Identification of sex determination locus and development of marker combination in Vitis based on genotyping by target sequencing

The grapevine is an important and economically valuable fruit crop, with flower sex being a key genetic trait that directly affects grapevine yield and quality. Despite its significance, there is a lack of studies on sex-linked molecular markers that can assist in grapevine breeding. In this study, we developed a grapevine single nucleotide polymorphism (SNP) marker array using a combination of genotyping by target sequencing (GBTS) and capture-in-solution technology and applied it to marker-assisted selection (MAS) of grapevine gender. The SNP array could detect a total of 20,597 core SNPs and 97,453 multiple SNPs (mSNPs), covering over 99% of the grapevine genome on each chromosome. A total of 131 progenies from a cross between Vitis vinifera 'Cabernet Sauvignon' and Vitis pseudoreticulata 'Huadong1058' that exhibited segregated sex phenotypes were sequenced using this array. Through locus mapping and a genome-wide association study (GWAS), a locus on chromosome 2 (54.74−58.80 cM) that explained 98.6% of the phenotypic variation was identified. To further utilize this locus, a sex prediction marker combination consisting of two SNPs was developed, which accurately predicted the sex of 34 natural grapevine varieties/accessions. This study demonstrates the application of GBTS in grapevine breeding and provides a reliable MAS marker set for early-stage sex selection.