Detection and characterization of genome-wide genetic variation associated with the early-ripening phenotype of grape mutants

Abstract Single nucleotide polymorphisms (SNPs), insertion-deletion mutations (InDels) and structural variation (SV) play an important role in the generation of mutant genotypes. In this study, we conducted whole genome resequencing analysis of ‘Kyoho’, ‘Zana’ and their early-ripening bud sports, ‘Fengzao’ and ‘90–1′, respectively, to identify variants related to the early ripening trait. First, we determined the variants between ‘Kyoho’ vs. ‘Fengzao’ and ‘Zana’ vs. ‘90–1′ comparison groups using Genome Analysis Tool Kit (GATK) and samtools. Then, 324 genes harboring 1,135 SNPs and InDels were identified, based on sequencing depth and variant allele frequency. We also detected 39,112 and 35,825 SVs specific to ‘Fengzao’ and ‘90–1′, based on their comparison with ‘Kyoho’ and ‘Zana’ sequence data, respectively. Among these SVs, 89 were common to both ‘Fengzao’ and ‘90–1′. Then, variants were found in the coding sequences (CDSs) or upstream regions of 204 genes, of which 96 mapped to early ripening-related quantitative trait loci (QTLs). Subsequently, transcriptome analysis of ‘Kyoho’ and ‘Fengzao’ genotypes at four development stages revealed that 69 genes affected by variants were differentially expressed at one or more time points. Finally, five SNPs were validated in ‘Kyoho’ and ‘Fengzao’ by Sanger sequencing. Overall, abundant genetic variation was detected in ‘Kyoho’ and ‘Fengzao’ genomes, which may play a role in their early ripening phenotype.