Accuracy of genomic selection and long-term genetic gain for resistance to Verticillium wilt in strawberry

Authors: PINCOT, DOMINIQUE - University Of California; HARDIGAN, MICHAEL - University Of California; COLE, GLENN - University Of California; FAMULA, RANDI - University Of California; Henry, Peter; GORDON, THOMAS - University Of California; KNAPP, STEVEN - University Of California

Submitted to: The Plant Genome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/27/2020
Publication Date: 9/24/2020
Citation: Pincot, D.D., Hardigan, M.A., Cole, G.S., Famula, R.A., Henry, P.M., Gordon, T.R., Knapp, S.J. 2020. Accuracy of genomic selection and long-term genetic gain for resistance to Verticillium wilt in strawberry. The Plant Genome. 13(3). Article e20054. https://doi.org/10.1002/tpg2.20054.
DOI: https://doi.org/10.1002/tpg2.20054

Interpretive Summary: Strawberry breeders have been trying for many years to improve resistance to Verticillium dahliae, a fungal pathogen that causes Verticillium wilt disease. Growing disease-resistant plants is an environmentally and economically sustainable way for farmers to reduce crop losses. We tested historic cultivars and wild strawberry varieties for resistance to Verticillium wilt, and found highly resistant strawberry cultivars and wild species. However, most varieties were susceptible or moderately resistant. Furthermore, the data show strawberry varieties have, overall, become more susceptible over the last century despite breeding efforts to improve resistance to Verticillium wilt. We found that resistance to Verticillium wilt does not result from a single or few genes. Instead, it is a phenomenon generated by the interaction of many different genes. Our results suggest it may be possible to accelerate selection for Verticillium resistance by analyzing the genomic “fingerprint” of resistant varieties, and highly resistant heirloom cultivars can improve the potential of breeding for this trait.

Technical Abstract: Verticillium wilt, a soil-borne disease caused by the fungal pathogen Verticillium dahliae, threatens strawberry (Fragaria × ananassa) production worldwide. The development of resistant cultivars has been a challenge since the disease was first reported on strawberry in the early 1900s. The empirical evidence suggests that genetic gains for resistance have been significant and that the genetics of resistance to this pathogen is quantitative. While resistant cultivars have been developed, a comparatively small percentage are highly resistant, whereas a large percentage are moderately to highly susceptible. To develop insights into the genetics of resistance, we studied a population of elite and exotic germplasm accessions (n = 984), including 245 cultivars developed in public breeding programs since 1854. We observed a full range of phenotypes, from highly susceptible to highly resistant. Broad-sense heritabilities ranged from 0.70 to 0.76, whereas narrow-sense heritabilities ranged from 0.33 to 0.45. Less than 3% of accessions were classified as highly resistant. Several of the most resistant accessions were heirloom cultivars or exotic germplasm accessions developed before the introduction of pre-plant soil fumigation in 1960. We show that genetic gains for resistance to Verticillium wilt have been negative over the last century and that genomic selection has significant potential to increase genetic gains. Genomic prediction accuracies ranged from 0.41 to 0.49 and generally increased as training population diversity increased. Heirloom cultivars and other exotic germplasm accessions carry favorable alleles for resistance to Verticillium wilt that are not present in modern cultivars.