Understanding divergent domestication traits from the whole-genome sequencing of swamp- and river-buffalo populations

Xier Luo; Yu Zhou; Bing Zhang; Yi Zhang; Xiaobo Wang; Tong Feng; Zhipeng Li; Kuiqing Cui; Zhiqiang Wang; Chan Luo; Hui Li; Yanfei Deng; Fenghua Lu; Jianlin Han; Yongwang Miao; Huaming Mao; Xiaoyan Yi; Cheng Ai; Shigang Wu; Alun Li; Zhichao Wu; Zijun Zhuo; Do Da Giang; Bikash Mitra; Mohammad Farhad Vahidi; Shahid Mansoor; Sahar Ahmed Al-Bayatti; Eka Meutia Sari; Neena Amatya Gorkhali; Sigit Prastowo; Laiba Shafique; Guoyou Ye; Qian Qian; Baoshan Chen; Deshun Shi; Jue Ruan; Qingyou Liu

doi:10.1093/nsr/nwaa024

Understanding divergent domestication traits from the whole-genome sequencing of swamp- and river-buffalo populations

Natl Sci Rev. 2020 Mar;7(3):686-701. doi: 10.1093/nsr/nwaa024. Epub 2020 Feb 17.

Authors

Xier Luo¹, Yu Zhou¹, Bing Zhang², Yi Zhang³, Xiaobo Wang^{1

4}, Tong Feng^{1

4}, Zhipeng Li¹, Kuiqing Cui¹, Zhiqiang Wang¹, Chan Luo¹, Hui Li¹, Yanfei Deng¹, Fenghua Lu¹, Jianlin Han^{5

6}, Yongwang Miao⁷, Huaming Mao⁷, Xiaoyan Yi⁴, Cheng Ai⁴, Shigang Wu⁴, Alun Li⁴, Zhichao Wu⁴, Zijun Zhuo⁴, Do Da Giang^{1

8}, Bikash Mitra⁹, Mohammad Farhad Vahidi¹⁰, Shahid Mansoor¹¹, Sahar Ahmed Al-Bayatti¹², Eka Meutia Sari¹³, Neena Amatya Gorkhali¹⁴, Sigit Prastowo¹⁵, Laiba Shafique¹, Guoyou Ye¹⁶, Qian Qian⁴, Baoshan Chen¹, Deshun Shi¹, Jue Ruan⁴, Qingyou Liu¹

Affiliations

¹ State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530005, China.
² CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.
³ National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing 100083, China.
⁴ Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China.
⁵ CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
⁶ International Livestock Research Institute, Nairobi 00100, Kenya.
⁷ Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China.
⁸ Bacgiang Agriculture and Forestry University, Bacgiang 230000, Vietnam.
⁹ Cellular Immunology Lab, Department of Zoology, University of North Bengal, Siligun 734013, India.
¹⁰ Animal Biotechnology Department, Agricultural Biotechnology Research Institute of Iran-North Region, Agricultural Research, Education and Extension Organization, Rasht 999067, Iran.
¹¹ National Institute for Biotechnology and Genetic Engineering, Faisalabad 999010, Pakistan.
¹² Animal Genetic Sources Department, Directorate of Animal Resources, Ministry of Agriculture, Baghdad 19207, Iraq.
¹³ Department of Animal Science, Faculty of Agriculture, Syiah Kuala University, Darussalam-Banda Aceh 23111, Indonesia.
¹⁴ Animal Breeding Division, National Animal Science Research Institute, Nepal Agriculture Research Council, Khumaltar 999098, Nepal.
¹⁵ Animal Science Department Universitas Sebelas Maret, Surakarta 999006, Indonesia.
¹⁶ International Rice Research Institute, Manila 999005, Philippines.

Abstract

Domesticated buffaloes have been integral to rice-paddy agro-ecosystems for millennia, yet relatively little is known about the buffalo genomics. Here, we sequenced and assembled reference genomes for both swamp and river buffaloes and we re-sequenced 230 individuals (132 swamp buffaloes and 98 river buffaloes) sampled from across Asia and Europe. Beyond the many actionable insights that our study revealed about the domestication, basic physiology and breeding of buffalo, we made the striking discovery that the divergent domestication traits between swamp and river buffaloes can be explained with recent selections of genes on social behavior, digestion metabolism, strengths and milk production.

Keywords: Bubalus bubalis genome; buffalo; domestication; re-sequencing; traits.