 30.0 - 55.7% (Violetta / VA09B-34) of the phenotypic variation for diastatic power (DU). These QTL are recommended for MAS in order to aid breeding strategies that aim to select for improved malting characteristics in Eastern U.S. malt barley breeding material. / Doctor of Philosophy / Wheat (Triticum aestivum, L) and barley (Hordeum vulgare) are staple crops throughout the world, and are the third and fourth most produced cereals crop according to the FAO. Primarily grown for human consumption, wheat and barley provide a significant percentage of the nutritional requirements for the human populations. According to the United Nations, wheat contributes 20% of all calories consumed by humans. Barley is the primary ingredient used to make beer. Increased productivity of all cropping and livestock systems is required in order to feed a growing human population while also restoring and preserving natural ecosystems. This can be accomplished through breeding and improved cropping systems management. Planting of existing cropland more frequently is fundamental to the improvement of cropping system productivity. In much of the U.S. (southern two-thirds of the lower 48), annual winter grains such as wheat and barley can be grown over the winter and spring in between the typical corn (Zea mays subsp. mays) and soybean (Glycine max, L. Merr.) growing seasons. Therefore, producing three crops in two years, as opposed to only two. Only between 6 and 11 million acres are double cropped in the US annually, for perspective, in 2018, 89 million acres of both corn and soybeans, which can only grow in summer, were planted. Over half of the soybean (~45 million) acres in Midwestern and Southeastern states could support double cropping. This is a major opportunity to maximize output per unit area, freeing up less productive land to be restored as natural ecosystems, potentially increasing carbon sequestration and species biodiversity. Winter annual grains have a very similar composition (high carbohydrate, low protein and oil) to corn, and could fill similar end-use markets currently dominated by corn (i.e. ethanol or livestock feed). For double cropping to be more widely deployed, it must be more profitable. Increased profitability of growing three crops in two years as opposed to two must outweigh the added cost of planting, managing, harvesting, and marketing the additional winter crop. Therefore, it is important to investigate management strategies that could increase production per unit area and develop new winter annual cultivars with improved end-use characteristics in order to make the winter annual more desirable to the end-users. Chapter I investigates sowing winter wheat earlier in the fall (i.e. 1st week of Oct. or last week of Sept.) in order to achieve an earlier harvest in the spring and earlier soybean planting (yield decreases 0.5 to 1 bu/ac per day that sowing is delayed), while also offering other benefits such as better-established root systems going into winter, which improves water infiltration and reduces erosion. At all environments, sowing earlier in the fall achieved an earlier heading date, while grain yields varied depending on environment and genotype. Genotype by sowing date interactions were non-significant at five site-years and significant at three site-years. Chapters II and III investigate the genetic architecture of winter wheat and winter barley breeding populations for end-use quality traits (milling/baking and malting). This was done in order to identify molecular markers that could be used to screen breeding material for improved end-use quality. The markers could then be used to assist breeders in developing soft red winter wheat cultivars with greater flour yields/improved baking performance and winter malt barley cultivars that can be grown in the Eastern U.S. and are suitable for the craft beer market. Chapter II describes 24 genomic regions that influences milling/baking performance in two soft red winter wheat breeding populations. Chapter III describes 6 genomic regions that influence malting performance in two winter barley breeding populations.