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Lyu Y, Wang F, Cheng H, Han J, Dang R, Xia X, Wang H, Zhong J, Lenstra JA, Zhang H, Han J, MacHugh DE, Medugorac I, Upadhyay M, Leonard AS, Ding H, Yang X, Wang MS, Quji S, Zhuzha B, Quzhen P, Wangmu S, Cangjue N, Wa D, Ma W, Liu J, Zhang J, Huang B, Qi X, Li F, Huang Y, Ma Y, Wang Y, Gao Y, Lu W, Lei C, Chen N. Recent selection and introgression facilitated high-altitude adaptation in cattle. Sci Bull (Beijing) 2024:S2095-9273(24)00380-3. [PMID: 38945748 DOI: 10.1016/j.scib.2024.05.030] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 05/09/2024] [Accepted: 05/13/2024] [Indexed: 07/02/2024]
Abstract
During the past 3000 years, cattle on the Qinghai-Xizang Plateau have developed adaptive phenotypes under the selective pressure of hypoxia, ultraviolet (UV) radiation, and extreme cold. The genetic mechanism underlying this rapid adaptation is not yet well understood. Here, we present whole-genome resequencing data for 258 cattle from 32 cattle breeds/populations, including 89 Tibetan cattle representing eight populations distributed at altitudes ranging from 3400 m to 4300 m. Our genomic analysis revealed that Tibetan cattle exhibited a continuous phylogeographic cline from the East Asian taurine to the South Asian indicine ancestries. We found that recently selected genes in Tibetan cattle were related to body size (HMGA2 and NCAPG) and energy expenditure (DUOXA2). We identified signals of sympatric introgression from yak into Tibetan cattle at different altitudes, covering 0.64%-3.26% of their genomes, which included introgressed genes responsible for hypoxia response (EGLN1), cold adaptation (LRP11), DNA damage repair (LATS1), and UV radiation resistance (GNPAT). We observed that introgressed yak alleles were associated with noncoding variants, including those in present EGLN1. In Tibetan cattle, three yak introgressed SNPs in the EGLN1 promoter region reduced the expression of EGLN1, suggesting that these genomic variants enhance hypoxia tolerance. Taken together, our results indicated complex adaptation processes in Tibetan cattle, where recently selected genes and introgressed yak alleles jointly facilitated rapid adaptation to high-altitude environments.
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Affiliation(s)
- Yang Lyu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China; Key Laboratory of Animal Production, Product Quality, and Security, Ministry of Education, College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China
| | - Fuwen Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Haijian Cheng
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China; Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Shandong Key Lab of Animal Disease Control and Breeding, Jinan 250000, China
| | - Jing Han
- College of Veterinary Medicine, Northwest A&F University, Yangling 712100, China
| | - Ruihua Dang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Xiaoting Xia
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Hui Wang
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Sichuan Province and Ministry of Education, Southwest Minzu University, Chengdu 610000, China
| | - Jincheng Zhong
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Sichuan Province and Ministry of Education, Southwest Minzu University, Chengdu 610000, China
| | - Johannes A Lenstra
- Faculty of Veterinary Medicine, Utrecht University, Utrecht 3584 CM, The Netherlands
| | - Hucai Zhang
- Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environmental Science, Yunnan University, Kunming 650500, China; Southwest United Graduate School, Kunming 650500, China
| | - Jianlin Han
- Yazhouwan National Laboratory, Sanya 572024, China; CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agriculture Sciences (CAAS), Beijing 100000, China
| | - David E MacHugh
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Dublin D04 V1W8, Ireland; UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin D04 V1W8, Ireland
| | - Ivica Medugorac
- Population Genomics Group, Department of Veterinary Sciences, LMU Munich, Martinsried 82152, Germany
| | - Maulik Upadhyay
- Population Genomics Group, Department of Veterinary Sciences, LMU Munich, Martinsried 82152, Germany
| | - Alexander S Leonard
- Animal Genomics, ETH Zurich, Universitaetstrasse 2, Zurich 8006, Switzerland
| | - He Ding
- Key Laboratory of Animal Production, Product Quality, and Security, Ministry of Education, College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China
| | - Xiaorui Yang
- Key Laboratory of Animal Production, Product Quality, and Security, Ministry of Education, College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China
| | - Ming-Shan 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 650223, China
| | - Suolang Quji
- Institute of Animal Husbandry and Veterinary Science, Xizang Autonomous Region Academy of Agricultural and Animal Husbandry Sciences, Lhasa 850000, China
| | - Basang Zhuzha
- Institute of Animal Husbandry and Veterinary Science, Xizang Autonomous Region Academy of Agricultural and Animal Husbandry Sciences, Lhasa 850000, China
| | - Pubu Quzhen
- Shigatse City Kangma County Shaogang Township Agriculture and Animal Husbandry Comprehensive Service Center, Shigatse 857000, China
| | - Silang Wangmu
- Institute of Animal Husbandry and Veterinary Science, Xizang Autonomous Region Academy of Agricultural and Animal Husbandry Sciences, Lhasa 850000, China
| | - Nima Cangjue
- Institute of Animal Husbandry and Veterinary Science, Xizang Autonomous Region Academy of Agricultural and Animal Husbandry Sciences, Lhasa 850000, China
| | - Da Wa
- Institute of Animal Husbandry and Veterinary Science, Xizang Autonomous Region Academy of Agricultural and Animal Husbandry Sciences, Lhasa 850000, China
| | - Weidong Ma
- Shaanxi Province Agriculture & Husbandry Breeding Farm, Fufeng 722203, China
| | - Jianyong Liu
- Yunnan Academy of Grassland and Animal Science, Kunming 650500, China
| | - Jicai Zhang
- Yunnan Academy of Grassland and Animal Science, Kunming 650500, China
| | - Bizhi Huang
- Yunnan Academy of Grassland and Animal Science, Kunming 650500, China
| | - Xingshan Qi
- Animal Husbandry Bureau in Biyang County, Biyang 463700, China
| | - Fuqiang Li
- Hunan Tianhua Industrial Corporation Ltd., Lianyuan 417126, China
| | - Yongzhen Huang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Yun Ma
- Key Laboratory of Ruminant Molecular and Cellular Breeding of Ningxia Hui Autonomous Region, School of Agriculture, Ningxia University, Yinchuan 750000, China
| | - Yu Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Yuanpeng Gao
- College of Veterinary Medicine, Northwest A&F University, Yangling 712100, China.
| | - Wenfa Lu
- Key Laboratory of Animal Production, Product Quality, and Security, Ministry of Education, College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China; Yazhouwan National Laboratory, Sanya 572024, China.
| | - Chuzhao Lei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China.
| | - Ningbo Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China.
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Petrov R, Yarkov D, Chakarov N. Genetic analysis of Saker Falcon ( Falcocherrug) subspecies. Biodivers Data J 2024; 12:e116889. [PMID: 38405379 PMCID: PMC10892141 DOI: 10.3897/bdj.12.e116889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 01/26/2024] [Indexed: 02/27/2024] Open
Abstract
Two subspecies of Saker Falcon are commonly accepted - Western (Falcocherrugcherrug) and Eastern (Falcocherrugmilvipes), which are differentiated by their distribution range and phenotype. In Bulgaria, Western Saker Falcons are breeding ex situ in the Wildlife Rehabilitation and Breeding Centre, part of Green Balkans - Stara Zagora NGO, with the aim of restoring the nesting population of the species in the country and both Western and Eastern - in the Breeding Centre for Birds of Prey in Burgas for the purpose of sale for the needs of falconry in the country and abroad. In 2021, a total of 115 birds from the two breeding centres were sampled. The samples were analysed in Bielefeld University (Germany) at nine microsatellite loci. Structure analyses were performed to establish the optimal explanatory number of groups. We compared the putative genetic groups with the known/expected origin of falcons. A separation in two groups best explained the allelic variation between samples. Out of 68 Saker Falcons with putatively Eastern origin, 66 were ascribed to genetic group 2 and two falcons had unclear, mixed or hybrid genetic fingerprints. Out of 42 Sakers with putatively Western origin, 33 were ascribed to genetic group 1, seven to genetic group 2 and two individuals appeared to have a mixed signature of genetic groups 1 and 2 with dominating alleles of group 2. Five known hybrids were scored as mixed signature with dominating genetic cluster 2. This suggests that the two (Eastern and Western) populations of Saker Falcon origin suggested by the subspecies' definitions are also adequate to be considered in breeding programmes. Genetic cluster 1 might represent the ancestral alleles shared with other falcons, while specific novel alleles allow the discrimination of secured Eastern Sakers (group 2), while these populations may be occasionally invaded by individuals from the west.
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Affiliation(s)
- Rusko Petrov
- Green Balkans - Stara Zagora NGO, Stara Zagora, BulgariaGreen Balkans - Stara Zagora NGOStara ZagoraBulgaria
- Trakia University - Stara Zagora, Stara Zagora, BulgariaTrakia University - Stara ZagoraStara ZagoraBulgaria
| | - Dobri Yarkov
- Trakia University - Stara Zagora, Stara Zagora, BulgariaTrakia University - Stara ZagoraStara ZagoraBulgaria
| | - Nayden Chakarov
- University of Bielefeld, Germany, Bielefeld, GermanyUniversity of Bielefeld, GermanyBielefeldGermany
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An X, Mao L, Wang Y, Xu Q, Liu X, Zhang S, Qiao Z, Li B, Li F, Kuang Z, Wan N, Liang X, Duan Q, Feng Z, Yang X, Liu S, Nevo E, Liu J, Storz JF, Li K. Genomic structural variation is associated with hypoxia adaptation in high-altitude zokors. Nat Ecol Evol 2024; 8:339-351. [PMID: 38195998 DOI: 10.1038/s41559-023-02275-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 11/20/2023] [Indexed: 01/11/2024]
Abstract
Zokors, an Asiatic group of subterranean rodents, originated in lowlands and colonized high-elevational zones following the uplift of the Qinghai-Tibet plateau about 3.6 million years ago. Zokors live at high elevation in subterranean burrows and experience hypobaric hypoxia, including both hypoxia (low oxygen concentration) and hypercapnia (elevated partial pressure of CO2). Here we report a genomic analysis of six zokor species (genus Eospalax) with different elevational ranges to identify structural variants (deletions and inversions) that may have contributed to high-elevation adaptation. Based on an assembly of a chromosome-level genome of the high-elevation species, Eospalax baileyi, we identified 18 large inversions that distinguished this species from congeners native to lower elevations. Small-scale structural variants in the introns of EGLN1, HIF1A, HSF1 and SFTPD of E. baileyi were associated with the upregulated expression of those genes. A rearrangement on chromosome 1 was associated with altered chromatin accessibility, leading to modified gene expression profiles of key genes involved in the physiological response to hypoxia. Multigene families that underwent copy-number expansions in E. baileyi were enriched for autophagy, HIF1 signalling and immune response. E. baileyi show a significantly larger lung mass than those of other Eospalax species. These findings highlight the key role of structural variants underlying hypoxia adaptation of high-elevation species in Eospalax.
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Affiliation(s)
- Xuan An
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Leyan Mao
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Yinjia Wang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Qinqin Xu
- Department of Medical Oncology, Qinghai Provincial People's Hospital, Xining, China
| | - Xi Liu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Shangzhe Zhang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Zhenglei Qiao
- College of Life Sciences and Technology, Mudanjiang Normal University, Mudanjiang, China
| | - Bowen Li
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Fang Li
- College of Life Sciences and Technology, Mudanjiang Normal University, Mudanjiang, China
| | - Zhuoran Kuang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Na Wan
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Xiaolong Liang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Qijiao Duan
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Zhilong Feng
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Xiaojie Yang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Sanyuan Liu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Eviatar Nevo
- Institute of Evolution, University of Haifa, Haifa, Israel
| | - Jianquan Liu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China.
| | - Jay F Storz
- School of Biological Sciences, University of Nebraska, Lincoln, NE, USA.
| | - Kexin Li
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China.
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Zinevich L, Prommer M, Laczkó L, Rozhkova D, Sorokin A, Karyakin I, Bagyura J, Cserkész T, Sramkó G. Phylogenomic insights into the polyphyletic nature of Altai falcons within eastern sakers (Falco cherrug) and the origins of gyrfalcons (Falco rusticolus). Sci Rep 2023; 13:17800. [PMID: 37853004 PMCID: PMC10584951 DOI: 10.1038/s41598-023-44534-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 10/10/2023] [Indexed: 10/20/2023] Open
Abstract
The Altai falcon from Central Asia always attracted the attention of humans. Long considered a totemic bird in its native area, modern falconers still much appreciated this large-bodied and mighty bird of prey due to its rarity and unique look. The peculiar body characteristics halfway between the saker falcon (Falco cherrug) and the gyrfalcon (F. rusticolus) triggered debates about its contentious taxonomy. The weak phylogenetic signal associated with traditional genetic methods could not resolve this uncertainty. Here, we address the controversial evolutionary origin of Altai falcons by means of a genome-wide approach, Restriction-site Associated DNA sequencing, using sympatric eastern sakers falcons, allopatric western saker falcons and gyrfalcons as outgroup. This approach provided an unprecedented insight into the phylogenetic relationships of the studied populations by delivering 17,095 unlinked SNPs shedding light on the polyphyletic nature of Altai falcons within eastern sakers. Thus we concluded that the former must correspond to a low taxonomic rank, probably an ecotype or form of the latter. Also, we found that eastern sakers are paraphyletic without gyrfalcons, thus, these latter birds are best regarded as the direct sister lineage of the eastern sakers. This evolutionary relationship, corroborated also by re-analyzing the dataset with the inclusion of outgroup samples (F. biarmicus and F. peregrinus), put eastern sakers into a new light as the potential ancestral genetic source of high latitude and altitude adaptation in descendent populations. Finally, conservation genomic values hint at the stable genetic background of the studied saker populations.
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Affiliation(s)
- Liudmila Zinevich
- Koltzov Institute of Developmental Biology Russian Academy of Sciences, Moscow, Russian Federation
- All-Russian Research Institute for Environmental Protection, Moscow, Russian Federation
| | | | - Levente Laczkó
- HUN-REN-UD Conservation Biology Research Group, Egyetem tér 1, Debrecen, 4032, Hungary
- Evolutionary Genomics Research Group, Department of Botany, University of Debrecen, Egyetem tér 1, Debrecen, 4032, Hungary
| | - Daria Rozhkova
- Koltzov Institute of Developmental Biology Russian Academy of Sciences, Moscow, Russian Federation
- All-Russian Research Institute for Environmental Protection, Moscow, Russian Federation
| | - Alexander Sorokin
- All-Russian Research Institute for Environmental Protection, Moscow, Russian Federation
| | | | - János Bagyura
- MME - BirdLife Hungary, Költő utca 21, Budapest, 1121, Hungary
| | - Tamás Cserkész
- Hungarian Natural History Museum, Baross utca 13, Budapest, 1088, Hungary
| | - Gábor Sramkó
- HUN-REN-UD Conservation Biology Research Group, Egyetem tér 1, Debrecen, 4032, Hungary.
- Evolutionary Genomics Research Group, Department of Botany, University of Debrecen, Egyetem tér 1, Debrecen, 4032, Hungary.
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