VIR genotyping and significant SNP effects on Tamar stage fruit color
The genomic region of the VIRESCENS gene (VIR gene) and Ibn Majid retrotransposon from the Barhee BC4 genome (Hazzouri et al . study,2019) were aligned against the PDK50 reference genome, and the coordinates of its insertion and termination codon in the VIR gene noted. Following the same procedure used in Hazzouri et al., we manually inspected all the QC filtered samples to identify the VIR genotypes (VIR+/VIR+, VIR+/VIRIM, and VIRIM/VIRIM) using JBrowse2 software. In this study, samples were classified into two groups (i): homozygous VIR+/VIR+ genotype (ii): homozygous VIRIM/VIRIM genotype. That is, only homozygous genotypes were used for further analysis to avoid confusion about the effect of the heterozygous genotypes. To investigate the effect of loci on dry fruit color identified in this study, analysis of our SNPs was conducted within each homozygous VIR sample group.