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Mahar K, Gurao A, Kumar A, Pratap Singh L, Chitkara M, Gowane GR, Ahlawat S, Niranjan SK, Pundir RK, Kataria RS, Dige MS. Genomic inbreeding analysis reveals resilience and genetic diversity in Indian yak populations. Gene 2024; 928:148787. [PMID: 39053660 DOI: 10.1016/j.gene.2024.148787] [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] [Received: 01/15/2024] [Revised: 07/02/2024] [Accepted: 07/19/2024] [Indexed: 07/27/2024]
Abstract
The yak (Bos grunniens), renowned for its adaptability to extreme cold and hypoxic conditions, stands as a remarkable domestic animal crucial for sustaining livelihoods in harsh climates. We conducted a comprehensive analysis of the whole genome sequence data from three distinct Indian yak populations: Arunachali yak (n = 10), Himachali yak (n = 10), and Ladakhi yak (n = 10). The genomic data for Indian yaks were meticulously generated by our laboratory and compared with their Chinese counterpart, the Jinchuan yak (n = 8), for a more nuanced understanding. Our investigation revealed a total of 37,437 runs of homozygosity (ROH) segments in 34 animals representing four distinct yak populations. The Jinchuan yak population exhibited the highest proportion, constituting 80.8 % of total ROHs, predominantly as small segments (<0.1 Mb), accounting for 63 % of the overall ROHs. Further analysis uncovered a significantly higher degree of inbreeding in Chinese yaks compared to their Indian counterparts. The Indian yak populations, in contrast, demonstrated relatively lower and consistent levels of inbreeding. Moreover, we identified ROH hotspots that covered at least 60 % of individuals in our study, indicating their pivotal role in environmental adaptation. A total of five hotspot regions were detected, housing genes such as ENSBGRG00000015023 (WNT2), YIPF4, SPAST, TLN2, and DSG4. These genes are associated with traits including hair follicle initiation, nutrient stress response, microtubule assembly, development of cardiac muscle, hair follicle, and coat color. This observation strongly suggests that there is substantial selection acting on these genes, emphasizing their important role in environmental adaptation among yak populations.
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Affiliation(s)
- Karan Mahar
- Division of Animal Genetics and Breeding, ICAR-National Dairy Research Institute, Karnal 132001, Haryana, India
| | - Ankita Gurao
- Division of Animal Genetic Resources, ICAR-National Bureau of Animal Genetic Resources, Karnal 132001, Haryana, India
| | - Amod Kumar
- Division of Animal Genetics, ICAR-National Bureau of Animal Genetic Resources, Karnal 132001, Haryana, India
| | - Lalit Pratap Singh
- Division of Animal Biotechnology, ICAR-National Dairy Research Institute, Karnal 132001, Haryana, India
| | - Meenakshi Chitkara
- Division of Animal Biotechnology, ICAR-National Dairy Research Institute, Karnal 132001, Haryana, India
| | - Gopal R Gowane
- Division of Animal Genetics and Breeding, ICAR-National Dairy Research Institute, Karnal 132001, Haryana, India
| | - Sonika Ahlawat
- Division of Animal Biotechnology, ICAR-National Bureau of Animal Genetic Resources, Karnal 132001, Haryana, India
| | - S K Niranjan
- Division of Animal Genetics, ICAR-National Bureau of Animal Genetic Resources, Karnal 132001, Haryana, India
| | - R K Pundir
- Division of Animal Genetic Resources, ICAR-National Bureau of Animal Genetic Resources, Karnal 132001, Haryana, India
| | - R S Kataria
- Division of Animal Biotechnology, ICAR-National Bureau of Animal Genetic Resources, Karnal 132001, Haryana, India
| | - M S Dige
- Division of Animal Genetic Resources, ICAR-National Bureau of Animal Genetic Resources, Karnal 132001, Haryana, India.
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Tiwari M, Gujar G, Shashank CG, Ponsuksili S. Selection signatures for high altitude adaptation in livestock: A review. Gene 2024; 927:148757. [PMID: 38986751 DOI: 10.1016/j.gene.2024.148757] [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] [Received: 03/24/2024] [Revised: 07/01/2024] [Accepted: 07/05/2024] [Indexed: 07/12/2024]
Abstract
High altitude adapted livestock species (cattle, yak, goat, sheep, and horse) has critical role in the human socioeconomic sphere and acts as good source of animal source products including milk, meat, and leather, among other things. These species sustain production and reproduction even in harsh environments on account of adaptation resulting from continued evolution of beneficial traits. Selection pressure leads to various adaptive strategies in livestock whose footprints are evident at the different genomic sites as the "Selection Signature". Scrutiny of these signatures provides us crucial insight into the evolutionary process and domestication of livestock adapted to diverse climatic conditions. These signatures have the potential to change the sphere of animal breeding and further usher the selection programmes in right direction. Technological revolution and recent strides made in genomic studies has opened the routes for the identification of selection signatures. Numerous statistical approaches and bioinformatics tools have been developed to detect the selection signature. Consequently, studies across years have identified candidate genes under selection region found associated with numerous traits which have a say in adaptation to high-altitude environment. This makes it pertinent to have a better understanding about the selection signature, the ways to identify and how to utilize them for betterment of livestock populations as well as farmers. This review takes a closer look into the general concept, various methodologies, and bioinformatics tools commonly employed in selection signature studies and summarize the results of recent selection signature studies related to high-altitude adaptation in various livestock species. This review will serve as an informative and useful insight for researchers and students in the field of animal breeding and evolutionary biology.
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Affiliation(s)
- Manish Tiwari
- ICAR-National Dairy Research Institute, Karnal, India; U.P. Pt. Deen Dayal Upadhyaya Veterinary Science University and Cattle Research Institute, Mathura, India.
| | | | - C G Shashank
- ICAR-National Dairy Research Institute, Karnal, India
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Chen SY, Luo Z, Jia X, Zhou J, Lai SJ. Evaluating genomic inbreeding of two Chinese yak (Bos grunniens) populations. BMC Genomics 2024; 25:712. [PMID: 39044139 PMCID: PMC11267844 DOI: 10.1186/s12864-024-10640-4] [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: 02/28/2024] [Accepted: 07/19/2024] [Indexed: 07/25/2024] Open
Abstract
BACKGROUND Yaks are a vital livestock in the Qinghai-Tibetan Plateau area for providing food products, maintaining sustainable ecosystems, and promoting cultural heritage. Because of uncontrolled mating, it is impossible to estimate inbreeding level of yak populations using the pedigree-based approaches. With the aims to accurately evaluate inbreeding level of two Chinese yak populations (Maiwa and Jiulong), we obtained genome-wide single nucleotide polymorphisms (SNPs) by DNA sequencing and calculated five SNP-by-SNP estimators ([Formula: see text], [Formula: see text], [Formula: see text], [Formula: see text], and [Formula: see text]), as well as two segment-based estimators of runs of homozygosity (ROH, [Formula: see text]) and homozygous-by-descent (HBD, [Formula: see text]). Functional implications were analyzed for the positional candidate genes located within the related genomic regions. RESULTS A total of 151,675 and 190,955 high-quality SNPs were obtained from 71 Maiwa and 30 Jiulong yaks, respectively. Jiulong had greater genetic diversity than Maiwa in terms of allele frequency and nucleotide diversity. The two populations could be genetically distinguished by principal component analysis, with the mean differentiation index (Fst) of 0.0054. The greater genomic inbreeding levels of Maiwa yaks were consistently supported by all five SNP-by-SNP estimators. Based on simple proportion of homozygous SNPs ([Formula: see text]), a lower inbreeding level was indicated by three successfully sequenced old leather samples that may represent historical Maiwa yaks about five generations ago. There were 3304 ROH detected among all samples, with mean and median length of 1.97 Mb and 1.0 Mb, respectively. A total of 94 HBD segments were found among all samples, whereas 92 of them belonged to the shortest class with the mean length of 10.9 Kb. Based on the estimates of [Formula: see text] and [Formula: see text], however, there was no difference in inbreeding level between Maiwa and Jiulong yaks. Within the genomic regions with the significant Fst or enriched by ROH, we found several candidate genes and pathways that have been reported to be related to diverse production traits in farm animals. CONCLUSIONS We successfully evaluated the genomic inbreeding level of two Chinese yak populations. Although different estimators resulted in inconsistent conclusions on their genomic inbreeding levels, our results may be helpful to implement the genetic conservation and utilization programs for the two yak populations.
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Affiliation(s)
- Shi-Yi Chen
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 211# Huimin Road, Wenjiang, Sichuan, 611130, China.
| | - Zhihao Luo
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 211# Huimin Road, Wenjiang, Sichuan, 611130, China
| | - Xianbo Jia
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 211# Huimin Road, Wenjiang, Sichuan, 611130, China
| | - Junkun Zhou
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 211# Huimin Road, Wenjiang, Sichuan, 611130, China
| | - Song-Jia Lai
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 211# Huimin Road, Wenjiang, Sichuan, 611130, China.
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Deng C, Li M, Wang T, Duan W, Guo A, Ma G, Yang F, Dai F, Li Q. Integrating genomics and transcriptomics to identify candidate genes for high-altitude adaptation and egg production in Nixi chicken. Br Poult Sci 2024:1-13. [PMID: 38922310 DOI: 10.1080/00071668.2024.2367228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 05/17/2024] [Indexed: 06/27/2024]
Abstract
1. This study combined genome-wide selection signal analysis with RNA-sequencing to identify candidate genes associated with high altitude adaptation and egg production performance in Nixi chickens (NXC).2. Based on the whole-genome data from 20 NXC (♂:10; ♀:10), the population selection signal was analysed by sliding window analysis. The selected genes were screened by combination with the population differentiation statistic (FST). The sequence diversity statistic (θπ). RNA-seq was performed on the ovarian tissues of NXC (n = 6) and Lohmann laying hens (n = 6) to analyse the differentially expressed genes (DEGs) between the two groups. The functional enrichment analysis of the selected genes and differentially expressed genes was performed.3. There were 742 genes under strong positive selection and 509 differentially expressed genes screened in NXC. Integrated analysis of the genome and transcriptome revealing 26 overlapping genes. The candidate genes for adaptation to a high-altitude environment, as well as for egg production, disease resistance, vision and pigmentation in NXC were preliminarily screened.4. The results provided theoretical guidance for further research on the genetic resource protection and utilisation of NXC.
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Affiliation(s)
- C Deng
- College of Biology and Food Engineering, Southwest Forestry University, Kunming, China
| | - M Li
- School of Mathematics and Computer Science, Yunnan Nationalities University, Kunming, China
| | - T Wang
- School of Pharmacy, Chengdu University, Chengdu, China
| | - W Duan
- College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - A Guo
- College of Biology and Food Engineering, Southwest Forestry University, Kunming, China
| | - G Ma
- Agricultural and Rural Bureau of Gejiu County, Honghe, China
| | - F Yang
- Agricultural and Rural Bureau of Gejiu County, Honghe, China
| | - F Dai
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming, China
| | - Q Li
- College of Biology and Food Engineering, Southwest Forestry University, Kunming, China
- Kunming Xianghao Technology Co. Ltd., Kunming, 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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Du X, Sun Y, Fu T, Gao T, Zhang T. Research Progress and Applications of Bovine Genome in the Tribe Bovini. Genes (Basel) 2024; 15:509. [PMID: 38674443 PMCID: PMC11050176 DOI: 10.3390/genes15040509] [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: 03/22/2024] [Revised: 04/16/2024] [Accepted: 04/17/2024] [Indexed: 04/28/2024] Open
Abstract
Various bovine species have been domesticated and bred for thousands of years, and they provide adequate animal-derived products, including meat, milk, and leather, to meet human requirements. Despite the review studies on economic traits in cattle, the genetic basis of traits has only been partially explained by phenotype and pedigree breeding methods, due to the complexity of genomic regulation during animal development and growth. With the advent of next-generation sequencing technology, genomics projects, such as the 1000 Bull Genomes Project, Functional Annotation of Animal Genomes project, and Bovine Pangenome Consortium, have advanced bovine genomic research. These large-scale genomics projects gave us a comprehensive concept, technology, and public resources. In this review, we summarize the genomics research progress of the main bovine species during the past decade, including cattle (Bos taurus), yak (Bos grunniens), water buffalo (Bubalus bubalis), zebu (Bos indicus), and gayal (Bos frontalis). We mainly discuss the development of genome sequencing and functional annotation, focusing on how genomic analysis reveals genetic variation and its impact on phenotypes in several bovine species.
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Affiliation(s)
- Xingjie Du
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China; (X.D.); (Y.S.); (T.F.); (T.G.)
- Henan International Joint Laboratory of Nutrition Regulation and Ecological Raising of Domestic Animal, College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Yu Sun
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China; (X.D.); (Y.S.); (T.F.); (T.G.)
- Henan International Joint Laboratory of Nutrition Regulation and Ecological Raising of Domestic Animal, College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Tong Fu
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China; (X.D.); (Y.S.); (T.F.); (T.G.)
- Henan International Joint Laboratory of Nutrition Regulation and Ecological Raising of Domestic Animal, College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Tengyun Gao
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China; (X.D.); (Y.S.); (T.F.); (T.G.)
- Henan International Joint Laboratory of Nutrition Regulation and Ecological Raising of Domestic Animal, College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Tianliu Zhang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China; (X.D.); (Y.S.); (T.F.); (T.G.)
- Henan International Joint Laboratory of Nutrition Regulation and Ecological Raising of Domestic Animal, College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
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Guo S, Yu T, Wang X, Zhao S, Zhao E, Ainierlitu, Ba T, Gan M, Dong C, Naerlima, Yin L, Ke X, Dana D, Guo X. Whole-genome resequencing reveals the uniqueness of Subei yak. J Anim Sci 2024; 102:skae152. [PMID: 38832496 PMCID: PMC11217902 DOI: 10.1093/jas/skae152] [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] [Received: 12/18/2023] [Accepted: 06/03/2024] [Indexed: 06/05/2024] Open
Abstract
Subei yak is an essential local yak in the Gansu Province, which genetic resource has recently been discovered. It is a meat-milk dual-purpose variety with high fecundity and relatively stable population genetic structure. However, its population genetic structure and genetic diversity are yet to be reported. Therefore, this study aimed to identify molecular markers of Subei yak genome by whole-genome resequencing, and to analyze the population structure and genetic diversity of Subei yak. This study screened 12,079,496 single nucleotide polymorphism (SNP) molecular markers in the 20 Subei yaks genome using whole-genome resequencing technology. Of these SNPs, 32.09% were located in the intronic region of the genome. Principal component analysis, phylogenetic analysis, and population structure analysis revealed that the Subei yak belonged to an independent group in the domestic yak population. A selective clearance analysis was carried out on Subei yak and other domestic yaks, and the genes under positive selection were annotated. The functional enrichment analysis showed that Subei yak possessed prominent selection characteristics in terms of external environment perception, hypoxia adaptation, and muscle development. Furthermore, Subei yak showed excellent muscle fat deposition and meat quality traits. Thus, this study will serve as a reference for discovering population structure, genetic evolution, and other unique traits of Subei yak and for expanding the genetic variation catalog of yaks.
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Affiliation(s)
- Shaoke Guo
- Key Laboratory of Yak Breeding Engineering in 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
| | - Tianjun Yu
- Center of Animal Husbandry and Veterinary Technology Services in Subei Mongolian Autonomous County of Gansu Province, Subei, 736300, China
| | - Xingdong Wang
- Key Laboratory of Yak Breeding Engineering in 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
| | - Shuangquan Zhao
- Center of Animal Husbandry and Veterinary Technology Services in Subei Mongolian Autonomous County of Gansu Province, Subei, 736300, China
| | - Erjun Zhao
- Center of Animal Husbandry and Veterinary Technology Services in Subei Mongolian Autonomous County of Gansu Province, Subei, 736300, China
| | - Ainierlitu
- Center of Animal Husbandry and Veterinary Technology Services in Subei Mongolian Autonomous County of Gansu Province, Subei, 736300, China
| | - Teer Ba
- Center of Animal Husbandry and Veterinary Technology Services in Subei Mongolian Autonomous County of Gansu Province, Subei, 736300, China
| | - Manyu Gan
- Center of Animal Husbandry and Veterinary Technology Services in Subei Mongolian Autonomous County of Gansu Province, Subei, 736300, China
| | - Cunmei Dong
- Center of Animal Husbandry and Veterinary Technology Services in Subei Mongolian Autonomous County of Gansu Province, Subei, 736300, China
| | - Naerlima
- Center of Animal Husbandry and Veterinary Technology Services in Subei Mongolian Autonomous County of Gansu Province, Subei, 736300, China
| | - Lian Yin
- Center of Animal Husbandry and Veterinary Technology Services in Subei Mongolian Autonomous County of Gansu Province, Subei, 736300, China
| | - Xikou Ke
- Center of Animal Husbandry and Veterinary Technology Services in Subei Mongolian Autonomous County of Gansu Province, Subei, 736300, China
| | - Dawuti Dana
- Center of Animal Husbandry and Veterinary Technology Services in Subei Mongolian Autonomous County of Gansu Province, Subei, 736300, China
| | - Xian Guo
- Key Laboratory of Yak Breeding Engineering in 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
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Chen N, Zhang Z, Hou J, Chen J, Gao X, Tang L, Wangdue S, Zhang X, Sinding MHS, Liu X, Han J, Lü H, Lei C, Marshall F, Liu X. Evidence for early domestic yak, taurine cattle, and their hybrids on the Tibetan Plateau. SCIENCE ADVANCES 2023; 9:eadi6857. [PMID: 38091398 PMCID: PMC10848728 DOI: 10.1126/sciadv.adi6857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 11/07/2023] [Indexed: 12/18/2023]
Abstract
Domestic yak, cattle, and their hybrids are fundamental to herder survival at high altitudes on the Tibetan Plateau. However, little is known about their history. Bos remains are uncommon in this region, and ancient domestic yak have not been securely identified. To identify Bos taxa and investigate their initial management, we conducted zooarchaeological analyses of 193 Bos specimens and sequenced five nuclear genomes from recently excavated assemblages at Bangga. Morphological data indicated that more cattle than yak were present. Ancient mitochondrial DNA and nuclear genome sequences identified taurine cattle and provided evidence for domestic yak and yak-cattle hybridization ~2500 years ago. Reliance on diverse Bos species and their hybrid has increased cattle adaptation and herder resilience to plateau conditions. Ancient cattle and yak at Bangga were closely related to contemporary livestock, indicating early herder legacies and the continuity of cattle and yak husbandry on the Tibetan Plateau.
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Affiliation(s)
- Ningbo Chen
- Key Laboratory of Animal Genetics Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, P. R. China
| | - Zhengwei Zhang
- Center for Archaeological Science, Sichuan University, Chengdu 610065, P. R. China
| | - Jiawen Hou
- Key Laboratory of Animal Genetics Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, P. R. China
| | - Jialei Chen
- Key Laboratory of Animal Genetics Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, P. R. China
| | - Xuan Gao
- Center for Archaeological Science, Sichuan University, Chengdu 610065, P. R. China
| | - Li Tang
- Department of Archaeology, Max Planck Institute of Geoanthropology, Jena 07745, Germany
- Domestication and Anthropogenic Evolution Research Group, Max Planck Institute of Geoanthropology, Jena 07745, Germany
| | - Shargan Wangdue
- Institute for Conservation and Research of Cultural Relics of Tibet Autonomous Region, Lhasa 850000, China
| | - Xiaoming Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), Kunming 650201, P. R. China
| | - Mikkel-Holger S. Sinding
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen DK-1350, Denmark
| | - Xuexue Liu
- National Germplasm Centre of Domestic Animal Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, P. R. China
- Centre for Anthropobiology and Genomics of Toulouse, CNRS UMR 5288, Université de Toulouse, Université Paul Sabatier, Toulouse 31000, France
| | - Jianlin Han
- Yazhouwan National Laboratory, Sanya 572024, P. R. China
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, P. R. China
| | - Hongliang Lü
- Center for Archaeological Science, Sichuan University, Chengdu 610065, P. R. China
| | - Chuzhao Lei
- Key Laboratory of Animal Genetics Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, P. R. China
| | - Fiona Marshall
- Department of Anthropology, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Xinyi Liu
- Department of Anthropology, Washington University in St. Louis, St. Louis, MO 63130, USA
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Li B, Yang J, Liu Y, Jiang M. Genome Variation Map of Domestic Qinghai-Tibet Plateau Yaks by SLAF-Seq Reveals Genetic Footprint during Artificial Selection. Animals (Basel) 2023; 13:2963. [PMID: 37760363 PMCID: PMC10525144 DOI: 10.3390/ani13182963] [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: 07/05/2023] [Revised: 09/14/2023] [Accepted: 09/18/2023] [Indexed: 09/29/2023] Open
Abstract
The yak (Bos grunniens) was domesticated in the high-altitude QTP. Research about their genetic diversity and population structure is limited. In this study, we resequenced the genome of 494 domestic yaks using Specific-Locus Amplified Fragment Sequencing (SLAF-seq). The survey was conducted on six populations sampled from isolated locations in China in order to analyze their structure and genetic diversity. These six domestic populations were clearly grouped into two independent clusters, with Jinchuan, Changtai, and Jiulong showing a tight genetic relationship with the wild yak. Nerve development pathways were enriched with GO enrichment analysis of 334 domesticated genes. Major genomic regions associated with the differentiation of domestic yaks were detected. These findings provide preliminary information on the yak genome variability, useful to understand the genomic characteristics of different populations in QTP.
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Affiliation(s)
- Biao Li
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Southwest Minzu University, Ministry of Education, Chengdu 610041, China; (B.L.)
- Key Laboratory of Animal Science of National Ethnic Affairs Commission of China, Southwest Minzu University, Chengdu 610041, China
| | - Jinzeng Yang
- Department of Human Nutrition, Food and Animal Sciences, University of Hawaii at Manoa, Honolulu, HI 96822, USA;
| | - Yili Liu
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Southwest Minzu University, Ministry of Education, Chengdu 610041, China; (B.L.)
| | - Mingfeng Jiang
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Southwest Minzu University, Ministry of Education, Chengdu 610041, China; (B.L.)
- College of Animal Husbandry and Veterinary Medicine, Southwest Minzu University, Chengdu 610041, China
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