Further, a consensus genetic map was constructed in LM3, where 150 progeny vines from each family were randomly chosen, and their genotypes were merged into a single VCF file in TASSEL using “Merge Genotype Table” plugin. The merged VCF file and pedigree information containing all four families were used in LM3 as an input to construct the sex averaged consensus genetic map as described above.
Genome wide association study of flower sex
The association between a well-characterized trait (flower sex) and genotypes was used to further evaluate rhAmpSeq marker transferability. Specifically, a genome-wide association study (GWAS) was conducted to map the flower sex locus in HC (F1) and RS (F2). The male allele (M) is dominant to hermaphroditic (H), which is dominant to female (f), that is, M>H>f. HC represents a cross of homozygous hermaphroditic flowers (HH) emasculated and pollinated with pollen from a male (Mf) vine, and should segregate 1 male (MH) : 1 hermaphrodite (Hf). RS represents self-pollination of heterozygous hermaphroditic flowers (Hf) and should segregate 3 hermaphrodite (HH/Hf/Hf) : 1 female (ff).