Using genomic selection to examine subgenome dominance and epistasis in allopolyploid strawberry

Allopolyploids are organisms that possess multiple sets of chromosomes derived from distinct ancestral species, resulting in multiple subgenomes. Many important crops are allopolyploid, including wheat (Triticum aestivum), cotton (Gossypium hirsutum), coffee (Coffea arabica), and strawberry (Fragaria × ananassa). In allopolyploids, subgenome dominance often emerges, with strong influence on gene expression, epigenetic regulation, and gene conservation. Subgenome dominance has been extensively characterized at the molecular level but very little at the phenotypic level. In this study, we investigated the importance of subgenome interactions for predicting nine phenotypes using a large dataset of 6718 genotypes from the University of Florida strawberry breeding population. We tested multi-kernel genomic selection models accounting for subgenome and epistasis effects to test the genetic contribution of each ancestral strawberry subgenome. Across three yield-related phenotypes, two fruit quality phenotypes, and four disease resistance phenotypes, the contributions of the four subgenomes were highly variable. On average, subgenome B contributed the most genetic variation, followed by subgenome A, then subgenome C, and lastly subgenome D. Using genomic selection models with epistasis kernels, we estimate that epistasis contributed between 12% and 46% of genetic variation for the nine phenotypes. Lastly, we used two different cross-validation scenarios to show that genomic selection models incorporating subgenome and epistatic effects improve predictive ability by 1%-34% depending on the phenotype and the genomic selection training set.