A genomic variation map provides insights into the genetic basis of cucumber domestication and diversity

Jianjian Qi, Xin Liu, Di Shen, Han Miao, Bingyan Xie, Xixiang Li, Peng Zeng, Shenhao Wang, Yi Shang, Xingfang Gu, Yongchen Du, Ying Li, Tao Lin, Jinhong Yuan, Xueyong Yang, Jinfeng Chen, Huiming Chen, Xingyao Xiong, Ke Huang, Zhangjun Fei & 8 others Linyong Mao, Li Tian, Thomas Städler, Susanne S. Renner, Sophien Kamoun, William J. Lucas, Zhonghua Zhang, Sanwen Huang

Research output: Contribution to journalArticle

160 Citations (Scopus)

Abstract

Most fruits in our daily diet are the products of domestication and breeding. Here we report a map of genome variation for a major fruit that encompasses ∼3.6 million variants, generated by deep resequencing of 115 cucumber lines sampled from 3,342 accessions worldwide. Comparative analysis suggests that fruit crops underwent narrower bottlenecks during domestication than grain crops. We identified 112 putative domestication sweeps; 1 of these regions contains a gene involved in the loss of bitterness in fruits, an essential domestication trait of cucumber. We also investigated the genomic basis of divergence among the cultivated populations and discovered a natural genetic variant in a β-carotene hydroxylase gene that could be used to breed cucumbers with enhanced nutritional value. The genomic history of cucumber evolution uncovered here provides the basis for future genomics-enabled breeding.

Original languageEnglish (US)
Pages (from-to)1510-1515
Number of pages6
JournalNature Genetics
Volume45
Issue number12
DOIs
StatePublished - Dec 2013

Fingerprint

Cucumis sativus
Fruit
Breeding
Nutritive Value
Carotenoids
Genomics
Mixed Function Oxygenases
Genes
History
Genome
Diet
Domestication
Population

ASJC Scopus subject areas

  • Genetics

Cite this

A genomic variation map provides insights into the genetic basis of cucumber domestication and diversity. / Qi, Jianjian; Liu, Xin; Shen, Di; Miao, Han; Xie, Bingyan; Li, Xixiang; Zeng, Peng; Wang, Shenhao; Shang, Yi; Gu, Xingfang; Du, Yongchen; Li, Ying; Lin, Tao; Yuan, Jinhong; Yang, Xueyong; Chen, Jinfeng; Chen, Huiming; Xiong, Xingyao; Huang, Ke; Fei, Zhangjun; Mao, Linyong; Tian, Li; Städler, Thomas; Renner, Susanne S.; Kamoun, Sophien; Lucas, William J.; Zhang, Zhonghua; Huang, Sanwen.

In: Nature Genetics, Vol. 45, No. 12, 12.2013, p. 1510-1515.

Research output: Contribution to journalArticle

Qi, J, Liu, X, Shen, D, Miao, H, Xie, B, Li, X, Zeng, P, Wang, S, Shang, Y, Gu, X, Du, Y, Li, Y, Lin, T, Yuan, J, Yang, X, Chen, J, Chen, H, Xiong, X, Huang, K, Fei, Z, Mao, L, Tian, L, Städler, T, Renner, SS, Kamoun, S, Lucas, WJ, Zhang, Z & Huang, S 2013, 'A genomic variation map provides insights into the genetic basis of cucumber domestication and diversity', Nature Genetics, vol. 45, no. 12, pp. 1510-1515. https://doi.org/10.1038/ng.2801
Qi, Jianjian ; Liu, Xin ; Shen, Di ; Miao, Han ; Xie, Bingyan ; Li, Xixiang ; Zeng, Peng ; Wang, Shenhao ; Shang, Yi ; Gu, Xingfang ; Du, Yongchen ; Li, Ying ; Lin, Tao ; Yuan, Jinhong ; Yang, Xueyong ; Chen, Jinfeng ; Chen, Huiming ; Xiong, Xingyao ; Huang, Ke ; Fei, Zhangjun ; Mao, Linyong ; Tian, Li ; Städler, Thomas ; Renner, Susanne S. ; Kamoun, Sophien ; Lucas, William J. ; Zhang, Zhonghua ; Huang, Sanwen. / A genomic variation map provides insights into the genetic basis of cucumber domestication and diversity. In: Nature Genetics. 2013 ; Vol. 45, No. 12. pp. 1510-1515.
@article{b4476cf21a234ac6bea3360ea7872616,
title = "A genomic variation map provides insights into the genetic basis of cucumber domestication and diversity",
abstract = "Most fruits in our daily diet are the products of domestication and breeding. Here we report a map of genome variation for a major fruit that encompasses ∼3.6 million variants, generated by deep resequencing of 115 cucumber lines sampled from 3,342 accessions worldwide. Comparative analysis suggests that fruit crops underwent narrower bottlenecks during domestication than grain crops. We identified 112 putative domestication sweeps; 1 of these regions contains a gene involved in the loss of bitterness in fruits, an essential domestication trait of cucumber. We also investigated the genomic basis of divergence among the cultivated populations and discovered a natural genetic variant in a β-carotene hydroxylase gene that could be used to breed cucumbers with enhanced nutritional value. The genomic history of cucumber evolution uncovered here provides the basis for future genomics-enabled breeding.",
author = "Jianjian Qi and Xin Liu and Di Shen and Han Miao and Bingyan Xie and Xixiang Li and Peng Zeng and Shenhao Wang and Yi Shang and Xingfang Gu and Yongchen Du and Ying Li and Tao Lin and Jinhong Yuan and Xueyong Yang and Jinfeng Chen and Huiming Chen and Xingyao Xiong and Ke Huang and Zhangjun Fei and Linyong Mao and Li Tian and Thomas St{\"a}dler and Renner, {Susanne S.} and Sophien Kamoun and Lucas, {William J.} and Zhonghua Zhang and Sanwen Huang",
year = "2013",
month = "12",
doi = "10.1038/ng.2801",
language = "English (US)",
volume = "45",
pages = "1510--1515",
journal = "Nature Genetics",
issn = "1061-4036",
publisher = "Nature Publishing Group",
number = "12",

}

TY - JOUR

T1 - A genomic variation map provides insights into the genetic basis of cucumber domestication and diversity

AU - Qi, Jianjian

AU - Liu, Xin

AU - Shen, Di

AU - Miao, Han

AU - Xie, Bingyan

AU - Li, Xixiang

AU - Zeng, Peng

AU - Wang, Shenhao

AU - Shang, Yi

AU - Gu, Xingfang

AU - Du, Yongchen

AU - Li, Ying

AU - Lin, Tao

AU - Yuan, Jinhong

AU - Yang, Xueyong

AU - Chen, Jinfeng

AU - Chen, Huiming

AU - Xiong, Xingyao

AU - Huang, Ke

AU - Fei, Zhangjun

AU - Mao, Linyong

AU - Tian, Li

AU - Städler, Thomas

AU - Renner, Susanne S.

AU - Kamoun, Sophien

AU - Lucas, William J.

AU - Zhang, Zhonghua

AU - Huang, Sanwen

PY - 2013/12

Y1 - 2013/12

N2 - Most fruits in our daily diet are the products of domestication and breeding. Here we report a map of genome variation for a major fruit that encompasses ∼3.6 million variants, generated by deep resequencing of 115 cucumber lines sampled from 3,342 accessions worldwide. Comparative analysis suggests that fruit crops underwent narrower bottlenecks during domestication than grain crops. We identified 112 putative domestication sweeps; 1 of these regions contains a gene involved in the loss of bitterness in fruits, an essential domestication trait of cucumber. We also investigated the genomic basis of divergence among the cultivated populations and discovered a natural genetic variant in a β-carotene hydroxylase gene that could be used to breed cucumbers with enhanced nutritional value. The genomic history of cucumber evolution uncovered here provides the basis for future genomics-enabled breeding.

AB - Most fruits in our daily diet are the products of domestication and breeding. Here we report a map of genome variation for a major fruit that encompasses ∼3.6 million variants, generated by deep resequencing of 115 cucumber lines sampled from 3,342 accessions worldwide. Comparative analysis suggests that fruit crops underwent narrower bottlenecks during domestication than grain crops. We identified 112 putative domestication sweeps; 1 of these regions contains a gene involved in the loss of bitterness in fruits, an essential domestication trait of cucumber. We also investigated the genomic basis of divergence among the cultivated populations and discovered a natural genetic variant in a β-carotene hydroxylase gene that could be used to breed cucumbers with enhanced nutritional value. The genomic history of cucumber evolution uncovered here provides the basis for future genomics-enabled breeding.

UR - http://www.scopus.com/inward/record.url?scp=84888360015&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84888360015&partnerID=8YFLogxK

U2 - 10.1038/ng.2801

DO - 10.1038/ng.2801

M3 - Article

VL - 45

SP - 1510

EP - 1515

JO - Nature Genetics

JF - Nature Genetics

SN - 1061-4036

IS - 12

ER -