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; Linyong Mao; Li Tian; Thomas Städler; Susanne S. Renner; Sophien Kamoun; William J. Lucas; Zhonghua Zhang; Sanwen Huang

doi:10.1038/ng.2801

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 FeiLinyong Mao, Li Tian, Thomas Städler, Susanne S. Renner, Sophien Kamoun, William J. Lucas, Zhonghua Zhang, Sanwen Huang

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329 Scopus citations

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 language	English
Pages (from-to)	1510-1515
Number of pages	6
Journal	Nature Genetics
Volume	45
Issue number	12
DOIs	https://doi.org/10.1038/ng.2801
State	Published - Dec 2013

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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., ... Huang, S. (2013). A genomic variation map provides insights into the genetic basis of cucumber domestication and diversity. Nature Genetics, 45(12), 1510-1515. https://doi.org/10.1038/ng.2801

@article{9e4e9e93232d46589e543eb7a3f3f517,

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",

note = "Funding Information: We thank J. Ross-Ibarra (University of California, Davis) and J.-Y. Li (Chinese Academy of Agricultural Sciences (CAAS)) for critical comments, D. DellaPenna (Michigan State University) for assistance in β-carotene pathway analysis and the three anonymous referees for their constructive comments. We thank F. Cunningham (University of Maryland) for providing the pAC-BETA plasmid. This work was supported by funding from the National Program on Key Basic Research Projects in China (the 973 Program; 2012CB113900), the National Funding Information: Natural Science Foundation of China (NSFC; 31225025) the National High-Tech Research Development Program in China (the 863 Program; 2010AA10A108 and 2012AA100101), and other NSFC grants (31030057, 30972011, 31101550, 31071797, 31171961, 31272161 and 31322047), the Chinese Ministry of Agriculture (the 948 program; 2008-Z42), the Chinese Ministry of Finance (1251610601001) and CAAS (seed grant to S.H.).",

year = "2013",

month = dec,

doi = "10.1038/ng.2801",

language = "English",

volume = "45",

pages = "1510--1515",

journal = "Nature Genetics",

issn = "1061-4036",

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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

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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

N1 - Funding Information: We thank J. Ross-Ibarra (University of California, Davis) and J.-Y. Li (Chinese Academy of Agricultural Sciences (CAAS)) for critical comments, D. DellaPenna (Michigan State University) for assistance in β-carotene pathway analysis and the three anonymous referees for their constructive comments. We thank F. Cunningham (University of Maryland) for providing the pAC-BETA plasmid. This work was supported by funding from the National Program on Key Basic Research Projects in China (the 973 Program; 2012CB113900), the National Funding Information: Natural Science Foundation of China (NSFC; 31225025) the National High-Tech Research Development Program in China (the 863 Program; 2010AA10A108 and 2012AA100101), and other NSFC grants (31030057, 30972011, 31101550, 31071797, 31171961, 31272161 and 31322047), the Chinese Ministry of Agriculture (the 948 program; 2008-Z42), the Chinese Ministry of Finance (1251610601001) and CAAS (seed grant to S.H.).

PY - 2013/12

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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.

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JO - Nature Genetics

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

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