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Wei X, Li S, Yan H, Chen S, Li R, Zhang W, Chao S, Guo W, Li W, Ahmed Z, Lei C, Ma Z. Unraveling genomic diversity and positive selection signatures of Qaidam cattle through whole-genome re-sequencing. Anim Genet 2024; 55:362-376. [PMID: 38480515 DOI: 10.1111/age.13417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 01/02/2024] [Accepted: 02/22/2024] [Indexed: 05/04/2024]
Abstract
Qaidam cattle are a typical Chinese native breed inhabiting northwest China. They bear the characteristics of high cold and roughage tolerance, low-oxygen adaptability and good meat quality. To analyze the genetic diversity of Qaidam cattle, 60 samples were sequenced using whole-genome resequencing technology, along with 192 published sets of whole-genome sequencing data of Indian indicine cattle, Chinese indicine cattle, North Chinese cattle breeds, East Asian taurine cattle, Eurasian taurine cattle and European taurine cattle as controls. It was found that Qaidam cattle have rich genetic diversity in Bos taurus, but the degree of inbreeding is also high, which needs further protection. The phylogenetic analysis, principal component analysis and ancestral component analysis showed that Qaidam cattle mainly originated from East Asian taurine cattle. Qaidam cattle had a closer genetic relationship with the North Chinese cattle breeds and the least differentiation from Mongolian cattle. Annotating the selection signals obtained by composite likelihood ratio, nucleotide diversity analysis, integrated haplotype score, genetic differentiation index, genetic diversity ratio and cross-population extended haplotype homozygosity methods, several genes associated with immunity, reproduction, meat, milk, growth and adaptation showed strong selection signals. In general, this study provides genetic evidence for understanding the germplasm characteristics of Qaidam cattle. At the same time, it lays a foundation for the scientific and reasonable protection and utilization of genetic resources of Chinese local cattle breeds, which has great theoretical and practical significance.
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Affiliation(s)
- Xudong Wei
- Academy of Animal Science and Veterinary Medicine, Qinghai University, Xining, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Xining, China
- Plateau Livestock Genetic Resources Protection and Innovative Utilization Key Laboratory of Qinghai Province, Xining, China
| | - Shuang Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Huixuan Yan
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Shengmei Chen
- Academy of Animal Science and Veterinary Medicine, Qinghai University, Xining, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Xining, China
- Plateau Livestock Genetic Resources Protection and Innovative Utilization Key Laboratory of Qinghai Province, Xining, China
| | - Ruizhe Li
- Academy of Animal Science and Veterinary Medicine, Qinghai University, Xining, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Xining, China
- Plateau Livestock Genetic Resources Protection and Innovative Utilization Key Laboratory of Qinghai Province, Xining, China
| | - Weizhong Zhang
- Golmud Animal Husbandry and Veterinary Station of Qinghai Province, Golmud, China
| | - Shengyu Chao
- Agro-Technical Extension and Service Center in Haixi Prefecture of Qinghai Province, Delingha, China
| | - Weixing Guo
- Academy of Animal Science and Veterinary Medicine, Qinghai University, Xining, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Xining, China
- Plateau Livestock Genetic Resources Protection and Innovative Utilization Key Laboratory of Qinghai Province, Xining, China
| | - Wenhao Li
- Academy of Animal Science and Veterinary Medicine, Qinghai University, Xining, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Xining, China
- Plateau Livestock Genetic Resources Protection and Innovative Utilization Key Laboratory of Qinghai Province, Xining, China
| | - Zulfiqar Ahmed
- Department of Livestock and Poultry Production, Faculty of Veterinary and Animal Sciences, University of Poonch Rawalakot, Rawalakot, Pakistan
| | - Chuzhao Lei
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Zhijie Ma
- Academy of Animal Science and Veterinary Medicine, Qinghai University, Xining, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Xining, China
- Plateau Livestock Genetic Resources Protection and Innovative Utilization Key Laboratory of Qinghai Province, Xining, China
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Zhang S, Li J, Zhao Y, Tang Y, Li H, Song T, An T, Guan J, Li X, Zhang M. Whole-genome resequencing reveals genetic diversity, differentiation, and selection signatures of yak breeds/populations in southwestern China. Front Genet 2024; 15:1382128. [PMID: 38873117 PMCID: PMC11169580 DOI: 10.3389/fgene.2024.1382128] [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: 02/05/2024] [Accepted: 04/17/2024] [Indexed: 06/15/2024] Open
Abstract
The Sichuan-Yunnan region is the main production area of yaks in southwestern China, with rich genetic resources of Yaks. Nevertheless, there have been limited study on the genetic characteristics of the entire yak populations in Tibet and southwestern China. In this study, we performed whole-genome resequencing to identify genetic variation information in a total of 198 individuals from six yak breeds (populations) in Sichuan (Muli yak, Jinchuan yak, Changtai yak, Maiwa yak), Yunnan (Zhongdian yak), and Tibet (Tibetan yak). The aim was to investigate the whole-genome genetic diversity, population genetic structure, and genome selection signatures. We observed that all six populations exhibit abundant genetic diversity. Except for Tibetan yaks, which showed low nucleotide diversity (0.00104), the remaining yak populations generally displayed high nucleotide diversity (0.00129-0.00153). Population genetic structure analysis revealed that, among the six yak populations, Muli yak exhibited greater differentiation from other yak populations and formed a distinct cluster independently. The Maiwa yak population displayed a complex genetic structure and exhibited gene exchange with Jinchuan and Changtai yaks. Positive selection signals were detected in candidate genes associated with growth (GNB4, HMGA2, TRPS1, and LTBP1), reproduction (PI4KB, DYNC1I1, and GRIP1), immunity (CD200 and IL1RAP), lactation (SNX13 and CPM), hypoxia adaptation (NDUFB6, PRKN, and MRPS9), hair (KRT24, KRT25, and KRT26), meat quality (SUCLG2), digestion and absorption (CLDN1), and pigment deposition (OCA2) using the integrated Pi and F ST methods. This study provides significant insights into understanding the whole-genome genetic characteristics of yak populations in Tibet and southwestern China.
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Affiliation(s)
- Shilin Zhang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Jing Li
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Yanhua Zhao
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Yujun Tang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Hao Li
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Tianzeng Song
- Institute of Animal Science, Tibet Academy of Agricultural and Animal Husbandry Science, Lhasa, China
| | - Tianwu An
- Sichuan Academy of Grassland Science, Chengdu, China
| | - Jiuqiang Guan
- Sichuan Academy of Grassland Science, Chengdu, China
| | - Xiaowei Li
- Breeding Fram of Longri, Agriculture and Rural Bureau of Aba Prefecture in Sichuan, Hongyuan, China
| | - Ming Zhang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
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Li R, Zhao Y, Liang B, Pu Y, Jiang L, Ma Y. Genome-Wide Signal Selection Analysis Revealing Genes Potentially Related to Sheep-Milk-Production Traits. Animals (Basel) 2023; 13:ani13101654. [PMID: 37238084 DOI: 10.3390/ani13101654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 05/10/2023] [Accepted: 05/11/2023] [Indexed: 05/28/2023] Open
Abstract
Natural selection and domestication have shaped modern sheep populations into a vast range of phenotypically diverse breeds. Among these breeds, dairy sheep have a smaller population than meat sheep and wool sheep, and less research is performed on them, but the lactation mechanism in dairy sheep is critically important for improving animal-production methods. In this study, whole-genome sequences were generated from 10 sheep breeds, including 57 high-milk-yield sheep and 44 low-milk-yield sheep, to investigate the genetic signatures of milk production in dairy sheep, and 59,864,820 valid SNPs (Single Nucleotide Polymorphisms) were kept after quality control to perform population-genetic-structure analyses, gene-detection analyses, and gene-function-validation analyses. For the population-genetic-structure analyses, we carried out PCA (Principal Component Analysis), as well as neighbor-joining tree and structure analyses to classify different sheep populations. The sheep used in our study were well distributed in ten groups, with the high-milk-yield-group populations close to each other and the low-milk-yield-group populations showing similar classifications. To perform an exact signal-selection analysis, we used three different methods to find SNPs to perform gene-annotation analyses within the 995 common regions derived from the fixation index (FST), nucleotide diversity (Ɵπ), and heterozygosity rate (ZHp) results. In total, we found 553 genes that were located in these regions. These genes mainly participate in the protein-binding pathway and the nucleoplasm-interaction pathway, as revealed by the GO- and KEGG-function-enrichment analyses. After the gene selection and function analyses, we found that FCGR3A, CTSK, CTSS, ARNT, GHR, SLC29A4, ROR1, and TNRC18 were potentially related to sheep-milk-production traits. We chose the strongly selected genes, FCGR3A, CTSK, CTSS, and ARNT during the signal-selection analysis to perform a RT-qPCR (Reale time Quantitative Polymerase Chain Reaction) experiment to validate their expression-level relationship with milk production, and the results showed that FCGR3A has a significant negative relationship with sheep-milk production, while other three genes did not show any positive or negative relations. In this study, it was discovered and proven that the candidate gene FCGR3A potentially contributes to the milk production of dairy sheep and a basis was laid for the further study of the genetic mechanism underlying the strong milk-production traits of sheep.
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Affiliation(s)
- Ruonan Li
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
- Key Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
- Teaching and Research Centre (TERRA), Gembloux Agro-Bio Tech, University of Liège, 5030 Gembloux, Belgium
| | - Yuhetian Zhao
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
- Key Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
| | - Benmeng Liang
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
- Key Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
| | - Yabin Pu
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
- Key Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
| | - Lin Jiang
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
- Key Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
| | - Yuehui Ma
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
- Key Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
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Li G, Luo J, Wang F, Xu D, Ahmed Z, Chen S, Li R, Ma Z. Whole-genome resequencing reveals genetic diversity, differentiation, and selection signatures of yak breeds/populations in Qinghai, China. Front Genet 2023; 13:1034094. [PMID: 36704337 PMCID: PMC9871260 DOI: 10.3389/fgene.2022.1034094] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 11/02/2022] [Indexed: 01/12/2023] Open
Abstract
The Qinghai Province of China is located in the northeast region of the Qinghai-Tibetan Plateau (QTP) and carries abundant yak genetic resources. Previous investigations of archaeological records, mitochondrial DNA, and Y chromosomal markers have suggested that Qinghai was the major center of yak domestication. In the present study, we examined the genomic diversity, differentiation, and selection signatures of 113 Qinghai yak, including 42 newly sequenced Qinghai yak and 71 publicly available individuals, from nine yak breeds/populations (wild, Datong, Huanhu, Xueduo, Yushu, Qilian, Geermu, Tongde, and Huzhu white) using high-depth whole-genome resequencing data. We observed that most of Qinghai yak breeds/populations have abundant genomic diversity based on four genomic parameters (nucleotide diversity, inbreeding coefficients, linkage disequilibrium decay, and runs of homozygosity). Population genetic structure analysis showed that Qinghai yak have two lineages with two ancestral origins and that nine yak breeds/populations are clustered into three distinct groups of wild yak, Geermu yak, and seven other domestic yak breeds/populations. F ST values showed moderate genetic differentiation between wild yak, Geermu yak, and the other Qinghai yak breeds/populations. Positive selection signals were detected in candidate genes associated with disease resistance (CDK2AP2, PLEC, and CYB5B), heat stress (NFAT5, HSF1, and SLC25A48), pigmentation (MCAM, RNF26, and BOP1), vision (C1QTNF5, MFRP, and TAX1BP3), milk quality (OPLAH and GRINA), neurodevelopment (SUSD4, INSYN1, and PPP1CA), and meat quality (ZRANB1), using the integrated PI, composite likelihood ratio (CLR), and F ST methods. These findings offer new insights into the genetic mechanisms underlying target traits in yak and provide important information for understanding the genomic characteristics of yak breeds/populations in Qinghai.
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Affiliation(s)
- Guangzhen Li
- Academy of Animal Science and Veterinary Medicine, Qinghai University, Xining, China,Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Xining, China,Plateau Livestock Genetic Resources Protection and Innovative Utilization Key Laboratory of Qinghai Province, Xining, China
| | - Jing Luo
- Academy of Animal Science and Veterinary Medicine, Qinghai University, Xining, China,Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Xining, China,Plateau Livestock Genetic Resources Protection and Innovative Utilization Key Laboratory of Qinghai Province, Xining, China
| | - Fuwen Wang
- College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Donghui Xu
- Academy of Animal Science and Veterinary Medicine, Qinghai University, Xining, China,Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Xining, China,Plateau Livestock Genetic Resources Protection and Innovative Utilization Key Laboratory of Qinghai Province, Xining, China
| | - Zulfiqar Ahmed
- Faculty of Veterinary and Animal Sciences, University of Poonch Rawalakot, Rawalakot, Pakistan
| | - Shengmei Chen
- Academy of Animal Science and Veterinary Medicine, Qinghai University, Xining, China,Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Xining, China,Plateau Livestock Genetic Resources Protection and Innovative Utilization Key Laboratory of Qinghai Province, Xining, China
| | - Ruizhe Li
- Academy of Animal Science and Veterinary Medicine, Qinghai University, Xining, China,Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Xining, China,Plateau Livestock Genetic Resources Protection and Innovative Utilization Key Laboratory of Qinghai Province, Xining, China
| | - Zhijie Ma
- Academy of Animal Science and Veterinary Medicine, Qinghai University, Xining, China,Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Xining, China,Plateau Livestock Genetic Resources Protection and Innovative Utilization Key Laboratory of Qinghai Province, Xining, China,*Correspondence: Zhijie Ma,
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Selection Signatures in Italian Livestock Guardian and Herding Shepherd Dogs. Vet Sci 2022; 10:vetsci10010003. [PMID: 36669004 PMCID: PMC9862740 DOI: 10.3390/vetsci10010003] [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: 10/21/2022] [Revised: 12/14/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022] Open
Abstract
Livestock guardian (LGD) and herding shepherd (HSD) dogs have distinct morphological and behavioural characteristics, long selected by farmers and breeders, to accomplish different tasks. This study aimed to find the genomic regions that best differentiate and characterise Italian LGD and HSD. Genomic data of 158 dogs of four LGD and five HSD breeds, obtained with the 170K canine SNPchip, were collected. The two groups were compared using FST and XP-EHH analyses, identifying regions containing 29 genes. Moreover, 16 islands of runs of homozygosity were found in LGD, and 15 in HSD; 4 of them were partially shared. Among the genes found that better differentiated HSD and LGD, several were associated with dog domestication and behavioural aspects; particularly, MSRB3 and LLPH were linked to herding behaviour in previous studies. Others, DYSK, MAP2K5, and RYR, were related to body size and muscle development. Prick ears prevailed in sampled HSD, and drop ears in LGD; this explains the identification of WIF1 and MSRB3 genes. Unexpectedly, a number of genes were also associated with eye development and functionality. These results shed further light on the differences that human selection introduced in dogs aimed at different duties, even in a limited geographic area such as Italy.
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Zhou C, Liu Y, Zheng X, Shang K, Cheng M, Wang L, Yang N, Yue B. Characterization of olfactory receptor repertoires provides insights into the high-altitude adaptation of the yak based on the chromosome-level genome. Int J Biol Macromol 2022; 209:220-230. [PMID: 35378160 DOI: 10.1016/j.ijbiomac.2022.03.194] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 03/25/2022] [Accepted: 03/28/2022] [Indexed: 11/15/2022]
Abstract
Olfaction in vertebrates plays pivotal parts in many aspects, such as localizing prey or food, mating behavior, avoiding predators, and social communication. Yak (Bos grunniens) is the only Bos species that can thrive in high-altitude areas. In view of the critical role of olfactory receptors (ORs) in the specific recognition of diverse stimuli, investigating the evolutionary dynamics of ORs in the yak means a lot. In this study, we used the chromosome-level genome of the yak to identify the ORs genes and discussed the effects of high altitude on the yak's olfaction by comparing the yak with other low-altitude living Bos species (Bos frontalis (gayal), Bos gaurus (gaur), Bos indicus (zebu) and Bos taurus (cattle)). The yak had 400 OR genes, including 264 functional genes, 16 partial genes and 120 OR pseudo genes. There were 387 OR genes mapped to yak 31 chromosomes, and chromosomes 13 and 8 had the most OR genes and functional OR genes. Among these five Bos species, yak had the least number of OR gene subfamilies, OR genes and functional OR genes, while the total number of OR genes in gayal (n = 784) was almost twice as many as that of yak, indicating that the olfaction of yak may be less developed. In addition, the phylogenetic relationships of the functional Bos OR genes were illustrated, which comprised 79 families and 466 subfamilies distributed in two classes (Class I and Class II). There were 76 OR gene subfamilies shared by these five Bos species and 17 OR gene subfamilies were unique to the yak. The potential odor specificity of 44 yak OR genes was identified through the similarity to human OR protein sequences. Remarkably, yak lacks β-ionone and Isovaleric acid(IVA)-related ORs, which may be related to the decline of high-altitude herbaceous plant diversity and underdeveloped yak sweat glands. The conserved motifs of OR genes were highly conserved in Bos species. These results provided a solid foundation for further studies on the molecular mechanisms of the yak's adaptation to the high-altitude environment in olfaction.
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Affiliation(s)
- Chuang Zhou
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064, PR China
| | - Yi Liu
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064, PR China
| | - Xiaofeng Zheng
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064, PR China
| | - Ke Shang
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064, PR China
| | - Meiling Cheng
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064, PR China
| | - Lei Wang
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064, PR China
| | - Nan Yang
- Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu 610064, PR China; Collaborative Innovation Center for Ecological Animal Husbandry of Qinghai- Tibetan plateau, Southwest Minzu University.
| | - Bisong Yue
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064, PR China.
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Beckman EJ, Martins F, Suzuki TA, Bi K, Keeble S, Good JM, Chavez AS, Ballinger MA, Agwamba K, Nachman MW. The genomic basis of high-elevation adaptation in wild house mice (Mus musculus domesticus) from South America. Genetics 2022; 220:iyab226. [PMID: 34897431 PMCID: PMC9097263 DOI: 10.1093/genetics/iyab226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 12/04/2021] [Indexed: 11/14/2022] Open
Abstract
Understanding the genetic basis of environmental adaptation in natural populations is a central goal in evolutionary biology. The conditions at high elevation, particularly the low oxygen available in the ambient air, impose a significant and chronic environmental challenge to metabolically active animals with lowland ancestry. To understand the process of adaptation to these novel conditions and to assess the repeatability of evolution over short timescales, we examined the signature of selection from complete exome sequences of house mice (Mus musculus domesticus) sampled across two elevational transects in the Andes of South America. Using phylogenetic analysis, we show that house mice colonized high elevations independently in Ecuador and Bolivia. Overall, we found distinct responses to selection in each transect and largely nonoverlapping sets of candidate genes, consistent with the complex nature of traits that underlie adaptation to low oxygen availability (hypoxia) in other species. Nonetheless, we also identified a small subset of the genome that appears to be under parallel selection at the gene and SNP levels. In particular, three genes (Col22a1, Fgf14, and srGAP1) bore strong signatures of selection in both transects. Finally, we observed several patterns that were common to both transects, including an excess of derived alleles at high elevation, and a number of hypoxia-associated genes exhibiting a threshold effect, with a large allele frequency change only at the highest elevations. This threshold effect suggests that selection pressures may increase disproportionately at high elevations in mammals, consistent with observations of some high-elevation diseases in humans.
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Affiliation(s)
- Elizabeth J Beckman
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Felipe Martins
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Taichi A Suzuki
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720, USA
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen 72076, Germany
| | - Ke Bi
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Sara Keeble
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
| | - Jeffrey M Good
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
- Wildlife Biology Program, University of Montana, Missoula, MT 59812, USA
| | - Andreas S Chavez
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720, USA
- Department of Evolution, Ecology, and Organismal Biology and the Translational Data Analytics Institute, The Ohio State University, Columbus, OH 43210, USA
| | - Mallory A Ballinger
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Kennedy Agwamba
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Michael W Nachman
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720, USA
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Kour A, Niranjan SK, Malayaperumal M, Surati U, Pukhrambam M, Sivalingam J, Kumar A, Sarkar M. Genomic Diversity Profiling and Breed-Specific Evolutionary Signatures of Selection in Arunachali Yak. Genes (Basel) 2022; 13:genes13020254. [PMID: 35205299 PMCID: PMC8872319 DOI: 10.3390/genes13020254] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 01/09/2022] [Accepted: 01/13/2022] [Indexed: 02/04/2023] Open
Abstract
Arunachali yak, the only registered yak breed of India, is crucial for the economic sustainability of pastoralist Monpa community. This study intended to determine the genomic diversity and to identify signatures of selection in the breed. Previously available double digest restriction-site associated DNA (ddRAD) sequencing data of Arunachali yak animals was processed and 99,919 SNPs were considered for further analysis. The genomic diversity profiled based on nucleotide diversity, π (π = 0.041 in 200 bp windows), effective population size, Ne (Ne = 83) and Runs of homozygosity (ROH) (predominance of shorter length ROHs) was found to be optimum. Subsequently, 207 regions were identified to be under selective sweeps through de-correlated composite of multiple signals (DCMS) statistic which combined three individual test statistics viz. π, Tajima’s D and |iHS| in non-overlapping 100 kb windows. Mapping of these regions revealed 611 protein-coding genes including KIT, KITLG, CDH12, FGG, FGA, FGB, PDGFRA, PEAR1, STXBP3, olfactory receptor genes (OR5K3, OR5H6 and OR1E1) and taste receptor genes (TAS2R1, TAS2R3 and TAS2R4). Functional annotation highlighted that biological processes like platelet aggregation and sensory perception were the most overrepresented and the associated regions could be considered as breed-specific signatures of selection in Arunachali yak. These findings point towards evolutionary role of natural selection in environmental adaptation of Arunachali yak population and provide useful insights for pursuing genome-wide association studies in future.
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Affiliation(s)
- Aneet Kour
- ICAR-National Research Centre on Yak, Dirang 790101, Arunachal Pradesh, India; (M.P.); (M.S.)
- Correspondence:
| | - Saket Kumar Niranjan
- ICAR-National Bureau of Animal Genetic Resources, Karnal 132001, Haryana, India; (S.K.N.); (A.K.)
| | - Mohan Malayaperumal
- ICAR-National Dairy Research Institute, Karnal 132001, Haryana, India; (M.M.); (U.S.)
| | - Utsav Surati
- ICAR-National Dairy Research Institute, Karnal 132001, Haryana, India; (M.M.); (U.S.)
| | - Martina Pukhrambam
- ICAR-National Research Centre on Yak, Dirang 790101, Arunachal Pradesh, India; (M.P.); (M.S.)
| | | | - Amod Kumar
- ICAR-National Bureau of Animal Genetic Resources, Karnal 132001, Haryana, India; (S.K.N.); (A.K.)
| | - Mihir Sarkar
- ICAR-National Research Centre on Yak, Dirang 790101, Arunachal Pradesh, India; (M.P.); (M.S.)
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Cheruiyot EK, Haile-Mariam M, Cocks BG, MacLeod IM, Xiang R, Pryce JE. New loci and neuronal pathways for resilience to heat stress in cattle. Sci Rep 2021; 11:16619. [PMID: 34404823 PMCID: PMC8371109 DOI: 10.1038/s41598-021-95816-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 07/30/2021] [Indexed: 02/07/2023] Open
Abstract
While understanding the genetic basis of heat tolerance is crucial in the context of global warming's effect on humans, livestock, and wildlife, the specific genetic variants and biological features that confer thermotolerance in animals are still not well characterized. We used dairy cows as a model to study heat tolerance because they are lactating, and therefore often prone to thermal stress. The data comprised almost 0.5 million milk records (milk, fat, and proteins) of 29,107 Australian Holsteins, each having around 15 million imputed sequence variants. Dairy animals often reduce their milk production when temperature and humidity rise; thus, the phenotypes used to measure an individual's heat tolerance were defined as the rate of milk production decline (slope traits) with a rising temperature-humidity index. With these slope traits, we performed a genome-wide association study (GWAS) using different approaches, including conditional analyses, to correct for the relationship between heat tolerance and level of milk production. The results revealed multiple novel loci for heat tolerance, including 61 potential functional variants at sites highly conserved across 100 vertebrate species. Moreover, it was interesting that specific candidate variants and genes are related to the neuronal system (ITPR1, ITPR2, and GRIA4) and neuroactive ligand-receptor interaction functions for heat tolerance (NPFFR2, CALCR, and GHR), providing a novel insight that can help to develop genetic and management approaches to combat heat stress.
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Affiliation(s)
- Evans K. Cheruiyot
- grid.1018.80000 0001 2342 0938School of Applied Systems Biology, La Trobe University, Bundoora, VIC 3083 Australia ,grid.452283.a0000 0004 0407 2669Agriculture Victoria Research, Centre for AgriBiosciences, AgriBio, Bundoora, VIC 3083 Australia
| | - Mekonnen Haile-Mariam
- grid.452283.a0000 0004 0407 2669Agriculture Victoria Research, Centre for AgriBiosciences, AgriBio, Bundoora, VIC 3083 Australia
| | - Benjamin G. Cocks
- grid.1018.80000 0001 2342 0938School of Applied Systems Biology, La Trobe University, Bundoora, VIC 3083 Australia ,grid.452283.a0000 0004 0407 2669Agriculture Victoria Research, Centre for AgriBiosciences, AgriBio, Bundoora, VIC 3083 Australia
| | - Iona M. MacLeod
- grid.452283.a0000 0004 0407 2669Agriculture Victoria Research, Centre for AgriBiosciences, AgriBio, Bundoora, VIC 3083 Australia
| | - Ruidong Xiang
- grid.452283.a0000 0004 0407 2669Agriculture Victoria Research, Centre for AgriBiosciences, AgriBio, Bundoora, VIC 3083 Australia ,grid.1008.90000 0001 2179 088XFaculty of Veterinary and Agricultural Science, The University of Melbourne, Parkville, VIC 3052 Australia
| | - Jennie E. Pryce
- grid.1018.80000 0001 2342 0938School of Applied Systems Biology, La Trobe University, Bundoora, VIC 3083 Australia ,grid.452283.a0000 0004 0407 2669Agriculture Victoria Research, Centre for AgriBiosciences, AgriBio, Bundoora, VIC 3083 Australia
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Adaptation Mechanisms of Yak ( Bos grunniens) to High-Altitude Environmental Stress. Animals (Basel) 2021; 11:ani11082344. [PMID: 34438801 PMCID: PMC8388626 DOI: 10.3390/ani11082344] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 07/29/2021] [Accepted: 08/03/2021] [Indexed: 11/16/2022] Open
Abstract
Living at a high altitude involves many environmental challenges. The combined effects of hypoxia and cold stress impose severe physiological challenges on endothermic animals. The yak is integral to the livelihood of the people occupying the vast, inhospitable Qinghai-Tibetan plateau and the surrounding mountainous region. Due to long-term selection, the yak exhibits stable and unique genetic characteristics which enable physiological, biochemical, and morphological adaptations to a high altitude. Thus, the yak is a representative model for mammalian plateau-adaptability studies. Understanding coping mechanisms provides unique insights into adaptive evolution, thus informing the breeding of domestic yaks. This review provides an overview of genetic adaptations in Bos grunniens to high-altitude environmental stress. Combined genomics and theoretical advances have informed the genetic basis of high-altitude adaptations.
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Pamenter ME, Hall JE, Tanabe Y, Simonson TS. Cross-Species Insights Into Genomic Adaptations to Hypoxia. Front Genet 2020; 11:743. [PMID: 32849780 PMCID: PMC7387696 DOI: 10.3389/fgene.2020.00743] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Accepted: 06/22/2020] [Indexed: 12/13/2022] Open
Abstract
Over millions of years, vertebrate species populated vast environments spanning the globe. Among the most challenging habitats encountered were those with limited availability of oxygen, yet many animal and human populations inhabit and perform life cycle functions and/or daily activities in varying degrees of hypoxia today. Of particular interest are species that inhabit high-altitude niches, which experience chronic hypobaric hypoxia throughout their lives. Physiological and molecular aspects of adaptation to hypoxia have long been the focus of high-altitude populations and, within the past decade, genomic information has become increasingly accessible. These data provide an opportunity to search for common genetic signatures of selection across uniquely informative populations and thereby augment our understanding of the mechanisms underlying adaptations to hypoxia. In this review, we synthesize the available genomic findings across hypoxia-tolerant species to provide a comprehensive view of putatively hypoxia-adaptive genes and pathways. In many cases, adaptive signatures across species converge on the same genetic pathways or on genes themselves [i.e., the hypoxia inducible factor (HIF) pathway). However, specific variants thought to underlie function are distinct between species and populations, and, in most cases, the precise functional role of these genomic differences remains unknown. Efforts to standardize these findings and explore relationships between genotype and phenotype will provide important clues into the evolutionary and mechanistic bases of physiological adaptations to environmental hypoxia.
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Affiliation(s)
- Matthew E. Pamenter
- Department of Biology, University of Ottawa, Ottawa, ON, Canada
- Ottawa Brain and Mind Research Institute, University of Ottawa, Ottawa, ON, Canada
| | - James E. Hall
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, School of Medicine, University of California, San Diego, San Diego, CA, United States
| | - Yuuka Tanabe
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, School of Medicine, University of California, San Diego, San Diego, CA, United States
| | - Tatum S. Simonson
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, School of Medicine, University of California, San Diego, San Diego, CA, United States
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Guang-Xin E, Yang BG, Zhu YB, Duang XH, Basang WD, Luo XL, An TW. Genome-wide selective sweep analysis of the high-altitude adaptability of yaks by using the copy number variant. 3 Biotech 2020; 10:259. [PMID: 32432020 DOI: 10.1007/s13205-020-02254-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 05/07/2020] [Indexed: 12/17/2022] Open
Abstract
The domestic yak (Bos grunniens) from the Qinghai-Tibet Plateau is an important animal model in high-altitude adaptation studies. Here, we performed the genome-wide selective sweep analysis to identify the candidate copy number variation (CNV) for the high-altitude adaptation of yaks. A total of 531 autosomal CNVs were determined from 29 yak genome-wide resequencing data (15 high- and 14 low-altitude distributions) by using a CNV caller with a CNV identification interval > 5 kb, CNV silhouette score > 0.7, and minimum allele frequency > 0.05. Most high-frequency CNVs were located at the exonic (44.63%) and intergenic (46.52%) regions. In accordance with the results of the selective sweep analysis, 7 candidate CNVs were identified from the interaction of the top 20 CNVs with highest divergence from the F ST and V ST between the low (LA) and high (HA) altitudes. Five genes (i.e., GRIK4, IFNLR1, LOC102275985, GRHL3, and LOC102275713) were also annotated from the seven candidate CNVs and their upstream and downstream ranges at 300 kb. GRIK4, IFNLR1, and LOC102275985 were enriched in five known signal pathways, namely, glutamatergic synapse, JAK-STAT signaling pathway, cytokine-cytokine receptor interaction, neuroactive ligand-receptor interaction, and olfactory transduction. These pathways are involved in the environmental adaptability and various physiological functions of animals, especially the physiological regulation under a hypoxic environment. The results of this study advanced the understanding of CNV as an important genomic structure variant type that contributes to HA adaptation and helped further explain the molecular mechanisms underlying the altitude adaptability of yaks.
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Affiliation(s)
- E Guang-Xin
- 1College of Animal Science and Technology, Southwest University, No. 2 Tiansheng Road, Chongqing, 400715 China
| | - Bai-Gao Yang
- 1College of Animal Science and Technology, Southwest University, No. 2 Tiansheng Road, Chongqing, 400715 China
| | - Yan-Bin Zhu
- 2State Key Laboratory of Barley and Yak Germplasm Resources and Genetic Improvement (Tibet Academy of Agricultural and Animal Husbandry Sciences (TAAAS)), Lhasa, 850002 China
| | - Xing-Hai Duang
- 1College of Animal Science and Technology, Southwest University, No. 2 Tiansheng Road, Chongqing, 400715 China
| | - Wang-Dui Basang
- 1College of Animal Science and Technology, Southwest University, No. 2 Tiansheng Road, Chongqing, 400715 China
| | - Xiao-Lin Luo
- 3Sichuan Academy of Grassland Sciences, Chengdu, 611731 Sichuan China
| | - Tian-Wu An
- 3Sichuan Academy of Grassland Sciences, Chengdu, 611731 Sichuan China
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Shi L, Wang L, Liu J, Deng T, Yan H, Zhang L, Liu X, Gao H, Hou X, Wang L, Zhao F. Estimation of inbreeding and identification of regions under heavy selection based on runs of homozygosity in a Large White pig population. J Anim Sci Biotechnol 2020; 11:46. [PMID: 32355558 PMCID: PMC7187514 DOI: 10.1186/s40104-020-00447-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 03/12/2020] [Indexed: 01/24/2023] Open
Abstract
Background Runs of homozygosity (ROHs) are homozygous segments of the genome where the two haplotypes inherited from the parents are identical. The current availability of genotypes for a very large number of single nucleotide polymorphisms (SNPs) is leading to more accurate characterization of ROHs in the whole genome. Here, we investigated the occurrence and distribution of ROHs in 3,692 Large White pigs and compared estimates of inbreeding coefficients calculated based on ROHs (FROH), homozygosity (FHOM), genomic relationship matrix (FGRM) and pedigree (FPED). Furthermore, we identified genomic regions with high ROH frequencies and annotated their candidate genes. Results In total, 176,182 ROHs were identified from 3,569 animals, and all individuals displayed at least one ROH longer than 1 Mb. The ROHs identified were unevenly distributed on the autosomes. The highest and lowest coverages of Sus scrofa chromosomes (SSC) by ROH were on SSC14 and SSC13, respectively. The highest pairwise correlation among the different inbreeding coefficient estimates was 0.95 between FROH_total and FHOM, while the lowest was − 0.083 between FGRM and FPED. The correlations between FPED and FROH using four classes of ROH lengths ranged from 0.18 to 0.37 and increased with increasing ROH length, except for ROH > 10 Mb. Twelve ROH islands were located on four chromosomes (SSC1, 4, 6 and 14). These ROH islands harboured genes associated with reproduction, muscular development, fat deposition and adaptation, such as SIRT1, MYPN, SETDB1 and PSMD4. Conclusion FROH can be used to accurately assess individual inbreeding levels compared to other inbreeding coefficient estimators. In the absence of pedigree records, FROH can provide an alternative to inbreeding estimates. Our findings can be used not only to effectively increase the response to selection by appropriately managing the rate of inbreeding and minimizing the negative effects of inbreeding depression but also to help detect genomic regions with an effect on traits under selection.
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Affiliation(s)
- Liangyu Shi
- Key Laboratory of Animal Genetics, Breeding and Reproduction (poultry) of Ministry of Agricuture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Ligang Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction (poultry) of Ministry of Agricuture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Jiaxin Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction (poultry) of Ministry of Agricuture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Tianyu Deng
- Key Laboratory of Animal Genetics, Breeding and Reproduction (poultry) of Ministry of Agricuture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Hua Yan
- Key Laboratory of Animal Genetics, Breeding and Reproduction (poultry) of Ministry of Agricuture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Longchao Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction (poultry) of Ministry of Agricuture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Xin Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction (poultry) of Ministry of Agricuture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Hongmei Gao
- Key Laboratory of Animal Genetics, Breeding and Reproduction (poultry) of Ministry of Agricuture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Xinhua Hou
- Key Laboratory of Animal Genetics, Breeding and Reproduction (poultry) of Ministry of Agricuture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Lixian Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction (poultry) of Ministry of Agricuture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Fuping Zhao
- Key Laboratory of Animal Genetics, Breeding and Reproduction (poultry) of Ministry of Agricuture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
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