Genome Resequencing, Improvement of Variant Calling, and Population Genomic Analyses Provide Insights into the Seedlessness in the Genus Vitis.

G3 : Genes - Genomes - Genetics
Myung-Shin KimSoon-Chun Jeong

Abstract

The seedlessness of grape derived from stenospermocarpy is one of the most prized traits of table or raisin grapes. It is controlled by a complex genetic system containing one dominant gene and multiple recessive genes. Here, we collected dense variation data from high-depth resequencing data of seeded, seedless, and wild relative grape genomes sequenced to > 37x mean depth. Variant calls were made using a modified variant calling pipeline that was suitable for highly diverse interspecific grape accessions. The modified pipeline enabled us to call several million more variants than the commonly recommended pipeline. The quality was validated by Sanger sequencing data and subsequently supported by the genetic population structure and the phylogenetic tree constructed using the obtained variation data, results of which were generally consistent with known pedigree and taxonomic classifications. Variation data enabled us to confirm a dominant gene and identify recessive loci for seedlessness. Incidentally, we found that grape cultivar Rizamat contains an ancestral chromosomal region of the dominant gene in Sultanina, a predominant seedlessness donor cultivar. Furthermore, we predicted new candidate causal genes including Vitvi01g0...Continue Reading

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Datasets Mentioned

BETA
PRJNA485199

Methods Mentioned

BETA
PCR
two hybrids
genotyping

Software Mentioned

qqman
Plot
GATK
Genome Analysis Toolkit ( GATK )
BEAGLE
OnePop
R
VCFtools
SAMtools
SMARTPCA

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