Whole-genome resequencing of 472 Vitis accessions revealed grapevine diversity and demographic history

On March 13, 2019, Nature Communications (IF=12.353) online published our research results entitled "Whole-genome research of 472 Vitis accessions for grapevine diversity and demographic history analysis". For the first time, this study constructed a high-resolution genome-wide genetic variation map of cultivated, wild grapes and other related species, systematically studies genetic mechanism of the origin and domestication of cultivated grapes, and proposed the viewpoint of "Pan-Black Sea Origin" of grapes.

Grape (Vitis vinifera ssp. vinifera) is the most cultivated fruit crop in the genus Vitis, which also contains about 60 fertile wild species. Among the native habitats in the world, there are about 28 wild grape species in North America and 30 wild species in East Asia. Vitis vinifera ssp. sylvestris is the only existing wild grape taxa in Europe and the Near East and is considered to be the wild ancestor of nearly 10,000 cultivated grape varieties today. Although viticulture has important cultural implications and economic value in human history, the lack of large-scale genomic genetic variation data has led to the inability to analyze its domestication history and seriously hinder the improvement of grape characteristics.

To assess the genetic diversity of wild and cultivated grape varieties, we mapped the genome resequencing data to the Pinot Noir reference genome. A total of 77,726,929 single nucleotide mutations (SNPs), 10,278,017 sequence insertions and deletions (Indels) and about 25,000 copy number variations (CNVs) were identified. Further filtering yielded a basic variant set comprising 37,859,960 SNPs and 3,854,659 Indels (< 40 bp) with a minor allele frequency (MAF) greater than 0.005. The core variation set included 12,549,273 SNPs and 904,280 Indels (< 40 bp) with a MAF greater than 0.05. Based on these datasets, we constructed a phylogenetic tree of 48 Vitis species and analyzed the historical population size changes of cultivated grapes and European wild grapes. At the same time, single-population analysis and double-population analysis methods were used to screen the selection signals related to evolution and domestication, and a large number of genes related to economic traits were identified, which provided genetic basis for grape breeding.

The completion of the grape re-sequencing project will help accelerate the breeding of new varieties, thus promoting the development of China's grape industry and enhancing the scientific influence of China's fruit industry in the world.

Paper Link: https://www.nature.com/articles/s41467-019-09135-8.pdf