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

Research output: Contribution to journalArticle

185 Scopus citations


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
Issue number12
StatePublished - Dec 2013


ASJC Scopus subject areas

  • Genetics

Cite this

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