Association Mapping and Genetic Diversity Studies of Agronomic and Quality Traits in Durum Wheat [Triticum turgidum L. var. durum (Desf.)]

Genetic diversity studies in breeding programs are important to identify parental lines for hybridization and introgression of desirable alleles into elite germplasm. The genetic diversity analysis of 283 North Dakota State University (NDSU) advanced durum wheat breeding lines developed during the last 20 years indicated that the population was structured according to its breeding history. Total genetic diversity analysis (HT = 0.334) showed adequate level of genetic variation. The results will help in breeding efforts to broaden the genetic base and select lines for crossing as well as for genetic and genomic studies to facilitate the combination of desirable alleles. The quantitative nature of important target traits, combined with environmental effects, makes it difficult to bring the desirable improvement in durum wheat to meet the expectations of all the stakeholders involved in the durum wheat industry. With an objective to identify molecular markers for marker-assisted breeding (MAB), the present study attempted to identify marker-trait associations for six agronomic and 29 quality traits using a genome-wide association study (GWAS) mapping approach. The study used two types of phenotypic datasets, a historic unbalanced dataset belonging to a total of 80 environments collected over a period of 16 years and a balanced dataset collected from two environments, to identify the applicability of historic unbalanced phenotypic data for GWAS analysis. A total of 292 QTL were identified for agronomic and quality traits, with 10 QTL showing major effects (R2 >15%). Over 45% of QTL for agronomic and quality traits were present in both the unbalanced and balanced datasets, with about 50% of those present in both environments in the balanced dataset. Genome-wide association mapping studies identified several candidate markers for use in marker-assisted selection (MAS) for height, gluten strength, distribution of small kernels, polyphenol oxidase (PPO) activity, and yield