Genome-wide association study of berry-related traits in grape [Vitis vinifera L.] based on genotyping-by-sequencing markers

Da-Long Guo,Hui-Li Zhao,Chong-Huai Liu,Qiong Li,Yi-He Yu,Jian-Fu Jiang,Guo-Hai Zhang

doi:10.1038/s41438-018-0089-z

Abstract

ABSTRACTDeciphering the genetic control of grape berry traits is crucial for optimizing yield, fruit quality, and consumer acceptability. In this study, an association panel of 179 grape genotypes comprising a mixture of ancient cultivars, landraces, and modern varieties collected worldwide were genotyped with genotyping-by-sequencing using a genome-wide association approach based on 32,311 single-nucleotide polymorphism (SNP) markers. Genome-wide efficient mixed-model association was selected as the optimal statistical model based on the results of known control loci of grape berry color traits. Many of the associated SNPs identified in this study were in accordance with the previous QTL analyses using biparental mapping. The grape skin color locus was found to be associated with a mybA transcription factor on chromosome 2. Two strong and distinct association signals associated with berry development periods were found on chromosome 16. Most candidate genes of the interval were highlighted as receptor-like protein kinase. For berry weight, significant association loci were identified on chromosome 18, as previously known, and on chromosome 19 and chromosome 17, as newly mapped. Berry flesh texture was newly located on chromosome 16; candidate genes in the interval were related to calcium. Berry flavor was determined on chromosome 5. Genomic regions were further investigated to reveal candidate genes. In this work, we identified interesting genetic determinants of grape berry-related traits. The identification of the markers closely associated with these berry traits may be useful for grape molecular breeding.

Highlights

Grape [Vitis vinifera L.] is an economically important fruit-tree crop in many temperate and subtropical countries
The data for the cluster density (CD), berry flesh texture (BFT), berry color (BC), berry shape (BS), and berry flavor (BF) traits were recorded as discrete data
The grape genotypes used in this study showed broad variation for three other traits: berry development period (BDP), Berry weight (BW), and cluster size (CS) (Supplementary Table S1)

Summary

Introduction

Grape [Vitis vinifera L.] is an economically important fruit-tree crop in many temperate and subtropical countries. As a result of long-term natural selection and artificial domestication and breeding, many fruit variations have accumulated in grape, with wide diversities of berry color, size, weight, texture, aroma, and shape. These variations could serve as important resources for grape breeding and. The genetic control of major berry-related traits in grape, such as phenology, berry weight, berry firmness, and seedlessness, has been explored via simple sequence repeat (SSR) markers in biparental populations[1,2,3,4,5,6]. A biparental population makes use only of the recent recombination information that arose during the crossing, which is often population

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