Advanced Science (Jan 2025)
Complete Genomic Landscape Reveals Hidden Evolutionary History and Selection Signature in Asian Water Buffaloes (Bubalus bubalis)
- Jingfang Si,
- Dongmei Dai,
- Neena Amatya Gorkhali,
- Mingshan Wang,
- Sheng Wang,
- Saroj Sapkota,
- Ram Chandra Kadel,
- Amir Sadaula,
- Aashish Dhakal,
- Md Omar Faruque,
- Abdullah Ibne Omar,
- Eka Meutia Sari,
- Hidayat Ashari,
- Muhammad Ihsan Andi Dagong,
- Marnoch Yindee,
- Hossam E. Rushdi,
- Hussein Elregalaty,
- Ahmed Amin,
- Mohamed A. Radwan,
- Lan Doan Pham,
- W. M. M. P. Hulugalla,
- G. L. L. Pradeepa Silva,
- Wei Zheng,
- Shahid Mansoor,
- Muhammad Basil Ali,
- Farhad Vahidi,
- Sahar Ahmed Al‐Bayatti,
- Alfredo Pauciullo,
- Johannes A. Lenstra,
- J. Stuart F. Barker,
- Lingzhao Fang,
- Dong‐Dong Wu,
- Jianlin Han,
- Yi Zhang
Affiliations
- Jingfang Si
- State Key Laboratory of Animal Biotech Breeding, 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 100193 China
- Dongmei Dai
- State Key Laboratory of Animal Biotech Breeding, 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 100193 China
- Neena Amatya Gorkhali
- National Animal Breeding and Genetics Research Centre National Animal Science Research Institute Nepal Agriculture Research Council Khumaltar Lalitpur Nepal
- Mingshan Wang
- State Key Laboratory of Genetic Resources and Evolution Yunnan Laboratory of Molecular Biology of Domestic Animals Kunming Institute of Zoology Chinese Academy of Sciences Kunming 650023 China
- Sheng Wang
- State Key Laboratory of Genetic Resources and Evolution Yunnan Laboratory of Molecular Biology of Domestic Animals Kunming Institute of Zoology Chinese Academy of Sciences Kunming 650023 China
- Saroj Sapkota
- National Animal Breeding and Genetics Research Centre National Animal Science Research Institute Nepal Agriculture Research Council Khumaltar Lalitpur Nepal
- Ram Chandra Kadel
- Ministry of Industry, Tourism, Forests and Environment Government of Gandaki Province Pokhara Nepal
- Amir Sadaula
- National Trust for Nature Conservation‐ Biodiversity Conservation Center Sauraha Chitwan Nepal
- Aashish Dhakal
- State Key Laboratory of Animal Biotech Breeding, 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 100193 China
- Md Omar Faruque
- Department of Animal Breeding and Genetics Bangladesh Agricultural University Mymensingh 2202 Bangladesh
- Abdullah Ibne Omar
- State Key Laboratory of Animal Biotech Breeding, 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 100193 China
- Eka Meutia Sari
- Department of Animal Science Faculty of Agriculture Syiah Kuala University Darussalam‐Banda Aceh 23111 Indonesia
- Hidayat Ashari
- Department of Animal Science Faculty of Agriculture Syiah Kuala University Darussalam‐Banda Aceh 23111 Indonesia
- Muhammad Ihsan Andi Dagong
- Animal Science Faculty Hasanuddin University Makassar Indonesia
- Marnoch Yindee
- Akkhraratchakumari Veterinary College Walailak University Thaiburi 222 Thailand
- Hossam E. Rushdi
- Department of Animal Production Faculty of Agriculture Cairo University Algammaa Street Giza 12613 Egypt
- Hussein Elregalaty
- Animal Production Research Institute Agricultural Research Center Dokki Giza Egypt
- Ahmed Amin
- Department of Animal Production Faculty of Agriculture Cairo University Algammaa Street Giza 12613 Egypt
- Mohamed A. Radwan
- Department of Animal Production Faculty of Agriculture Cairo University Algammaa Street Giza 12613 Egypt
- Lan Doan Pham
- Key Laboratory of Animal Cell Technology National Institute of Animal Sciences Tu Liem Hanoi 100000 Vietnam
- W. M. M. P. Hulugalla
- Department of Animal Science Faculty of Agriculture University of Peradeniya Sri Lanka
- G. L. L. Pradeepa Silva
- Department of Animal Science Faculty of Agriculture University of Peradeniya Sri Lanka
- Wei Zheng
- Guangxi Key Laboratory of Buffalo Genetics, Reproduction and Breeding Guangxi Buffalo Research Institute Chinese Academy of Agricultural Sciences Nanning 530001 China
- Shahid Mansoor
- National Institute for Biotechnology and Genetic Engineering (NIBGE) Faisalabad Pakistan
- Muhammad Basil Ali
- National Institute for Biotechnology and Genetic Engineering (NIBGE) Faisalabad Pakistan
- Farhad Vahidi
- Department of Genomics Agricultural Biotechnology Research Institute of Iran‐North Branch (ABRII) Rasht Iran
- Sahar Ahmed Al‐Bayatti
- Medical Laboratory Techniques Department Al‐Farabi University College Ministry of Higher Education and Scientific Research Baghdad Iraq
- Alfredo Pauciullo
- Department of Agricultural, Forest and Food Sciences University of Turin Grugliasco (TO) 10095 Italy
- Johannes A. Lenstra
- Faculty of Veterinary Medicine Utrecht University Yalelaan 104 Utrecht CM 3584 The Netherlands
- J. Stuart F. Barker
- School of Environmental and Rural Science University of New England Armidale NSW 2351 Australia
- Lingzhao Fang
- The Center for Quantitative Genetics and Genomics (QGG) Aarhus University Aarhus 8000 Denmark
- Dong‐Dong Wu
- State Key Laboratory of Genetic Resources and Evolution Yunnan Laboratory of Molecular Biology of Domestic Animals Kunming Institute of Zoology Chinese Academy of Sciences Kunming 650023 China
- Jianlin Han
- Yazhouwan National Laboratory Sanya 572024 China
- Yi Zhang
- State Key Laboratory of Animal Biotech Breeding, 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 100193 China
- DOI
- https://doi.org/10.1002/advs.202407615
- Journal volume & issue
-
Vol. 12,
no. 4
pp. n/a – n/a
Abstract
Abstract To identify the genetic determinants of domestication and productivity of Asian water buffaloes (Bubalus bubalis), 470 genomes of domesticated river and swamp buffaloes along with their putative ancestors, the wild water buffaloes (Bubalus arnee) are sequenced and integrated. The swamp buffaloes inherit the morphology of the wild buffaloes. In contrast, most river buffaloes are unique in their morphology, but their genomes cluster with the wild buffaloes. The levels of genomic diversity in Italian river and Indonesian swamp buffaloes decrease at opposite extremes of their distribution range. Purifying selection prevented the accumulation of harmful loss‐of‐function variants in the Indonesian buffaloes. Genes that evolved rapidly (e.g., GKAP1) following differential selections in the river and swamp buffaloes are involved in their reproduction. Genes related to milk production (e.g., CSN2) and coat color (e.g., MC1R) underwent strong selections in the dairy river buffaloes via soft and hard selective sweeps, respectively. The selective sweeps and single‐cell RNA‐seq data revealed the luminal cells as the key cell type in response to artificial selection for milk production of the dairy buffaloes. These findings show how artificial selection has been driving the evolutionary divergence and genetic differentiation in morphology and productivity of Asian water buffaloes.
Keywords
