Genomic prediction of strawberry resistance to post-harvest fruit decay caused by the fungal pathogen Botrytis cinerea

Authors: PETRASCH, STEFAN - University Of California, Davis; MESQUIDA-PESCI, SASKIA - University Of California, Davis; PINCOT, DOMINIQUE - University Of California, Davis; FELDMANN, MITCHELL - University Of California, Davis; LOPEZ, CINDY - University Of California, Davis; FAMULA, RANDI - University Of California, Davis; Hardigan, Michael; COLE, GLENN - University Of California, Davis; KNAPP, STEVEN - University Of California, Davis; BLANCO-ULATE, BARBARA - University Of California, Davis

Submitted to: G3, Genes/Genomes/Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/28/2021
Publication Date: 11/13/2021
Citation: Petrasch, S., Mesquida-Pesci, S.D., Pincot, D.D., Feldmann, M.J., Lopez, C.M., Famula, R., Hardigan, M.A., Cole, G.S., Knapp, S.J., Blanco-Ulate, B. 2021. Genomic prediction of strawberry resistance to post-harvest fruit decay caused by the fungal pathogen Botrytis cinerea. G3, Genes/Genomes/Genetics. 12(1). Article jkab378. https://doi.org/10.1093/g3journal/jkab378.
DOI: https://doi.org/10.1093/g3journal/jkab378

Interpretive Summary: Gray mold growth on strawberry fruit caused by the common fungus Botrytis cinerea is one of the main drivers behind the loss of marketable fruit quality and fruit deterioration following harvest. This results in a significant economic impact caused by the reduction of strawberry shelf-life. This study examined susceptibility to Botrytis in a large population of cultivated strawberry individuals. Genetic markers were used to estimate the heritability of Botrytis resistance/susceptibility in strawberry fruit, and perform genome-wide association and genomic prediction analyses. No individual genes contributed significant resistance in the study population, confirming that Botrytis resistance is a genetically complex trait. However, there was sufficient heritability to perform genomic prediction for Botrytis resistance with moderate prediction accuracy, suggesting that genomic selection may be a useful tool for improving strawberry shelf-life and delaying the onset of gray mold.

Technical Abstract: Gray mold, a disease of strawberry (Fragaria × ananassa) caused by the ubiquitous necrotroph Botrytis cinerea, renders fruit unmarketable and causes economic losses under post-harvest conditions favorable for pathogen growth. To explore the feasibility of selecting for increased resistance to gray mold, we undertook genetic and genomic prediction studies in strawberry populations segregating for fruit quality and shelf life traits hypothesized to pleiotropically affect susceptibility. As predicted, resistance to gray mold was heritable but genetically complex. While every individual was susceptible, the speed of symptom progression and severity differed. Narrow-sense heritability ranged from 0.38-0.71 for lesion diameter (LD) and 0.39-0.44 for speed of emergence of external mycelium (EM). Even though significant additive genetic variation was observed for LD and EM, the phenotypic ranges were comparatively narrow and genome-wide analyses did not identify any large effect loci. Genomic selection accuracy ranged from 0.28-0.59 for LD and 0.37-0.47 for EM. Additive genetic correlations between fruit quality and gray mold resistance traits were consistent with prevailing hypotheses: LD decreased as titratable acidity increased, whereas EM increased as soluble solid content decreased and firmness increased. We concluded that phenotypic and genomic selection could be effective for reducing LD and increasing EM, especially in long shelf life populations, but that a significant fraction of the genetic variation for resistance to gray mold was caused by the pleiotropic effects of fruit quality traits that differ among market and shelf life classes.