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.