UC Davis

This thesis explores advanced strategies to enhance strawberry breeding by applying genomic prediction, harnessing underutilized genetic diversity, and investigating key genetic mutations affecting fruit quality traits. The first chapter focuses on enhancing strawberry resistance to Phytophthora crown rot (PhCR), a soil-borne disease that thrives in warm, wet conditions and severely impacts yields. It addresses the limited genetic gains in breeding for PhCR resistance and the discovery of a significant locus, RPc2, which explains a substantial portion of genetic variance. Incorporating underutilized gene bank resources doubled additive genetic variance and improved genomic prediction accuracy, highlighting the potential of genomic selection for enhancing PhCR resistance.

The second chapter further solidifies the success of these strategies, evaluating the use of useful heterosis and genomic prediction to improve fruit quality traits and shelf life in strawberries. It examines the introgression of favorable alleles from exotic genetic resources into elite breeding pools, resulting in significant improvements in total soluble solids and titratable acidity. The study not only highlights the genetic correlations among fruit traits and the impact of genotype combinations on hybrid performance but also underscores the importance of genomic prediction in efficiently selecting superior genotypes and optimizing breeding programs.

The third chapter investigates the domestication of strawberry for improved fruit firmness and shelf life. It identifies a loss-of-function mutation in the polygalacturonase gene PG1-6A1, significantly increasing fruit firmness and reducing perishability. This mutation and several structural variants have been positively correlated with fruit firmness and negatively with gene expression. Developing high-throughput genotyping assays for these mutations facilitates marker-assisted selection, enabling the breeding of firmer and longer-lasting strawberry cultivars.

Collectively, these studies provide valuable insights into the genetic basis of key traits in strawberries and showcase the potential of genomic technologies to accelerate breeding efforts and improve fruit quality and disease resistance.