Natural and induced variation in faba bean protein traits

Focusing on the genetic improvement of protein traits in faba bean, the aims of this thesis were: to quantitatively investigate patterns of variation and covariation among important protein and field traits; to use GWAS to identify DNA markers associated with positive trait variation; and to characterize novel sources of protein quality variation. Over 200 diverse inbred lines were phenotyped for amino acid contents, protein sub-unit composition, protein and sulphur contents, yield, and seed weight. The genetic and environmental components of trait (co)variation were estimated using multivariate methods. A well-supported (posterior probability = 1.00) negative genetic relationship between yield and protein content was observed, while the relationships between protein content and nutritionally favourable protein quality traits, such as relative cysteine content, were found to be generally positive. Using simulated phenotypes, an experiment was carried out to assess the suitability of different published GWAS methods for use in the study population. Some commonly used frequentist methods were found to perform poorly in terms of prioritizing causal variants and providing reliable measures of significance while two lesser used Bayesian methods performed uniformly best by these metrics. Using real phenotype data, univariate and multivariate GWAS were carried out using the best performing methods from the simulation study. Almost 150 unique significant associations, some of which replicated earlier findings, were reported across 44 univariate and multivariate traits. One locus on chromosome 6 was found to be significantly linked to higher yields and higher protein contents. Finally, a novel protein variant was discovered in an induced mutant line and, using biparental crosses, a putatively causal genetic mutation was mapped to the proximal end of chromosome 4. Together, these results, by identifying markers for use in molecular selection and by quantifying genetic trade-offs to be avoided, could help expedite breeding for faba protein traits.