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

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 persistent challenge, in part because the genetics of resistance is complex. The heritability of resistance and genetic gains in breeding for resistance to this pathogen have not been well documented. To elucidate the genetics, assess long-term genetic gains, and estimate the accuracy of genomic selection for resistance to Verticillium wilt, we analyzed a genetically diverse population of elite and exotic germplasm accessions (n = 984), including 245 cultivars developed since 1854. We observed a full range of phenotypes, from highly susceptible to highly resistant: < 3% were classified as highly resistant, whereas > 50% were classified as moderately to highly susceptible. Broad-sense heritability estimates ranged from 0.70-0.76, whereas narrow-sense genomic heritability estimates ranged from 0.33-0.45. We found that genetic gains in breeding for resistance to Verticillium wilt have been negative over the last 165 years (mean resistance has decreased over time). We identified several highly resistant accessions that might harbor favorable alleles that are either rare or non-existent in modern populations. We did not observe the segregation of large-effect loci. The accuracy of genomic predictions ranged from 0.38-0.53 among years and whole-genome regression methods. We show that genomic selection has promise for increasing genetic gains and accelerating the development of resistant cultivars in strawberry by shortening selection cycles and enabling selection in early developmental stages without phenotyping.

Genomic Selection for F1 Hybrid Breeding in Strawberry (Fragaria × ananassa)

“…In addition, sufficient prior information such as genotype of population in a simple pedigree is necessary, especially in allo-polyploids ( Clark et al, 2019 ). Preparation of both data is difficult in strawberry genetic study, and therefore, subgenome-specific loci were used for GS in this study and the previous studies ( Gezan et al, 2017 ; Pincot et al, 2020 ). Recent advances not only in throughput of sequencers but also experimental methods are increasing accuracy of genotype calling for SNPs with higher ploidy levels ( Wadl et al, 2018 ).…”

“… Gezan et al (2017) assessed the potential of GS to improve basic agronomic traits such as fruit quality and yield performance. Pincot et al (2020) evaluated GS model accuracy for soil-borne disease resistance by using a genetically diverse population. However, to the best of our knowledge, no study has applied GS for F 1 hybrid breeding in strawberry.…”

Novel Fusarium wilt resistance genes uncovered in natural and cultivated strawberry populations are found on three non-homoeologous chromosomes

“…DNA was isolated from newly emerged leaves harvested from field grown plants using a previously described protocol (Pincot et al. 2020 ). Leaf samples were placed into 1.5 ml tubes or coin envelopes and freeze-dried in a Benchtop Pro (VirTis SP Scientific, Stone Bridge, NY).…”

Novel Fusarium Wilt Resistance Genes Uncovered in the Wild Progenitors and Heirloom Cultivars of Strawberry

“…DNA was isolated from newly emerged leaves harvested from field grown plants using a previously described protocol (Pincot et al, 2020). Leaf samples were placed into 1.5 ml tubes or coin envelopes and freeze-dried in a Benchtop Pro (VirTis SP Scientific, Stone Bridge, NY).…”