Improving Small Grains: Dissecting the Genetic Control of End-Use Quality and Stagonospora Resistance in Wheat, and Freeze Tolerance in Oat

Small grains production in North Carolina faces a number of challenges, from disease pressure to abiotic stresses. In addition to improving varieties for these traits, breeders must seek to improve yield while maintaining acceptable levels of end-use quality. The majority of these traits are highly quantitative in nature, with low to moderate levels of heritability. Breeding efforts can potentially be facilitated through the use of molecular markers in a marker assisted selection scheme.;Soft wheats are used in the production of a diverse range of food products and require different flour characteristics compared to hard wheats. While the selection of varieties with superior end-use quality could be enhanced through marker assisted selection (MAS), few linkage or association mapping studies have been conducted using soft wheat germplasm. A total of 171 recombinant inbred lines (RILs) from the cross 'AGS 2000' x 'NC-Neuse' were assessed for eight milling and baking quality parameters, based on samples collected from six environments. Trait heritabilities ranged from 0.71-0.93, with a significant proportion of transgressive segregation among the RILs for most traits. A total of twenty significant logarithm of odds (LOD) peaks were detected in at least three of the six environments for the eight quality parameters and grouped into 11 putative QTL on eight separate chromosomes. The proportion of desirable parental alleles was evenly split between NC-Neuse and AGS 2000 amongst the 11 QTL, and many progeny showed superior quality to either parent for most of the quality traits. These loci can be targeted for marker assisted selection, especially within soft red winter wheat germplasm in the southern United States.;Stagonospora nodorum blotch (SNB; causal agent: Parastagonospora nodorum) is a common and potentially severe pathogen of wheat which reduces both yield and grain quality. In this study, a collection of 382 soft winter wheat landraces, breeding lines, and cultivars from the eastern United States were evaluated for resistance to SNB, and a genome-wide association analysis using marker data from 3492 SNP markers was conducted. Significant differences (p < 0.01) were observed amongst lines and environments and their interaction. Genetic association analyses using the LS means from within and across environments identified a total of eleven loci that were detected in three or more out of six environments. These loci represent a stable source of resistance to SNB for the southeastern United States.;Oat is the least cold hardy small grain, and production of winter oat in North Carolina is frequently reduced due to severe freezing events during the winter. Access to a set of molecular markers linked to QTL for crown freezing tolerance could facilitate efforts to improve winter hardiness in elite winter oat germplasm. A panel of 213 diverse oat lines were evaluated in a controlled environment chamber for their survivability following freezing at -9 °C. Significant differences were observed both between lines, and across runs of the experiment. However, analysis of the check lines only showed significant differences between lines, indicating that much of the variability between runs can be ascribed to the moderately freeze tolerant lines. All lines were previously genotyped using both a 6K Illumina Infinium SNP chip, and via genotyping by sequencing (GBS). A total of eight significant markers were detected on chromosomes 5C, 6C, 11A, and either 8A or 14D, with R2 ranging between 0.039 and 0.06. These markers may be helpful in screening parents and their progeny when breeding for improved freeze tolerance in oats.