Toward identification of haplotypes that control seedlessness of grape by genome resequencing

Seedlessness is one of the most prized traits in table or raisin grapes. Seedlessness of grape derived from stenospermocarpy is thought to be controlled by one major dominant gene and multiple minor recessive genes. In the present study, we obtained dense variation data from an analysis of high-depth resequencing data of a diverse group of eight seeded, 18 seedless, and two wild grape genomes sequenced to >41× mean depth. The genetic structure of the population and the relationships of the accessions sequenced were generally consistent with their known pedigree and origin. However, a phylogenetic tree of a chromosomal region surrounding the major seedless-regulating locus SDI supported the conclusion that grouping of our sequenced grape genomes was consistent with grouping based on seeded or seedless phenotypes. The grape genome resequencing data provided in this study could be of tremendous value to grape breeders who are striving to develop superior seedless grape cultivars and grape genome researchers in general.