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Wang T, Ma X, Ma C, Wu X, ZhaXi T, Yin L, Li W, Li Y, Liang C, Yan P. Whole genome resequencing-based analysis of plateau adaptation in Meiren yak ( Bos grunniens). Anim Biotechnol 2024; 35:2298406. [PMID: 38193808 DOI: 10.1080/10495398.2023.2298406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2024]
Abstract
The Meiren yak is an important genetic resource in Gansu Province, China. In this study, we aimed to explore the evolutionary history and population structure of the genetic resource of Meiren yak and to mine the characteristic genes of Meiren yak. We analysed a total of 93 yaks of eight yak breeds based on whole genome resequencing combined with population genomics and used θπ ratio and Fst method to screen the selected sites in the genome region. The results proved that Meiren yak can be used as a potential genetic resource in Gansu Province. The genes in Meiren yak with positive selection in selection signal analysis were subjected to the Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) functional enrichment analyses, which indicated that the genes were related to the adaptability to high altitude and hypoxic environment. By analysing the genetic variation of Meiren yak at the genome-wide level, this study provided a theoretical basis for genetic improvement of Meiren yak and for the development of high-quality yak resources.
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Affiliation(s)
- Tong Wang
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou, China
- Life science and Engineering College, Northwest Minzu University, Lanzhou, China
| | - XiaoMing Ma
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou, China
| | - ChaoFan Ma
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou, China
- Life science and Engineering College, Northwest Minzu University, Lanzhou, China
| | - XiaoYun Wu
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou, China
| | - Ta ZhaXi
- Qilian County Veterinary Animal Husbandry Station, Qinghai, China
| | - LiXin Yin
- Huazhi Biotech Co. Ltd, Changsha, China
| | - WeiGuo Li
- Huazhi Biotech Co. Ltd, Changsha, China
| | - YuFei Li
- Huazhi Biotech Co. Ltd, Changsha, China
| | - ChunNian Liang
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou, China
| | - Ping Yan
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou, 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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Lan D, Fu W, Ji W, Mipam TD, Xiong X, Ying S, Xiong Y, Sheng P, Ni J, Bai L, Shan T, Kong X, Li J. Pangenome and multi-tissue gene atlas provide new insights into the domestication and highland adaptation of yaks. J Anim Sci Biotechnol 2024; 15:64. [PMID: 38706000 PMCID: PMC11071219 DOI: 10.1186/s40104-024-01027-2] [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: 12/12/2023] [Accepted: 03/18/2024] [Indexed: 05/07/2024] Open
Abstract
BACKGROUND The genetic diversity of yak, a key domestic animal on the Qinghai-Tibetan Plateau (QTP), is a vital resource for domestication and breeding efforts. This study presents the first yak pangenome obtained through the de novo assembly of 16 yak genomes. RESULTS We discovered 290 Mb of nonreference sequences and 504 new genes. Our pangenome-wide presence and absence variation (PAV) analysis revealed 5,120 PAV-related genes, highlighting a wide range of variety-specific genes and genes with varying frequencies across yak populations. Principal component analysis (PCA) based on binary gene PAV data classified yaks into three new groups: wild, domestic, and Jinchuan. Moreover, we proposed a 'two-haplotype genomic hybridization model' for understanding the hybridization patterns among breeds by integrating gene frequency, heterozygosity, and gene PAV data. A gene PAV-GWAS identified a novel gene (BosGru3G009179) that may be associated with the multirib trait in Jinchuan yaks. Furthermore, an integrated transcriptome and pangenome analysis highlighted the significant differences in the expression of core genes and the mutational burden of differentially expressed genes between yaks from high and low altitudes. Transcriptome analysis across multiple species revealed that yaks have the most unique differentially expressed mRNAs and lncRNAs (between high- and low-altitude regions), especially in the heart and lungs, when comparing high- and low-altitude adaptations. CONCLUSIONS The yak pangenome offers a comprehensive resource and new insights for functional genomic studies, supporting future biological research and breeding strategies.
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Affiliation(s)
- Daoliang Lan
- Ministry of Education of Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource and Utilization, Southwest Minzu University, Chengdu, China.
- College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu, China.
- Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu, China.
| | - Wei Fu
- College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu, China
- Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu, China
| | - Wenhui Ji
- College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu, China
| | - Tserang-Donko Mipam
- Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu, China
| | - Xianrong Xiong
- Ministry of Education of Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource and Utilization, Southwest Minzu University, Chengdu, China
- College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu, China
| | - Shi Ying
- College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu, China
| | - Yan Xiong
- Ministry of Education of Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource and Utilization, Southwest Minzu University, Chengdu, China
- College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu, China
| | - Peng Sheng
- Jiguang Gene Biotechnology Co., Ltd., Nanjing, China
| | - Jiangping Ni
- Jiguang Gene Biotechnology Co., Ltd., Nanjing, China
| | - Lijun Bai
- Chengdu Genepre Technology Co., Ltd., Chengdu, China
| | - Tongling Shan
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | | | - Jian Li
- Ministry of Education of Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource and Utilization, Southwest Minzu University, Chengdu, China
- College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu, China
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Zhou C, Zheng X, Peng K, Feng K, Yue B, Wu Y. Chromosome-level genome assembly of the kiang (Equus kiang) illuminates genomic basis for its high-altitude adaptation. Integr Zool 2023. [PMID: 38151756 DOI: 10.1111/1749-4877.12795] [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] [Indexed: 12/29/2023]
Abstract
The kiang (Equus kiang) can only be observed in the Qinghai-Tibet Plateau (QTP). The kiang displayed excellent athletic performance in the high-altitude environment, which attracted wide interest in the investigation of the potential adaptive mechanisms to the extreme environment. Here, we assembled a chromosome-level genome of the kiang based on Hi-C sequencing technology. A total of 324.14 Gb clean data were generated, and the chromosome-level genome with 26 chromosomes (25 + X) and scaffold N50 of 101.77 Mb was obtained for the kiang. The genomic synteny analysis revealed large-scale chromosomal rearrangement during the evolution process of Equus species. Phylogenetic and divergence analyses revealed that the kiang was the sister branch to the ass and diverged from a common ancestor at approximately 13.5 Mya. The expanded gene families were mainly related to the hypoxia response, metabolism, and immunity. The kiang suffered a significant loss of olfaction-related genes, which might indicate decreased olfactory sensibility. Positively selected genes (PSGs) detected in the kiang were mainly associated with hypoxia response. Especially, there were two species-specific missense amino acid mutations in the PSG STAT3 annotated in the hypoxia-inducible factor 1 signal pathway, which may play an important role in the high-altitude adaptation of the kiang. Moreover, structure variations in the kiang genome were also identified, which possibly contributed to the high-altitude adaptation of the kiang. Comparative analysis revealed a lot of species-specific insertions and deletions in the kiang genome, such as PIK3CB and AKT with 3258 and 189 bp insertions in the intron region, respectively, possibly affecting the expression and regulation of hypoxia-related downstream pathways. This study provided valuable genomic resources, and our findings help a better understanding of the underlying adaptive strategies to the high-altitude environment in the kiang.
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Affiliation(s)
- Chuang Zhou
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, China
| | - Xiaofeng Zheng
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, China
| | - Kexin Peng
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, China
| | - Kaize Feng
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, China
| | - Bisong Yue
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, China
| | - Yongjie Wu
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, China
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Liu X, Liu W, Lenstra JA, Zheng Z, Wu X, Yang J, Li B, Yang Y, Qiu Q, Liu H, Li K, Liang C, Guo X, Ma X, Abbott RJ, Kang M, Yan P, Liu J. Evolutionary origin of genomic structural variations in domestic yaks. Nat Commun 2023; 14:5617. [PMID: 37726270 PMCID: PMC10509194 DOI: 10.1038/s41467-023-41220-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 08/23/2023] [Indexed: 09/21/2023] Open
Abstract
Yak has been subject to natural selection, human domestication and interspecific introgression during its evolution. However, genetic variants favored by each of these processes have not been distinguished previously. We constructed a graph-genome for 47 genomes of 7 cross-fertile bovine species. This allowed detection of 57,432 high-resolution structural variants (SVs) within and across the species, which were genotyped in 386 individuals. We distinguished the evolutionary origins of diverse SVs in domestic yaks by phylogenetic analyses. We further identified 334 genes overlapping with SVs in domestic yaks that bore potential signals of selection from wild yaks, plus an additional 686 genes introgressed from cattle. Nearly 90% of the domestic yaks were introgressed by cattle. Introgression of an SV spanning the KIT gene triggered the breeding of white domestic yaks. We validated a significant association of the selected stratified SVs with gene expression, which contributes to phenotypic variations. Our results highlight that SVs of different origins contribute to the phenotypic diversity of domestic yaks.
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Affiliation(s)
- Xinfeng Liu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystem, College of Ecology, Lanzhou University, Lanzhou, 730000, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China
- Academy of Plateau Science and Sustainability, Qinghai Normal University, Xining, 810016, China
| | - Wenyu Liu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystem, College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Johannes A Lenstra
- Faculty of Veterinary Medicine, Utrecht University, Utrecht, 3508 TD, The Netherlands
| | - Zeyu Zheng
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystem, College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Xiaoyun Wu
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China
| | - Jiao Yang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystem, College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Bowen Li
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystem, College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Yongzhi Yang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystem, College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Qiang Qiu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystem, College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Hongyu Liu
- Anhui Provincial Laboratory of Local Livestock and Poultry Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, China
| | - Kexin Li
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystem, College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Chunnian Liang
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China
| | - Xian Guo
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China
| | - Xiaoming Ma
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China
| | - Richard J Abbott
- School of Biology, University of St Andrews, St Andrews, KY16 9AJ, UK
| | - Minghui Kang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystem, College of Ecology, Lanzhou University, Lanzhou, 730000, China.
| | - Ping Yan
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China.
| | - Jianquan Liu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystem, College of Ecology, Lanzhou University, Lanzhou, 730000, China.
- Academy of Plateau Science and Sustainability, Qinghai Normal University, Xining, 810016, China.
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Collado GA, Torres-Díaz C, Vidal MA, Valladares MA. Genetic Diversity, Morphometric Characterization, and Conservation Reassessment of the Critically Endangered Freshwater Snail, Heleobia atacamensis, in the Atacama Saltpan, Northern Chile. BIOLOGY 2023; 12:791. [PMID: 37372077 DOI: 10.3390/biology12060791] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 02/22/2023] [Accepted: 02/28/2023] [Indexed: 06/29/2023]
Abstract
Evaporitic ecosystems of the Atacama Desert contain a rich endemic fauna, including mollusk species. A recent study performed in the freshwater snail Heleobia atacamensis, endemic to the Atacama Saltpan, revealed a strong interdependence of genetic patterns with climatic fluctuations and landscape physiography. The species is currently listed as Critically Endangered at regional scale and as Data Deficient on the International Union for Conservation of Nature (IUCN) Red List. Here, we studied genetic diversity and demographic history of several populations of the species occurring on a connectivity gradient, including snails from new peripherical localities (Peine and Tilomonte), which were compared with topotype specimens. In addition, we reassessed the conservation status using the IUCN Red List categories and criteria considering species-specific idiosyncrasy. Phylogenetic and phylogeographical analyses indicated that snails from Peine and Tilomonte belong to H. atacamensis. We discovered significant differentiation in shell morphology, which was generally greater in geographically isolated populations. We also inferred six genetic clusters and a demographic expansion congruent with the wet periods that occurred at the end of the Pleistocene. Considering the highest risk category obtained, H. atacamensis was reassessed as Endangered at regional scale. Future conservation plans should consider the genetic assemblages as conservation units.
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Affiliation(s)
- Gonzalo A Collado
- Departamento de Ciencias Básicas, Facultad de Ciencias, Universidad del Bío-Bío, Avenida Andrés Bello 720, Chillán 3800708, Chile
- Grupo de Investigación en Biodiversidad y Cambio Global, Universidad del Bío-Bío, Avenida Andrés Bello 720, Chillán 3800708, Chile
| | - Cristian Torres-Díaz
- Departamento de Ciencias Básicas, Facultad de Ciencias, Universidad del Bío-Bío, Avenida Andrés Bello 720, Chillán 3800708, Chile
- Grupo de Investigación en Biodiversidad y Cambio Global, Universidad del Bío-Bío, Avenida Andrés Bello 720, Chillán 3800708, Chile
| | - Marcela A Vidal
- Departamento de Ciencias Básicas, Facultad de Ciencias, Universidad del Bío-Bío, Avenida Andrés Bello 720, Chillán 3800708, Chile
- Grupo de Investigación en Biodiversidad y Cambio Global, Universidad del Bío-Bío, Avenida Andrés Bello 720, Chillán 3800708, Chile
| | - Moisés A Valladares
- Departamento de Ciencias Básicas, Facultad de Ciencias, Universidad del Bío-Bío, Avenida Andrés Bello 720, Chillán 3800708, Chile
- Grupo de Investigación en Biodiversidad y Cambio Global, Universidad del Bío-Bío, Avenida Andrés Bello 720, Chillán 3800708, Chile
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7
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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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8
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Li X, Yuan L, Wang W, Zhang D, Zhao Y, Chen J, Xu D, Zhao L, Li F, Zhang X. Whole genome re-sequencing reveals artificial and natural selection for milk traits in East Friesian sheep. Front Vet Sci 2022; 9:1034211. [PMID: 36330154 PMCID: PMC9623881 DOI: 10.3389/fvets.2022.1034211] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 09/30/2022] [Indexed: 08/23/2023] Open
Abstract
The East Friesian sheep is one of the important high-yielding dairy sheep breeds, but still little is known about their genetic and genomic variation during domestication. Therefore, we analyzed the genomic data of 46 sheep with the aim of identifying candidate genes that are closely related to milk production traits. Our genomic data consisted of 20 East Friesian sheep and 26 Asian Mouflon wild sheep. Finally, a total of 32590241 SNPs were identified, of which 0.61% (198277) SNPs were located in exonic regions. After further screening, 122 shared genomic regions in the top 1% of F ST and top 1% of Nucleotide diversity ratio were obtained. After genome annotation, these 122 candidate genomic regions were found to contain a total of 184 candidate genes. Finally, the results of KEGG enrichment analysis showed four significantly enriched pathways (P < 0.05): beta-Alanine metabolism (SMOX, HIBCH), Pathways in cancer (GLI2, AR, TXNRD3, TRAF3, FGF16), Non-homologous end-joining (MRE11), Epstein-Barr virus infection (TRAF3, PSMD13, SIN3A). Finally, we identified four important KEGG enrichment pathways and 10 candidate genes that are closely related to milk production in East Friesian sheep. These results provide valuable candidate genes for the study of milk production traits in East Friesian sheep and lay an important foundation for the study of milk production traits.
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Affiliation(s)
- Xiaolong Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Lvfeng Yuan
- Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Weimin Wang
- The State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Deyin Zhang
- The State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Yuan Zhao
- The State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Jiangbo Chen
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Dan Xu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Liming Zhao
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Fadi Li
- The State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Xiaoxue Zhang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
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9
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Kang Y, Guo S, Wang X, Cao M, Pei J, Li R, Bao P, Wang J, Lamao J, Gongbao D, Lamao J, Liang C, Yan P, Guo X. Whole-Genome Resequencing Highlights the Unique Characteristics of Kecai Yaks. Animals (Basel) 2022; 12:ani12192682. [PMID: 36230423 PMCID: PMC9559661 DOI: 10.3390/ani12192682] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Revised: 09/29/2022] [Accepted: 10/03/2022] [Indexed: 12/01/2022] Open
Abstract
Kecai yaks are regarded as an important genetic resource in China owing to their high fecundity and flavorful meat. However, the genetic characteristics of Kecai yaks have not been effectively characterized to date, and the relationship between Kecai yaks and other yak breeds remains to be fully characterized. In this paper, the resequencing of the Kecai yak genome is performed leading to the identification of 11,491,383 high-quality single nucleotide polymorphisms (SNPs). Through principal component, phylogenetic, and population genetic structure analyses based on these SNPs, Kecai yaks were confirmed to represent an independent population of yaks within China. In this study, marker and functional enrichment analysis of genes related to positive selection in Kecai yak was carried out, and the results show that such selection in Kecai yaks is associated with the adaptation to alpine environments and the deposition of muscle fat. Overall, these results offer a theoretical foundation for the future utilization of Kecai yak genetic resources.
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Affiliation(s)
- Yandong Kang
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Shaoke Guo
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Xingdong Wang
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Mengli Cao
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Jie Pei
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Ruiwu Li
- Station of Animal Husbandry in Xiahe County, Xiahe 747199, China
| | - Pengjia Bao
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Jiefeng Wang
- Station of Animal Husbandry in Xiahe County, Xiahe 747199, China
| | - Jiebu Lamao
- Station of Animal Husbandry in Xiahe County, Xiahe 747199, China
| | - Dangzhi Gongbao
- Station of Animal Husbandry in Xiahe County, Xiahe 747199, China
| | - Ji Lamao
- Station of Animal Husbandry in Xiahe County, Xiahe 747199, China
| | - Chunnian Liang
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Ping Yan
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Xian Guo
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
- Correspondence: ; Tel.: +86-1899-3037-854
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10
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Lyu T, Yang X, Zhao C, Wang L, Zhou S, Shi L, Dong Y, Dou H, Zhang H. Comparative transcriptomics of high-altitude Vulpes and their low-altitude relatives. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.999411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The harsh environment of Qinghai-Tibet Plateau (QTP) imposes strong selective stresses (e.g., hypoxia, high UV-radiation, and extreme temperature) to the native species, which have driven striking phenotypic and genetic adaptations. Although the mechanisms of high-altitude adaptation have been explored for many plateau species, how the phylogenetic background contributes to genetic adaption to high-altitude of Vulpes is largely unknown. In this study, we sequenced transcriptomic data across multiple tissues of two high-altitude Vulpes (Vulpes vulpes montana and Vulpes ferrilata) and their low-altitude relatives (Vulpes corsac and Vulpes lagopus) to search the genetic and gene expression changes caused by high-altitude environment. The results indicated that the positive selection genes (PSGs) identified by both high-altitude Vulpes are related to angiogenesis, suggesting that angiogenesis may be the result of convergent evolution of Vulpes in the face of hypoxic selection pressure. In addition, more PSGs were detected in V. ferrilata than in V. v. montana, which may be related to the longer adaptation time of V. ferrilata to plateau environment and thus more genetic changes. Besides, more PSGs associated with high-altitude adaptation were identified in V. ferrilata compared with V. v. montana, indicating that the longer the adaptation time to the high-altitude environment, the more genetic alterations of the species. Furthermore, the result of expression profiles revealed a tissue-specific pattern between Vulpes. We also observed that differential expressed genes in the high-altitude group exhibited species-specific expression patterns, revealed a convergent expression pattern of Vulpes in high-altitude environment. In general, our research provides a valuable transcriptomic resource for further studies, and expands our understanding of high-altitude adaptation within a phylogenetic context.
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11
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Long read genome assemblies complemented by single cell RNA-sequencing reveal genetic and cellular mechanisms underlying the adaptive evolution of yak. Nat Commun 2022; 13:4887. [PMID: 36068211 PMCID: PMC9448747 DOI: 10.1038/s41467-022-32164-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 07/20/2022] [Indexed: 12/04/2022] Open
Abstract
Wild yak (Bos mutus) and domestic yak (Bos grunniens) are adapted to high altitude environment and have ecological, economic, and cultural significances on the Qinghai-Tibetan Plateau (QTP). Currently, the genetic and cellular bases underlying adaptations of yak to extreme conditions remains elusive. In the present study, we assembled two chromosome-level genomes, one each for wild yak and domestic yak, and screened structural variants (SVs) through the long-read data of yak and taurine cattle. The results revealed that 6733 genes contained high-FST SVs. 127 genes carrying special type of SVs were differentially expressed in lungs of the taurine cattle and yak. We then constructed the first single-cell gene expression atlas of yak and taurine cattle lung tissues and identified a yak-specific endothelial cell subtype. By integrating SVs and single-cell transcriptome data, we revealed that the endothelial cells expressed the highest proportion of marker genes carrying high-FST SVs in taurine cattle lungs. Furthermore, we identified pathways which were related to the medial thickness and formation of elastic fibers in yak lungs. These findings provide new insights into the high-altitude adaptation of yak and have important implications for understanding the physiological and pathological responses of large mammals and humans to hypoxia. The genetic bases of yak adaptations to extreme conditions remains elusive. This study compares yak and cattle at a genomic and transcriptomic level, revealing a new type of endothelial cell and candidate genes related with elastic fiber formation in yak lungs that might contribute to high altitude adaptation.
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12
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Chen S, Holyoak M, Liu H, Bao H, Ma Y, Dou H, Li G, Roberts NJ, Jiang G. Global warming responses of gut microbiota in moose (
Alces alces
) populations with different dispersal patterns. J Zool (1987) 2022. [DOI: 10.1111/jzo.12998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- S. Chen
- Feline Research Center of National Forestry and Grassland Administration, College of Wildlife and Protected Area Northeast Forestry University Harbin China
- Northeast Asia Biodiversity Research Center Northeast Forestry University Harbin China
| | - M. Holyoak
- Department of Environmental Science and Policy University of California Davis California USA
| | - H. Liu
- Feline Research Center of National Forestry and Grassland Administration, College of Wildlife and Protected Area Northeast Forestry University Harbin China
- Northeast Asia Biodiversity Research Center Northeast Forestry University Harbin China
- College of Forestry Hainan University Haikou China
| | - H. Bao
- Feline Research Center of National Forestry and Grassland Administration, College of Wildlife and Protected Area Northeast Forestry University Harbin China
- Northeast Asia Biodiversity Research Center Northeast Forestry University Harbin China
| | - Y. Ma
- Feline Research Center of National Forestry and Grassland Administration, College of Wildlife and Protected Area Northeast Forestry University Harbin China
- Northeast Asia Biodiversity Research Center Northeast Forestry University Harbin China
- Key Lab of Animal Ecology and Conservation Biology, Institute of Zoology Chinese Academy of Sciences Beijing China
| | - H. Dou
- Feline Research Center of National Forestry and Grassland Administration, College of Wildlife and Protected Area Northeast Forestry University Harbin China
- Northeast Asia Biodiversity Research Center Northeast Forestry University Harbin China
- Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization Guangdong Academy of Forestry Guangzhou China
| | - G. Li
- State Key Laboratory of Integrated Pest Management, Institute of Zoology Chinese Academy of Sciences Beijing China
| | - N. J. Roberts
- Feline Research Center of National Forestry and Grassland Administration, College of Wildlife and Protected Area Northeast Forestry University Harbin China
- Northeast Asia Biodiversity Research Center Northeast Forestry University Harbin China
| | - G. Jiang
- Feline Research Center of National Forestry and Grassland Administration, College of Wildlife and Protected Area Northeast Forestry University Harbin China
- Northeast Asia Biodiversity Research Center Northeast Forestry University Harbin China
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13
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Yang X, Sun G, Xia T, Cha M, Zhang L, Pang B, Tang Q, Dou H, Zhang H. Transcriptome analysis provides new insights into cold adaptation of corsac fox (
Vulpes Corsac
). Ecol Evol 2022; 12:e8866. [PMID: 35462974 PMCID: PMC9019142 DOI: 10.1002/ece3.8866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 12/10/2021] [Accepted: 04/06/2022] [Indexed: 11/11/2022] Open
Abstract
Vulpesare widely distributed throughout the world and have undergone drastic physiological and phenotypic changes in response to their environment. However, little is known about the underlying genetic causes of these traits, especially Vulpes corsac. In this study, RNA‐Seq was used to obtain a comprehensive dataset for multiple pooled tissues of corsac fox, and selection analysis of orthologous genes was performed to identify the genes that may be influenced by the low‐temperature environment. More than 6.32 Gb clean reads were obtained and assembled into a total of 173,353 unigenes with an average length of 557 bp for corsac fox. Selective pressure analysis showed that 16 positively selected genes (PSGs) were identified in corsac fox, red fox, and arctic fox. Enrichment analysis of PSGs showed that the LRP11 gene was enriched in several pathways related to the low‐temperature response and might play a key role in response to environmental stimuli of foxes. In addition, several positively selected genes were related to DNA damage repair (ELP2 and CHAF1A), innate immunity (ARRDC4 and S100A12), and the respiratory chain (NDUFA5), and these positively selected genes might play a role in adaptation to harsh wild fox environments. The results of common orthologous gene analysis showed that gene flow or convergent evolution might be an important factor in promoting regional differentiation of foxes. Our study provides a valuable transcriptomic resource for the evolutionary history of the corsac fox and the adaptations to the extreme environments.
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Affiliation(s)
- Xiufeng Yang
- College of Life Science Qufu Normal University Qufu China
| | - Guolei Sun
- College of Life Science Qufu Normal University Qufu China
| | - Tian Xia
- College of Life Science Qufu Normal University Qufu China
| | - Muha Cha
- Hulunbuir Academy of Inland Lakes in Northern Cold & Arid Areas Hulunbuir China
| | - Lei Zhang
- College of Life Science Qufu Normal University Qufu China
| | - Bo Pang
- Hulunbuir Academy of Inland Lakes in Northern Cold & Arid Areas Hulunbuir China
| | - Qingming Tang
- Hulun Buir Forestry and Grassland Business Development Center Hulunbuir China
| | - Huashan Dou
- Hulunbuir Academy of Inland Lakes in Northern Cold & Arid Areas Hulunbuir China
| | - Honghai Zhang
- College of Life Science Qufu Normal University Qufu China
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14
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Yue Y, Hua Y, Zhang J, Guo Y, Zhao D, Huo W, Xiong Y, Chen F, Lin Y, Xiong X, Li J. Establishment of a subcutaneous adipogenesis model and distinct roles of LKB1 regulation on adipocyte lipid accumulation in high-altitude Bos grunniens. JOURNAL OF APPLIED ANIMAL RESEARCH 2022. [DOI: 10.1080/09712119.2022.2042001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Yongqi Yue
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Ministry of Education, Chengdu, People’s Republic of China
- College of Animal &Veterinary Sciences, Southwest Minzu University, Chengdu, People’s Republic of China
| | - Yonglin Hua
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Ministry of Education, Chengdu, People’s Republic of China
- College of Animal &Veterinary Sciences, Southwest Minzu University, Chengdu, People’s Republic of China
| | - Jing Zhang
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Ministry of Education, Chengdu, People’s Republic of China
- College of Animal &Veterinary Sciences, Southwest Minzu University, Chengdu, People’s Republic of China
| | - Yu Guo
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Ministry of Education, Chengdu, People’s Republic of China
- College of Animal &Veterinary Sciences, Southwest Minzu University, Chengdu, People’s Republic of China
| | - Dan Zhao
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Ministry of Education, Chengdu, People’s Republic of China
- College of Animal &Veterinary Sciences, Southwest Minzu University, Chengdu, People’s Republic of China
| | - Wentao Huo
- College of Animal &Veterinary Sciences, Southwest Minzu University, Chengdu, People’s Republic of China
| | - Yan Xiong
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Ministry of Education, Chengdu, People’s Republic of China
- Key Laboratory of Animal Science of National Ethnic Affairs Commission of China, Southwest Minzu University, Chengdu, People’s Republic of China
- College of Animal &Veterinary Sciences, Southwest Minzu University, Chengdu, People’s Republic of China
| | - Fenfen Chen
- School of Life Sciences, Southwest Forestry University, Kunming, People’s Republic of China
| | - Yaqiu Lin
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Ministry of Education, Chengdu, People’s Republic of China
- Key Laboratory of Animal Science of National Ethnic Affairs Commission of China, Southwest Minzu University, Chengdu, People’s Republic of China
- College of Animal &Veterinary Sciences, Southwest Minzu University, Chengdu, People’s Republic of China
| | - Xianrong Xiong
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Ministry of Education, Chengdu, People’s Republic of China
- Key Laboratory of Animal Science of National Ethnic Affairs Commission of China, Southwest Minzu University, Chengdu, People’s Republic of China
- College of Animal &Veterinary Sciences, Southwest Minzu University, Chengdu, People’s Republic of China
| | - Jian Li
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Ministry of Education, Chengdu, People’s Republic of China
- Key Laboratory of Animal Science of National Ethnic Affairs Commission of China, Southwest Minzu University, Chengdu, People’s Republic of China
- College of Animal &Veterinary Sciences, Southwest Minzu University, Chengdu, People’s Republic of China
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15
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Geng HL, Ni HB, Li JH, Jiang J, Wang W, Wei XY, Zhang Y, Sun HT. Prevalence of Cryptosporidium spp. in Yaks ( Bos grunniens) in China: A Systematic Review and Meta-Analysis. Front Cell Infect Microbiol 2021; 11:770612. [PMID: 34733797 PMCID: PMC8558464 DOI: 10.3389/fcimb.2021.770612] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Accepted: 09/27/2021] [Indexed: 12/24/2022] Open
Abstract
Cryptosporidium spp., the causative agent of cryptosporidiosis, can infect a variety of hosts. So far, there has been limited information regarding Cryptosporidium spp. infection in yaks (Bos grunniens). Here, we performed the first systematic review and meta-analysis for Cryptosporidium spp. infection in yaks in China. To perform the meta-analysis, five databases (Chinese National Knowledge Infrastructure (CNKI), VIP Chinese journal database, WanFang Data, PubMed, and ScienceDirect) were employed to search for studies related to the prevalence of Cryptosporidium spp. in yaks in China. The total number of samples was 8,212, and the pooled Cryptosporidium spp. prevalence in yaks was estimated to be 10.52% (1192/8012). The prevalence of Cryptosporidium spp. in yaks was 13.54% (1029/5277) and 4.49% (148/2132) in northwestern and southwestern China, respectively. In the sampling year subgroups, the prevalence before 2012 (19.79%; 650/2662) was significantly higher than that after 2012 (6.07%; 437/4476). The prevalence of Cryptosporidium spp. in cold seasons (20.55%; 188/794) was higher than that in warm seasons (4.83%; 41/1228). In the age subgroup, the yaks with age < 12 months had a higher prevalence (19.47%; 231/1761) than that in yaks with age ≥12 months (16.63%; 365/2268). Among 12 Cryptosporidium spp. species/genotypes, the C. bovis had the highest prevalence. Moreover, the effects of geography (latitude, longitude, precipitation, temperature, and altitude) and climate on Cryptosporidium spp. infection in yaks were evaluated. Through analyzing the risk factors correlated with the prevalence of Cryptosporidium spp., we recommend that effective management measures should be formulated according to the differences of different geographical factors, in order to prevent cryptosporidiosis and reduce economic losses in yaks in China.
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Affiliation(s)
- Hong-Li Geng
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Hong-Bo Ni
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Jing-Hao Li
- General Monitoring Station for Wildlife-Borne Infectious Diseases, State forestry and Grass Administration, Shenyang, China
| | - Jing Jiang
- College of Life Sciences, Changchun Sci-Tech University, Shuangyang, China
| | - Wei Wang
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Xin-Yu Wei
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Yuan Zhang
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - He-Ting Sun
- General Monitoring Station for Wildlife-Borne Infectious Diseases, State forestry and Grass Administration, Shenyang, China
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