Abstract Oat ( Avena sativa L.) seed is a rich resource of beneficial lipids, soluble fiber, protein, and antioxidants, and is considered a healthful food for humans. Despite these characteristics, little is known regarding the genetic controllers of variation for these compounds in oat seed. We sought to characterize natural variation in the mature seed metabolome using untargeted metabolomics on 367 diverse lines and leverage this information to improve prediction for seed quality traits. We used a latent factor approach to define unobserved variables that may drive covariance among metabolites. One hundred latent factors were identified, of which 21% were enriched for compounds associated with lipid metabolism. Through a combination of whole-genome regression and association mapping, we show that latent factors that generate covariance for many metabolites tend to have a complex genetic architecture. Nonetheless, we recovered significant associations for 23% of the latent factors. These associations were used to inform a multi-kernel genomic prediction model, which was used to predict seed lipid and protein traits in two independent studies. Predictions for eight of the 12 traits were significantly improved compared to genomic best linear unbiased prediction when this prediction model was informed using associations from lipid-enriched factors. This study provides new insights into variation in the oat seed metabolome and provides genomic resources for breeders to improve selection for health-promoting seed quality traits. More broadly, we outline an approach to distill high-dimensional ‘omics’ data to a set of biologically-meaningful variables and translate inferences on these data into improved breeding decisions.

Translating insights from the seed metabolome into improved prediction for healthful compounds in oat (Avena sativa L.)