Journal Article

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

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

2019

Overview

ABSTRACT Deciphering 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. Grapes: The genetic basis of fruit traits Genetic analysis of 179 types of vine has revealed regions of the genome and associated genes and proteins that control many of the key traits in the grapes. These traits are crucial for determining fruit quality and yield, in addition to conferring flavors that are highly valued by consumers and wine makers. Researchers in China, led by Da-Long Guo at Henan University of Science and Technology, used DNA sequencing to analyze genetic markers in a mixture of ancient, traditionally cultivated and modern grape varieties. The analysis identified specific regions of the genome linked to grape fruit development, weight, texture, skin color and flavor. The molecular basis of the effects of the identified genetic regions were also explored. The findings will help generate new varieties of grapes for the food and wine industries.

• Publisher: Nature Publishing Group UK,Oxford University Press
• Subject: 631/208/711 / 631/449/1870 / Agriculture / Biomedical and Life Sciences / Calcium / Chromosome 16 / Chromosome 17 / Chromosome 18 / Chromosome 19 / Chromosome 2 / Chromosome 5 / Chromosomes / Color / Cultivars / Ecology / Flavors / Fruits / Gene mapping / Gene polymorphism / Gene sequencing / Genes / Genetic control / Genome-wide association studies / Genomes / Genotypes / Genotyping / Grapes / Kinases / Life Sciences / Mapping / Markers / Mathematical models / Optimization / Plant Breeding/Biotechnology / Plant Genetics and Genomics / Plant Sciences / Polymorphism / Protein kinase / Proteins / Quantitative trait loci / Single-nucleotide polymorphism / Skin / Statistical models / Vitis vinifera / Weight