Technical Advances in Octoploid Strawberry Genomics and Genome-Informed Breeding

Cultivated strawberry (Fragaria × ananassa) is one of our youngest domesticates, originating from interspecific hybrids in the early eighteenth century between geographically isolated allo-octoploid (2n = 8x = 56) species (F. chiloensis} and F. virginiana). The global F. × ananassa population has been reshaped through the introduction of alleles from nearly 200 wild octoploid founders, migration, admixture, directional selection, and population bottlenecks. Over the last century, several agriculturally important traits have been enhanced by modern plant breeding, thereby enabling the global expansion of strawberry production. The cultivars grown around the world today have primarily been developed through traditional breeding, partly because the genomics revolution came late to strawberry. Here, we review explosive changes in breeding approaches that have resulted from the assembly of a reference genome for octoploid strawberry, the development of octoploid genome-anchored SNP arrays, and other technical advances. We developed 50K and 850K Affymetrix SNP genotyping arrays to support genome-informed breeding and genetic studies in strawberry. These were constructed by identifying paralog- and homeolog-specific DNA variants across the genome. We will review the applications and importance of these SNP arrays and highlight the range of genome-informed studies that have been enabled by recent technical advances in strawberry. Genomic selection and other predictive genome-informed approaches, in particular, have significant potential to increase genetic gains and accelerate the development of genetically superior strawberry cultivars.