Diversification and independent domestication of Asian and European pears

Jun Wu, Yingtao Wang, Jiabao Xu, Schuyler S. Korban, Zhangjun Fei, Shutian Tao, Ray Ming, Shuaishuai Tai, Awais M. Khan, Joseph D. Postman, Chao Gu, Hao Yin, Danman Zheng, Kaijie Qi, Yong Li, Runze Wang, Cecilia H. Deng, Satish Kumar, David Chagné, Xiaolong LiJuyou Wu, Xiaosan Huang, Huping Zhang, Zhihua Xie, Xiao Li, Mingyue Zhang, Yanhong Li, Zhen Yue, Xiaodong Fang, Jiaming Li, Leiting Li, Cong Jin, Mengfan Qin, Jiaying Zhang, Xiao Wu, Yaqi Ke, Jian Wang, Huanmimg Yang, Shaoling Zhang

Research output: Contribution to journalArticle

Abstract

Background: Pear (Pyrus) is a globally grown fruit, with thousands of cultivars in five domesticated species and dozens of wild species. However, little is known about the evolutionary history of these pear species and what has contributed to the distinct phenotypic traits between Asian pears and European pears. Results: We report the genome resequencing of 113 pear accessions from worldwide collections, representing both cultivated and wild pear species. Based on 18,302,883 identified SNPs, we conduct phylogenetics, population structure, gene flow, and selective sweep analyses. Furthermore, we propose a model for the divergence, dissemination, and independent domestication of Asian and European pears in which pear, after originating in southwest China and then being disseminated throughout central Asia, has eventually spread to western Asia, and then on to Europe. We find evidence for rapid evolution and balancing selection for S-RNase genes that have contributed to the maintenance of self-incompatibility, thus promoting outcrossing and accounting for pear genome diversity across the Eurasian continent. In addition, separate selective sweep signatures between Asian pears and European pears, combined with co-localized QTLs and differentially expressed genes, underline distinct phenotypic fruit traits, including flesh texture, sugar, acidity, aroma, and stone cells. Conclusions: This study provides further clarification of the evolutionary history of pear along with independent domestication of Asian and European pears. Furthermore, it provides substantive and valuable genomic resources that will significantly advance pear improvement and molecular breeding efforts.

Original languageEnglish (US)
Article number77
JournalGenome biology
Volume19
Issue number1
DOIs
StatePublished - Jun 11 2018

Fingerprint

Pyrus
domestication
pears
genome
fruit
self incompatibility
outcrossing
gene
history
gene flow
population structure
acidity
cultivar
sugar
genomics
texture
divergence
breeding
phylogenetics
Domestication

Keywords

  • Fruit-related traits
  • Independent domestication
  • Origin and evolution
  • Pear (Pyrus)
  • Re-sequencing genomes
  • Self-incompatibility

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics
  • Cell Biology

Cite this

Wu, J., Wang, Y., Xu, J., Korban, S. S., Fei, Z., Tao, S., ... Zhang, S. (2018). Diversification and independent domestication of Asian and European pears. Genome biology, 19(1), [77]. https://doi.org/10.1186/s13059-018-1452-y

Diversification and independent domestication of Asian and European pears. / Wu, Jun; Wang, Yingtao; Xu, Jiabao; Korban, Schuyler S.; Fei, Zhangjun; Tao, Shutian; Ming, Ray; Tai, Shuaishuai; Khan, Awais M.; Postman, Joseph D.; Gu, Chao; Yin, Hao; Zheng, Danman; Qi, Kaijie; Li, Yong; Wang, Runze; Deng, Cecilia H.; Kumar, Satish; Chagné, David; Li, Xiaolong; Wu, Juyou; Huang, Xiaosan; Zhang, Huping; Xie, Zhihua; Li, Xiao; Zhang, Mingyue; Li, Yanhong; Yue, Zhen; Fang, Xiaodong; Li, Jiaming; Li, Leiting; Jin, Cong; Qin, Mengfan; Zhang, Jiaying; Wu, Xiao; Ke, Yaqi; Wang, Jian; Yang, Huanmimg; Zhang, Shaoling.

In: Genome biology, Vol. 19, No. 1, 77, 11.06.2018.

Research output: Contribution to journalArticle

Wu, J, Wang, Y, Xu, J, Korban, SS, Fei, Z, Tao, S, Ming, R, Tai, S, Khan, AM, Postman, JD, Gu, C, Yin, H, Zheng, D, Qi, K, Li, Y, Wang, R, Deng, CH, Kumar, S, Chagné, D, Li, X, Wu, J, Huang, X, Zhang, H, Xie, Z, Li, X, Zhang, M, Li, Y, Yue, Z, Fang, X, Li, J, Li, L, Jin, C, Qin, M, Zhang, J, Wu, X, Ke, Y, Wang, J, Yang, H & Zhang, S 2018, 'Diversification and independent domestication of Asian and European pears', Genome biology, vol. 19, no. 1, 77. https://doi.org/10.1186/s13059-018-1452-y
Wu, Jun ; Wang, Yingtao ; Xu, Jiabao ; Korban, Schuyler S. ; Fei, Zhangjun ; Tao, Shutian ; Ming, Ray ; Tai, Shuaishuai ; Khan, Awais M. ; Postman, Joseph D. ; Gu, Chao ; Yin, Hao ; Zheng, Danman ; Qi, Kaijie ; Li, Yong ; Wang, Runze ; Deng, Cecilia H. ; Kumar, Satish ; Chagné, David ; Li, Xiaolong ; Wu, Juyou ; Huang, Xiaosan ; Zhang, Huping ; Xie, Zhihua ; Li, Xiao ; Zhang, Mingyue ; Li, Yanhong ; Yue, Zhen ; Fang, Xiaodong ; Li, Jiaming ; Li, Leiting ; Jin, Cong ; Qin, Mengfan ; Zhang, Jiaying ; Wu, Xiao ; Ke, Yaqi ; Wang, Jian ; Yang, Huanmimg ; Zhang, Shaoling. / Diversification and independent domestication of Asian and European pears. In: Genome biology. 2018 ; Vol. 19, No. 1.
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AU - Wang, Yingtao

AU - Xu, Jiabao

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AU - Fei, Zhangjun

AU - Tao, Shutian

AU - Ming, Ray

AU - Tai, Shuaishuai

AU - Khan, Awais M.

AU - Postman, Joseph D.

AU - Gu, Chao

AU - Yin, Hao

AU - Zheng, Danman

AU - Qi, Kaijie

AU - Li, Yong

AU - Wang, Runze

AU - Deng, Cecilia H.

AU - Kumar, Satish

AU - Chagné, David

AU - Li, Xiaolong

AU - Wu, Juyou

AU - Huang, Xiaosan

AU - Zhang, Huping

AU - Xie, Zhihua

AU - Li, Xiao

AU - Zhang, Mingyue

AU - Li, Yanhong

AU - Yue, Zhen

AU - Fang, Xiaodong

AU - Li, Jiaming

AU - Li, Leiting

AU - Jin, Cong

AU - Qin, Mengfan

AU - Zhang, Jiaying

AU - Wu, Xiao

AU - Ke, Yaqi

AU - Wang, Jian

AU - Yang, Huanmimg

AU - Zhang, Shaoling

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