Abstract

Understanding the Vitis species at the genomic level is important for cultivar improvement of grapevine. Here we report whole-genome genetic variation at single-base resolution of 472 Vitis accessions, which cover 48 out of 60 extant Vitis species from a wide geographic distribution. The variation helps to identify a recent dramatic expansion and contraction of effective population size in the domesticated grapevines and that cultivars from the pan-Black Sea region have a unique demographic history in comparison to the other domesticated cultivars. We also find selective sweeps for berry edibility and stress resistance improvement. Furthermore, we find associations between candidate genes and important agronomic traits, such as berry shape and aromatic compounds. These results demonstrate resource value of the resequencing data for illuminating the evolutionary biology of Vitis species and providing targets for grapevine genetic improvement.

Despite the importance of grapevine cultivation in human history and the economic values of cultivar improvement, large-scale genomic variation data are lacking. Here the authors resequence 472 Vitis accessions and use the identified genetic variations for domestication history, demography, and GWAS analyses.

Details

Title
Whole-genome resequencing of 472 Vitis accessions for grapevine diversity and demographic history analyses
Author
Liang Zhenchang 1 ; Duan Shengchang 2 ; Sheng, Jun 3 ; Zhu Shusheng 4 ; Ni Xuemei 5 ; Shao Jianhui 6 ; Liu Chonghuai 7 ; Nick, Peter 8 ; Du, Fei 6 ; Fan Peige 9 ; Mao Ruzhi 6 ; Zhu, Yifan 4 ; Deng Weiping 6 ; Yang, Min 6 ; Huang Huichuan 6   VIAFID ORCID Logo  ; Liu, Yixiang 6 ; Ding Yiqing 10 ; Liu Xianju 10 ; Jiang Jianfu 7 ; Zhu Youyong 3 ; Li, Shaohua 9 ; He Xiahong 4 ; Chen, Wei 11 ; Yang, Dong 11 

1  Chinese Academy of Sciences, Beijing Key Laboratory of Grape Sciences and Enology, Laboratory of Plant Resources, Institute of Botany, Beijing, China (GRID:grid.9227.e) (ISNI:0000000119573309); Chinese Academy of Sciences, Sino-Africa Joint Research Center, Wuhan, China (GRID:grid.9227.e) (ISNI:0000000119573309) 
2  Yunnan Agricultural University, State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Kunming, China (GRID:grid.410696.c) (ISNI:0000 0004 1761 2898); Nowbio Biotechnology Company, Kunming, China (GRID:grid.410696.c) 
3  Yunnan Agricultural University, State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Kunming, China (GRID:grid.410696.c) (ISNI:0000 0004 1761 2898); Yunnan Research Institute for Local Plateau Agriculture and Industry, Kunming, China (GRID:grid.410696.c); Yunnan Agricultural University, Key Laboratory for Agro-biodiversity and Pest Control of Ministry of Education, Kunming, China (GRID:grid.410696.c) (ISNI:0000 0004 1761 2898) 
4  Yunnan Agricultural University, State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Kunming, China (GRID:grid.410696.c) (ISNI:0000 0004 1761 2898); Yunnan Agricultural University, Key Laboratory for Agro-biodiversity and Pest Control of Ministry of Education, Kunming, China (GRID:grid.410696.c) (ISNI:0000 0004 1761 2898) 
5  BGI-Shenzhen, BGI, Shenzhen, China (GRID:grid.21155.32) (ISNI:0000 0001 2034 1839); BGI-Shenzhen, BGI Institute of Applied Agriculture, Shenzhen, China (GRID:grid.21155.32) (ISNI:0000 0001 2034 1839) 
6  Yunnan Agricultural University, Key Laboratory for Agro-biodiversity and Pest Control of Ministry of Education, Kunming, China (GRID:grid.410696.c) (ISNI:0000 0004 1761 2898) 
7  Chinese Academy of Agricultural Sciences, Zhengzhou Fruit Research Institute, Zhengzhou, China (GRID:grid.410727.7) (ISNI:0000 0001 0526 1937) 
8  Karlsruhe Institute of Technology, Botanical Institute, Karlsruhe, Germany (GRID:grid.7892.4) (ISNI:0000 0001 0075 5874) 
9  Chinese Academy of Sciences, Beijing Key Laboratory of Grape Sciences and Enology, Laboratory of Plant Resources, Institute of Botany, Beijing, China (GRID:grid.9227.e) (ISNI:0000000119573309) 
10  Chinese Academy of Sciences, Beijing Key Laboratory of Grape Sciences and Enology, Laboratory of Plant Resources, Institute of Botany, Beijing, China (GRID:grid.9227.e) (ISNI:0000000119573309); University of Chinese Academy of Sciences, Beijing, China (GRID:grid.410726.6) (ISNI:0000 0004 1797 8419) 
11  Yunnan Agricultural University, State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Kunming, China (GRID:grid.410696.c) (ISNI:0000 0004 1761 2898); Yunnan Research Institute for Local Plateau Agriculture and Industry, Kunming, China (GRID:grid.410696.c) 
Publication year
2019
Publication date
2019
Publisher
Nature Publishing Group
e-ISSN
20411723
Source type
Scholarly Journal
Language of publication
English
DOI
https://doi.org/10.1038/s41467-019-09135-8
ProQuest document ID
2190995878
Copyright
© The Author(s) 2019. This work is published under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.