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Cai B, Wu X, Shi Y, Kang Y, Ding Z, Guo S, Cao M, Hu L, Zhang B, Wang X, Pei J, Ge Q, Xiong L, Zhang S, Guo X. Whole-Genome Sequencing Unveils the Uniqueness of Yushu Yaks ( Bos grunniens). Int J Mol Sci 2025; 26:3879. [PMID: 40332613 PMCID: PMC12027638 DOI: 10.3390/ijms26083879] [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: 01/30/2025] [Revised: 04/12/2025] [Accepted: 04/17/2025] [Indexed: 05/08/2025] Open
Abstract
The Yushu yak is one of China's distinctive yak breeds, primarily distributed in the Yushu Tibetan Autonomous Prefecture of Qinghai Province and its surrounding areas. Yushu yaks are not only economically and culturally significant but also play a crucial role in protecting the ecosystem of the Qinghai-Tibet Plateau and promoting sustainable development. However, there are no clear records regarding the ancestry, population structure, and unique traits of Yushu yaks. Therefore, this study conducted an analysis of genetic diversity, population structure, and selection signals in Yushu yak populations, aiming to provide references for the conservation and utilization of the breed genetic resources. The results of the analysis showed that the Yushu yak population has high genetic diversity and low inbreeding coefficients, indicating a stable genetic structure. Population structure analysis revealed that the Yushu yak lineage is unique, with limited gene flow between domestic and wild yaks. Functional enrichment analysis of positively selected genes in Yushu yaks indicated prominent selection features related to growth and development as well as energy metabolism. Additionally, we classified the Yushu yak breeding bulls into family lineages based on kinship, which is essential for improving the efficiency of utilizing genetic resources and scientifically managing the population.
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Affiliation(s)
- Bao Cai
- Key Laboratory of Yak Breeding of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (B.C.); (X.W.); (Y.S.); (Y.K.); (Z.D.); (S.G.); (M.C.); (L.H.); (B.Z.); (X.W.); (J.P.); (Q.G.); (L.X.)
| | - Xiaoyun Wu
- Key Laboratory of Yak Breeding of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (B.C.); (X.W.); (Y.S.); (Y.K.); (Z.D.); (S.G.); (M.C.); (L.H.); (B.Z.); (X.W.); (J.P.); (Q.G.); (L.X.)
| | - Yilin Shi
- Key Laboratory of Yak Breeding of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (B.C.); (X.W.); (Y.S.); (Y.K.); (Z.D.); (S.G.); (M.C.); (L.H.); (B.Z.); (X.W.); (J.P.); (Q.G.); (L.X.)
| | - Yandong Kang
- Key Laboratory of Yak Breeding of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (B.C.); (X.W.); (Y.S.); (Y.K.); (Z.D.); (S.G.); (M.C.); (L.H.); (B.Z.); (X.W.); (J.P.); (Q.G.); (L.X.)
| | - Ziqiang Ding
- Key Laboratory of Yak Breeding of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (B.C.); (X.W.); (Y.S.); (Y.K.); (Z.D.); (S.G.); (M.C.); (L.H.); (B.Z.); (X.W.); (J.P.); (Q.G.); (L.X.)
| | - Shaoke Guo
- Key Laboratory of Yak Breeding of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (B.C.); (X.W.); (Y.S.); (Y.K.); (Z.D.); (S.G.); (M.C.); (L.H.); (B.Z.); (X.W.); (J.P.); (Q.G.); (L.X.)
| | - Mengli Cao
- Key Laboratory of Yak Breeding of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (B.C.); (X.W.); (Y.S.); (Y.K.); (Z.D.); (S.G.); (M.C.); (L.H.); (B.Z.); (X.W.); (J.P.); (Q.G.); (L.X.)
| | - Liyan Hu
- Key Laboratory of Yak Breeding of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (B.C.); (X.W.); (Y.S.); (Y.K.); (Z.D.); (S.G.); (M.C.); (L.H.); (B.Z.); (X.W.); (J.P.); (Q.G.); (L.X.)
| | - Ben Zhang
- Key Laboratory of Yak Breeding of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (B.C.); (X.W.); (Y.S.); (Y.K.); (Z.D.); (S.G.); (M.C.); (L.H.); (B.Z.); (X.W.); (J.P.); (Q.G.); (L.X.)
| | - Xingdong Wang
- Key Laboratory of Yak Breeding of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (B.C.); (X.W.); (Y.S.); (Y.K.); (Z.D.); (S.G.); (M.C.); (L.H.); (B.Z.); (X.W.); (J.P.); (Q.G.); (L.X.)
| | - Jie Pei
- Key Laboratory of Yak Breeding of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (B.C.); (X.W.); (Y.S.); (Y.K.); (Z.D.); (S.G.); (M.C.); (L.H.); (B.Z.); (X.W.); (J.P.); (Q.G.); (L.X.)
| | - Qianyun Ge
- Key Laboratory of Yak Breeding of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (B.C.); (X.W.); (Y.S.); (Y.K.); (Z.D.); (S.G.); (M.C.); (L.H.); (B.Z.); (X.W.); (J.P.); (Q.G.); (L.X.)
| | - Lin Xiong
- Key Laboratory of Yak Breeding of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (B.C.); (X.W.); (Y.S.); (Y.K.); (Z.D.); (S.G.); (M.C.); (L.H.); (B.Z.); (X.W.); (J.P.); (Q.G.); (L.X.)
| | - Songshan Zhang
- Beijing Institute of Animal Husbandry and Veterinary Medicine, Chinese Academy of Agricultural Sciences, Beijing 100080, China
| | - Xian Guo
- Key Laboratory of Yak Breeding of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (B.C.); (X.W.); (Y.S.); (Y.K.); (Z.D.); (S.G.); (M.C.); (L.H.); (B.Z.); (X.W.); (J.P.); (Q.G.); (L.X.)
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Xu S, Akhatayeva Z, Liu J, Feng X, Yu Y, Badaoui B, Esmailizadeh A, Kantanen J, Amills M, Lenstra JA, Johansson AM, Coltman DW, Liu GE, Curik I, Orozco-terWengel P, Paiva SR, Zinovieva NA, Zhang L, Yang J, Liu Z, Wang Y, Yu Y, Li M. Genetic advancements and future directions in ruminant livestock breeding: from reference genomes to multiomics innovations. SCIENCE CHINA. LIFE SCIENCES 2025; 68:934-960. [PMID: 39609363 DOI: 10.1007/s11427-024-2744-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2024] [Accepted: 09/24/2024] [Indexed: 11/30/2024]
Abstract
Ruminant livestock provide a rich source of products, such as meat, milk, and wool, and play a critical role in global food security and nutrition. Over the past few decades, genomic studies of ruminant livestock have provided valuable insights into their domestication and the genetic basis of economically important traits, facilitating the breeding of elite varieties. In this review, we summarize the main advancements for domestic ruminants in reference genome assemblies, population genomics, and the identification of functional genes or variants for phenotypic traits. These traits include meat and carcass quality, reproduction, milk production, feed efficiency, wool and cashmere yield, horn development, tail type, coat color, environmental adaptation, and disease resistance. Functional genomic research is entering a new era with the advancements of graphical pangenomics and telomere-to-telomere (T2T) gap-free genome assembly. These advancements promise to improve our understanding of domestication and the molecular mechanisms underlying economically important traits in ruminant livestock. Finally, we provide new perspectives and future directions for genomic research on ruminant genomes. We suggest how ever-increasing multiomics datasets will facilitate future studies and molecular breeding in livestock, including the potential to uncover novel genetic mechanisms underlying phenotypic traits, to enable more accurate genomic prediction models, and to accelerate genetic improvement programs.
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Affiliation(s)
- Songsong Xu
- Frontiers Science Center for Molecular Design Breeding (MOE); State Key Laboratory of Animal Biotech Breeding; College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Zhanerke Akhatayeva
- Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot, 010010, China
| | - Jiaxin Liu
- Frontiers Science Center for Molecular Design Breeding (MOE); State Key Laboratory of Animal Biotech Breeding; College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Xueyan Feng
- Frontiers Science Center for Molecular Design Breeding (MOE); State Key Laboratory of Animal Biotech Breeding; College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Yi Yu
- Frontiers Science Center for Molecular Design Breeding (MOE); State Key Laboratory of Animal Biotech Breeding; College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Bouabid Badaoui
- Laboratory of Biodiversity, Ecology and Genome, Department of Biology, Faculty of Sciences Rabat, Mohammed V University, Rabat, 10106, Morocco
| | - Ali Esmailizadeh
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, 76169-133, Iran
| | - Juha Kantanen
- Production Systems, Natural Resources Institute Finland (Luke), Jokioinen, FI-31600, Finland
| | - Marcel Amills
- Department of Animal Genetics, Center for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus de la Universitat Autónoma de Barcelona, Bellaterra, 08193, Spain
- Departament de Ciència Animal i dels Aliments, Universitat Autónoma de Barcelona, Bellaterra, 08193, Spain
| | - Johannes A Lenstra
- Faculty of Veterinary Medicine, Utrecht University, Utrecht, 3584, The Netherlands
| | - Anna M Johansson
- Department of Animal Breeding and Genetics, Faculty of Veterinary Medicine and Animal Science, Swedish University of Agricultural Sciences, Uppsala, 75007, Sweden
| | - David W Coltman
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, T6G 2E9, Canada
- Department of Biology, Western University, London, Ontario, N6A 5B7, Canada
| | - George E Liu
- Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Beltsville, MD, 20705, USA
| | - Ino Curik
- Department of Animal Science, Faculty of Agriculture, University of Zagreb, Zagreb, 10000, Croatia
- Institute of Animal Sciences, Hungarian University of Agriculture and Life Sciences (MATE), Kaposvár, 7400, Hungary
| | | | - Samuel R Paiva
- Embrapa Genetic Resources and Biotechnology, Laboratory of Animal Genetics, Brasília, Federal District, 70770917, Brazil
| | - Natalia A Zinovieva
- L.K. Ernst Federal Science Center for Animal Husbandry, Moscow Region, Podolsk, 142132, Russian Federation
| | - Linwei Zhang
- Department of Neurology, China-Japan Friendship Hospital, Beijing, 100029, China
| | - Ji Yang
- Frontiers Science Center for Molecular Design Breeding (MOE); State Key Laboratory of Animal Biotech Breeding; College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Zhihong Liu
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Yachun Wang
- Frontiers Science Center for Molecular Design Breeding (MOE); State Key Laboratory of Animal Biotech Breeding; College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Ying Yu
- Frontiers Science Center for Molecular Design Breeding (MOE); State Key Laboratory of Animal Biotech Breeding; College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Menghua Li
- Frontiers Science Center for Molecular Design Breeding (MOE); State Key Laboratory of Animal Biotech Breeding; College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
- Sanya Institute of China Agricultural University, Sanya, 572024, China.
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Ma C, Andersson L. Population genomic analysis identifies the complex structural variation at the fibromelanosis (FM) locus in chicken. Sci Rep 2025; 15:9239. [PMID: 40102581 PMCID: PMC11920206 DOI: 10.1038/s41598-025-94250-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2024] [Accepted: 03/12/2025] [Indexed: 03/20/2025] Open
Abstract
Phenotypic diversity and its genetic basis are central questions in biology, with domesticated animals offering valuable insights due to their rapid evolution the last 10,000 years. In chickens, fibromelanosis (FM) is a striking pigmentation phenotype characterized by hyperpigmentation. A previous study identified a complex structural variant involving both two large duplications (127.4 and 170.5 kb in size) and inversions associated with upregulated expression of the Endothelin 3 (EDN3) gene. However, the detailed organization of the structural arrangements have remained unclear. In this study, we conducted a comprehensive genomic survey of 517 FM chickens representing 44 different populations. Our results elucidate the complex arrangement of the duplications and inversions at the FM locus based on the large-scale genomic survey, population level genotyping, and linkage disequilibrium analysis, providing conclusive support for one specific configuration of the two large duplications, resolving a controversy that has been unresolved for more than a decade. Our results show that the birth of this complex structural variant must have involved an interchromosomal rearrangement creating fixed heterozygosity due to sequence differences between the two copies of the 127.4 kb duplication. This study shows how population genomics can be used to understand complex structural variations that underlie phenotypic variation.
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Affiliation(s)
- Cheng Ma
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.
| | - Leif Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, USA.
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Yang B, Zhang H, Feng X, Yu Z, Cao J, Niu Y, Wan P, Liu G, Zhao X. Genetic Diversity Estimation and Genome-Wide Selective Sweep Analysis of the Bazhou Yak. Animals (Basel) 2025; 15:849. [PMID: 40150378 PMCID: PMC11939585 DOI: 10.3390/ani15060849] [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: 01/28/2025] [Revised: 03/01/2025] [Accepted: 03/14/2025] [Indexed: 03/29/2025] Open
Abstract
The Bazhou yak, a major native meat yak breed in Xinjiang, China, is renowned for its fast growth rate, strong adaptability, and particularly high intramuscular fat (IMF) content. However, limited knowledge regarding its phylogenetic history and genomic composition has hindered its long-term conservation and utilization. This study evaluated the genetic diversity, population phylogenetics, and genome-wide selective sweep analysis (GWSA) of 100 newly obtained Bazhou yaks through genome resequencing, as well as 340 public yak genomes from nine other populations on the Qinghai-Tibet Plateau. The results revealed moderate diversity, lower genomic inbreeding levels, and rapid linkage disequilibrium (LD) decay in Bazhou yaks. Principal component analysis (PCA) and phylogenetic analysis showed a clear separation of Bazhou yaks from other yak populations, indicating the Bazhou yak as an independent genetic population. Furthermore, less genetic differentiation was found between the Bazhou yak and the Huanhu yak, while ADMIXTURE analysis revealed a common ancestral lineage between Bazhou yaks and Huanhu yaks, indicating an important genetic contribution of the Qinghai yak population to Bazhou yaks. The GWSA identified a total of 833 selected genes in Bazhou yaks using the top 5% interaction windows of both parameters (FST, Pi ratio, and XP-EHH). A significant number of these genes are related to fat synthesis and deposition, such as MTOR, APOA1, and GPAT4. In summary, this study sheds light on the phylogenetic status and distinctive genomic features of Bazhou yaks, which facilitates our understanding of the genetic basis of the IMF phenotype in Bazhou yaks.
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Affiliation(s)
- Baigao Yang
- Institute of Animal Sciences (IAS), Chinese Academy of Agricultural Sciences (CAAS), No. 2 Yuanmingyuan Western Road, Haidian District, Beijing 100193, China; (B.Y.); (H.Z.); (X.F.); (Z.Y.); (J.C.); (Y.N.)
| | - Hang Zhang
- Institute of Animal Sciences (IAS), Chinese Academy of Agricultural Sciences (CAAS), No. 2 Yuanmingyuan Western Road, Haidian District, Beijing 100193, China; (B.Y.); (H.Z.); (X.F.); (Z.Y.); (J.C.); (Y.N.)
| | - Xiaoyi Feng
- Institute of Animal Sciences (IAS), Chinese Academy of Agricultural Sciences (CAAS), No. 2 Yuanmingyuan Western Road, Haidian District, Beijing 100193, China; (B.Y.); (H.Z.); (X.F.); (Z.Y.); (J.C.); (Y.N.)
| | - Zhou Yu
- Institute of Animal Sciences (IAS), Chinese Academy of Agricultural Sciences (CAAS), No. 2 Yuanmingyuan Western Road, Haidian District, Beijing 100193, China; (B.Y.); (H.Z.); (X.F.); (Z.Y.); (J.C.); (Y.N.)
| | - Jianhua Cao
- Institute of Animal Sciences (IAS), Chinese Academy of Agricultural Sciences (CAAS), No. 2 Yuanmingyuan Western Road, Haidian District, Beijing 100193, China; (B.Y.); (H.Z.); (X.F.); (Z.Y.); (J.C.); (Y.N.)
| | - Yifan Niu
- Institute of Animal Sciences (IAS), Chinese Academy of Agricultural Sciences (CAAS), No. 2 Yuanmingyuan Western Road, Haidian District, Beijing 100193, China; (B.Y.); (H.Z.); (X.F.); (Z.Y.); (J.C.); (Y.N.)
| | - Pengcheng Wan
- State Key Laboratory of Sheep Genetic Improvement and Healthy Breeding, Institute of Animal Husbandry and Veterinary Sciences, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi 832000, China;
| | - Gang Liu
- National Animal Husbandry Service, Beijing 100193, China
| | - Xueming Zhao
- Institute of Animal Sciences (IAS), Chinese Academy of Agricultural Sciences (CAAS), No. 2 Yuanmingyuan Western Road, Haidian District, Beijing 100193, China; (B.Y.); (H.Z.); (X.F.); (Z.Y.); (J.C.); (Y.N.)
- State Key Laboratory of Sheep Genetic Improvement and Healthy Breeding, Institute of Animal Husbandry and Veterinary Sciences, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi 832000, China;
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Yang Q, Sun J, Wang X, Wang J, Liu Q, Ru J, Zhang X, Wang S, Hao R, Bian P, Dai X, Gong M, Zhang Z, Wang A, Bai F, Li R, Cai Y, Jiang Y. SVLearn: a dual-reference machine learning approach enables accurate cross-species genotyping of structural variants. Nat Commun 2025; 16:2406. [PMID: 40069188 PMCID: PMC11897243 DOI: 10.1038/s41467-025-57756-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2024] [Accepted: 03/04/2025] [Indexed: 03/15/2025] Open
Abstract
Structural variations (SVs) are diverse forms of genetic alterations and drive a wide range of human diseases. Accurately genotyping SVs, particularly occurring at repetitive genomic regions, from short-read sequencing data remains challenging. Here, we introduce SVLearn, a machine-learning approach for genotyping bi-allelic SVs. It exploits a dual-reference strategy to engineer a curated set of genomic, alignment, and genotyping features based on a reference genome in concert with an allele-based alternative genome. Using 38,613 human-derived SVs, we show that SVLearn significantly outperforms four state-of-the-art tools, with precision improvements of up to 15.61% for insertions and 13.75% for deletions in repetitive regions. On two additional sets of 121,435 cattle SVs and 113,042 sheep SVs, SVLearn demonstrates a strong generalizability to cross-species genotype SVs with a weighted genotype concordance score of up to 90%. Notably, SVLearn enables accurate genotyping of SVs at low sequencing coverage, which is comparable to the accuracy at 30× coverage. Our studies suggest that SVLearn can accelerate the understanding of associations between the genome-scale, high-quality genotyped SVs and diseases across multiple species.
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Affiliation(s)
- Qimeng Yang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Jianfeng Sun
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Xinyu Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Jiong Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Quanzhong Liu
- College of Information Engineering, Northwest A&F University, Yangling, Shaanxi, China
| | - Jinlong Ru
- Institute of Virology, Helmholtz Centre Munich - German Research Centre for Environmental Health, Neuherberg, Germany
| | - Xin Zhang
- College of Information Engineering, Northwest A&F University, Yangling, Shaanxi, China
| | - Sizhe Wang
- College of Information Engineering, Northwest A&F University, Yangling, Shaanxi, China
| | - Ran Hao
- College of Information Engineering, Northwest A&F University, Yangling, Shaanxi, China
| | - Peipei Bian
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Xuelei Dai
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
- Yazhouwan National Laboratory, Sanya, Hainan, China
| | - Mian Gong
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Zhuangbiao Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Ao Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Fengting Bai
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Ran Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Yudong Cai
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China.
| | - Yu Jiang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China.
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Ahmad SF, Gangwar M, Kumar A, Kumar A, Dige MS, Jha GK, Gaur GK, Dutt T. Dissecting genomes of multiple yak populations: unveiling ancestry and high-altitude adaptation through whole-genome resequencing analysis. BMC Genomics 2025; 26:214. [PMID: 40033180 PMCID: PMC11877770 DOI: 10.1186/s12864-025-11387-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2024] [Accepted: 02/19/2025] [Indexed: 03/05/2025] Open
Abstract
The present study was undertaken to elucidate the population structure and differentiation of Indian yak from Chinese and wild cohorts on genome-wide scale by identifying the selection sweeps and genomic basis of their adaptation across different comparisons while analyzing whole genome sequencing (WGS) data using latest bioinformatics tools. The study included 105 individuals from three distinct yak populations i.e., Indian yak (n = 29); Chinese yak (n = 61) and wild yak (n = 15), hypothesized to be related along the evolutionary timescale. Efficient variant calling and quality control in GATK and PLINK programs resulted in around 1 million (1,002,970) high-quality (LD-independent) SNPs with an average genotyping rate of 96.55%. The PCA, ADMIXTURE and TREEMIX analysis revealed stratification of the yak groups into three distinct clusters. The empirical distribution pattern of minor allele frequency (MAF) of SNPs on genome-wide scale was also elucidated for three yak cohorts revealing unique distribution across five different bins. The selection signature analysis revealed candidate genes that are important for the adaptation of Indian yak against harsh environmental conditions in their habitats. Under iHS analysis, several genes were identified to be under selection pressure in Indian yak including ABCA12, EXOC1, JUNB, KLF1, PRDX2, NANOS3, RFX1, RFX2, and CACNG7. On the other hand, across population analysis revealed the genes like NR2F2, OSBPL10, CIDEC, WFIKKN2, ADCY, THSD7A, ADGRB3, TRPC1, VASH2, and ABHD5 to be part of selective sweeps under these comparisons. A total of 53 genes were found common between intra- and inter-population selection signature analysis of Indian yak. Notably, the genes harbouring the SNPs under selection pressure were significant for adaptation traits including lipidogenesis, energy metabolism, thermogenesis, hair follicle formation, oxidation-reduction reactions, hypoxia and reproduction. These genes may be evaluated as candidate genes for livestock adaptation to harsh environmental conditions and to further the research and application in the present era of climate change.
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Affiliation(s)
- Sheikh Firdous Ahmad
- ICAR-Indian Veterinary Research Institute, Uttar Pradesh, Izatnagar, Bareilly, 243 122, India.
| | - Munish Gangwar
- ICAR-Indian Veterinary Research Institute, Uttar Pradesh, Izatnagar, Bareilly, 243 122, India
| | - Amit Kumar
- ICAR-Indian Veterinary Research Institute, Uttar Pradesh, Izatnagar, Bareilly, 243 122, India.
| | - Amod Kumar
- ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, 132 001, India
| | | | - Girish Kumar Jha
- ICAR-Indian Agricultural Statistics Research Institute, Pusa, New Delhi, 110 012, India
| | - Gyanendra Kumar Gaur
- ICAR-Indian Veterinary Research Institute, Uttar Pradesh, Izatnagar, Bareilly, 243 122, India
- Assistant Director General (Animal Production and Breeding), Indian Council of Agricultural Research, Krishi Bhawan, New Delhi, 110 001, India
| | - Triveni Dutt
- ICAR-Indian Veterinary Research Institute, Uttar Pradesh, Izatnagar, Bareilly, 243 122, India
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Li H, Wang H, Gao Y, Zhao X, Liang J, Pei L, Yao Y, Tang D. Bacterial community structure and metabolomic profiles of yak milk and cattle-yak milk during refrigeration in Gannan region: Analysis of interspecific differences in milk spoilage. Food Chem 2025; 463:141022. [PMID: 39243606 DOI: 10.1016/j.foodchem.2024.141022] [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: 05/28/2024] [Revised: 08/05/2024] [Accepted: 08/25/2024] [Indexed: 09/09/2024]
Abstract
The bacterial community dynamics and metabolomic profiles in raw yak (Y) milk and cattle-yak (CY) milk during refrigeration at 4 °C were investigated, followed by the elucidation of interspecific differences in milk storage. Bacterial communities and succession patterns were significantly different between the two milk types during refrigeration, with Lactococcus and Pseudomonas being the key distinguishing genera. Moreover, higher network complexity and tighter interactions were observed for the microbial community in CY milk than in Y milk. Furthermore, 7 proteases and 1 lipase potentially contributed to milk spoilage. The metabolomic profiles significantly differed between the milk types during refrigeration. Extended storage time decreased the relative abundances of organic nitrogen compounds and lipids and lipid-like molecules, with a concomitant increase in organic acids and derivatives, particularly in Y milk. Moreover, 9 metabolites, whose levels gradually increased with storage time, were strongly correlated with psychrophiles and thus considered potential markers of deterioration in plateau-characteristic milk. These findings offer a theoretical foundation for augmenting the quality and safety of plateau-characteristic milk and its derivatives, while also helping us understand the microbial and metabolic dynamics in raw milk under extreme environments.
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Affiliation(s)
- Hongqiang Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Hongbo Wang
- Laboratory of Quality & Safety Risk Assessment for Livestock Products of Ministry of Agriculture, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Yaqin Gao
- Laboratory of Quality & Safety Risk Assessment for Livestock Products of Ministry of Agriculture, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Xiangmin Zhao
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Jing Liang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Longying Pei
- College of Food Science and Engineering, Xinjiang Institute of Technology, Aksu 843100, China
| | - Yali Yao
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Defu Tang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China.
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8
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Ren P, Zhang M, Khan MZ, Yang L, Jing Y, Liu X, Yang X, Zhang C, Zhang M, Zhu Z, Zheng N, Zhang L, Zhang S, Zhu M. Genome-Wide Structural Variation Analysis and Breed Comparison of Local Domestic Ducks in Shandong Province, China. Animals (Basel) 2024; 14:3657. [PMID: 39765561 PMCID: PMC11672513 DOI: 10.3390/ani14243657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2024] [Revised: 11/27/2024] [Accepted: 12/16/2024] [Indexed: 01/11/2025] Open
Abstract
Structural variations in the duck genome significantly impact the environmental adaptability and phenotypic diversity of duck populations. Characterizing these SVs in local domestic duck breeds from Shandong province offers valuable insights for breed selection and the development of new breeds. This study aimed to profile the genomic SVs in three local duck breeds (Matahu duck, Weishan partridge duck, and Wendeng black duck) and explore their differential distributions. A total of 21,673 SVs were detected using LUMPY (v0.2.13) and DELLY (v1.0.3) software, with 46% located in intergenic regions, 33% in intronic regions, and frameshift deletions being the most prevalent in exonic regions (3%). SVs distribution showed a decreasing trend with shorter chromosome lengths. Population structure analysis revealed distinct genetic profiles, with Matahu and Weishan partridge ducks showing closer affinities and the Wendeng black duck having a more homogeneous genetic background, likely due to geographic isolation. Functional annotation identified genes related to nervous system development, mitosis, spindle assembly, and energy metabolism. Notable genes included PLXNA4, NRP2, SEMA3A, PTEN, MYBL2, ADK, and COX4I1. Additionally, genes such as PRKG1, GABRA2, and FSHR were linked to energy metabolism and reproductive activity. The study provides a comprehensive analysis of SVs, revealing significant genetic differentiation and identifying genes associated with economically important traits, offering valuable resources for the genetic improvement and breeding of local duck breeds.
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Affiliation(s)
- Pengwei Ren
- College of Agriculture and Biology, Liaocheng University, Liaocheng 252000, China
| | - Meixia Zhang
- College of Agriculture and Biology, Liaocheng University, Liaocheng 252000, China
| | - Muhammad Zahoor Khan
- College of Agriculture and Biology, Liaocheng University, Liaocheng 252000, China
| | - Liu Yang
- College of Agriculture and Biology, Liaocheng University, Liaocheng 252000, China
| | - Yadi Jing
- College of Agriculture and Biology, Liaocheng University, Liaocheng 252000, China
| | - Xiang Liu
- College of Agriculture and Biology, Liaocheng University, Liaocheng 252000, China
| | - Xiaohui Yang
- College of Agriculture and Biology, Liaocheng University, Liaocheng 252000, China
| | - Chaoran Zhang
- College of Agriculture and Biology, Liaocheng University, Liaocheng 252000, China
| | - Min Zhang
- Shandong Animal Husbandry Station, Jinan 250010, China
| | - Zhiming Zhu
- Fujian Key Laboratory of Animal Genetics and Breeding, Institute of Animal Husbandry and Veterinary Medicine of Fujian Academy of Agricultural Sciences, Fuzhou 350013, China
| | - Nenzhu Zheng
- Fujian Key Laboratory of Animal Genetics and Breeding, Institute of Animal Husbandry and Veterinary Medicine of Fujian Academy of Agricultural Sciences, Fuzhou 350013, China
| | - Lujiao Zhang
- Weihai Wendeng District Animal Husbandry and Veterinary Career Development Center, Weihai 264400, China
| | - Shuer Zhang
- Shandong Animal Husbandry Station, Jinan 250010, China
| | - Mingxia Zhu
- College of Agriculture and Biology, Liaocheng University, Liaocheng 252000, China
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9
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Wu S, Chen Z, Zhou X, Lu J, Tian Y, Jiang Y, Liu Q, Wang Z, Li H, Qu L, Zhang F. Analysis of genetic diversity and genetic structure of indigenous chicken populations in Guizhou province based on genome-wide single nucleotide polymorphism markers. Poult Sci 2024; 103:104383. [PMID: 39447329 PMCID: PMC11539430 DOI: 10.1016/j.psj.2024.104383] [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: 05/24/2024] [Revised: 08/23/2024] [Accepted: 10/01/2024] [Indexed: 10/26/2024] Open
Abstract
Guizhou province in China is rich in indigenous chicken breeds, playing an essential role in the genetic improvement of modern chickens. Genetic diversity has decreased in recent decades due to accelerated breeding processes and changing conservation priorities. To determine the genetic diversity and population structure of Guizhou indigenous chicken breeds, we used 55K genotyping arrays to conduct population genetic analysis on 233 individuals from 8 Guizhou indigenous breeds and 263 individuals from 9 Guizhou indigenous chicken populations. We evaluated the genetic diversity parameter (heterozygosity, proportion of polymorphic markers, and nucleotide diversity), linkage disequilibrium (LD), population structure, and genetic differentiation (FST and genetics distance). Genetic diversity results indicated that the genetic diversity of chicken breeds in Guizhou province is relatively affluent. Among Guizhou breeds, Baiyi black-bone and Guizhou yellow chicken displayed the lowest genetic diversity, as the 2 breeds exhibit lower PN and heterozygosity, the extent of linkage disequilibrium is higher. According to the LD pattern, Guizhou indigenous breeds can be divided into 3 categories. Population structure analysis showed a certain degree of genetic differentiation among local chickens in Guizhou. We argue that Chishui black-bone and Puan black-bone chickens are 2 different geographical regional groups of the same breed. In principal component analysis, individuals from the 2 groups clustered together, and the phylogenetic tree results showed that the 2 groups clustered together to form a branch independent of other breeds, and they displayed an identical pattern of ancestral lineage composition. The research results will provide a reference for protecting local chicken genetic resources in Guizhou Province and promote the protection and utilization of genetic resources.
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Affiliation(s)
- Sheng Wu
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, College of Animal Sciences, Guizhou University, Guiyang, 550025, Guizhou Province, China
| | - Zhiwen Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, College of Animal Sciences, Guizhou University, Guiyang, 550025, Guizhou Province, China
| | - Xiaohong Zhou
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, College of Animal Sciences, Guizhou University, Guiyang, 550025, Guizhou Province, China
| | - Juanhong Lu
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, College of Animal Sciences, Guizhou University, Guiyang, 550025, Guizhou Province, China
| | - Yingping Tian
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, College of Animal Sciences, Guizhou University, Guiyang, 550025, Guizhou Province, China
| | - Yaozhou Jiang
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, College of Animal Sciences, Guizhou University, Guiyang, 550025, Guizhou Province, China
| | - Qinsong Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, College of Animal Sciences, Guizhou University, Guiyang, 550025, Guizhou Province, China
| | - Zhong Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, College of Animal Sciences, Guizhou University, Guiyang, 550025, Guizhou Province, China
| | - Hui Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, College of Animal Sciences, Guizhou University, Guiyang, 550025, Guizhou Province, China
| | - Lujiang Qu
- Department of Animal Genetics and Breeding, State Key Laboratory of Animal Nutrition, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Fuping Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, College of Animal Sciences, Guizhou University, Guiyang, 550025, Guizhou Province, China.
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She H, Liu Z, Xu Z, Zhang H, Wu J, Cheng F, Wang X, Qian W. Pan-genome analysis of 13 Spinacia accessions reveals structural variations associated with sex chromosome evolution and domestication traits in spinach. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:3102-3117. [PMID: 39095952 PMCID: PMC11501001 DOI: 10.1111/pbi.14433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 06/12/2024] [Accepted: 06/27/2024] [Indexed: 08/04/2024]
Abstract
Structural variations (SVs) are major genetic variants that can be involved in the origin, adaptation and domestication of species. However, the identification and characterization of SVs in Spinacia species are rare due to the lack of a pan-genome. Here, we report eight chromosome-scale assemblies of cultivated spinach and its two wild species. After integration with five existing assemblies, we constructed a comprehensive Spinacia pan-genome and identified 193 661 pan-SVs, which were genotyped in 452 Spinacia accessions. Our pan-SVs enabled genome-wide association study identified signals associated with sex and clarified the evolutionary direction of spinach. Most sex-linked SVs (86%) were biased to occur on the Y chromosome during the evolution of the sex-linked region, resulting in reduced Y-linked gene expression. The frequency of pan-SVs among Spinacia accessions further illustrated the contribution of these SVs to domestication, such as bolting time and seed dormancy. Furthermore, compared with SNPs, pan-SVs act as efficient variants in genomic selection (GS) because of their ability to capture missing heritability information and higher prediction accuracy. Overall, this study provides a valuable resource for spinach genomics and highlights the potential utility of pan-SV in crop improvement and breeding programmes.
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Affiliation(s)
- Hongbing She
- State Key Laboratory of Vegetable BiobreedingInstitute of Vegetables and Flowers, Chinese Academy of Agricultural SciencesBeijingChina
| | - Zhiyuan Liu
- State Key Laboratory of Vegetable BiobreedingInstitute of Vegetables and Flowers, Chinese Academy of Agricultural SciencesBeijingChina
| | - Zhaosheng Xu
- State Key Laboratory of Vegetable BiobreedingInstitute of Vegetables and Flowers, Chinese Academy of Agricultural SciencesBeijingChina
| | - Helong Zhang
- State Key Laboratory of Vegetable BiobreedingInstitute of Vegetables and Flowers, Chinese Academy of Agricultural SciencesBeijingChina
| | - Jian Wu
- State Key Laboratory of Vegetable BiobreedingInstitute of Vegetables and Flowers, Chinese Academy of Agricultural SciencesBeijingChina
| | - Feng Cheng
- State Key Laboratory of Vegetable BiobreedingInstitute of Vegetables and Flowers, Chinese Academy of Agricultural SciencesBeijingChina
| | - Xiaowu Wang
- State Key Laboratory of Vegetable BiobreedingInstitute of Vegetables and Flowers, Chinese Academy of Agricultural SciencesBeijingChina
| | - Wei Qian
- State Key Laboratory of Vegetable BiobreedingInstitute of Vegetables and Flowers, Chinese Academy of Agricultural SciencesBeijingChina
- Zhongyuan Research Center, Chinese Academy of Agricultural SciencesXinxiangChina
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11
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Yang Y, Yuan H, Yao B, Zhao S, Wang X, Xu L, Zhang L. Genetic Adaptations of the Tibetan Pig to High-Altitude Hypoxia on the Qinghai-Tibet Plateau. Int J Mol Sci 2024; 25:11303. [PMID: 39457085 PMCID: PMC11508817 DOI: 10.3390/ijms252011303] [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: 08/19/2024] [Revised: 10/05/2024] [Accepted: 10/09/2024] [Indexed: 10/28/2024] Open
Abstract
The Tibetan Plateau's distinctive high-altitude environment, marked by extreme cold and reduced oxygen levels, presents considerable survival challenges for both humans and mammals. Natural selection has led to the accumulation of adaptive mutations in Tibetan pigs, enabling them to develop distinctive adaptive phenotypes. Here, we aim to uncover the genetic mechanisms underlying the adaptation of Tibetan pigs to high-altitude hypoxia. Therefore, we conducted a systematic analysis of 140 whole-genome sequencing (WGS) data points from different representing pig populations. Our analysis identified a total of 27,614,561 mutations, including 22,386,319 single-nucleotide variants (SNVs) and 5,228,242 insertions/deletions (INDELs, size < 50 bp). A total of 11% (2,678,569) of the SNVs were newly identified in our project, significantly expanding the dataset of genetic variants in Tibetan pigs. Compared to other pig breeds, Tibetan pigs are uniquely adapted to high-altitude environments, exhibiting the highest genetic diversity and the lowest inbreeding coefficient. Employing the composite of multiple signals (CMS) method, we scanned the genome-wide Darwinian positive selection signals and identified 32,499 Tibetan pig positively selected SNVs (TBPSSs) and 129 selected genes (TBPSGs), including 213 newly discovered genes. Notably, we identified eight genes (PHACTR1, SFI1, EPM2A, SLC30A7, NKAIN2, TNNI3K, and PLIN2) with strong nature selection signals. They are likely to improve cardiorespiratory function and fat metabolism to help Tibetan pigs become adapted to the high-altitude environment. These findings provide new insights into the genetic mechanisms of high-altitude adaptation and the adaptive phenotypes of Tibetan pigs.
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Affiliation(s)
- Yanan Yang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (H.Y.); (B.Y.); (S.Z.); (X.W.); (L.X.); (L.Z.)
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12
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Fu Y, Yan J, Lan L, Zhang H, Wang P, Wang Y, Xiong X, Li J, He H. Cloning, bioinformatics analysis and expression of the cysteine dioxygenase type 1 (CDO1) gene in domestic yak. Front Vet Sci 2024; 11:1488782. [PMID: 39493813 PMCID: PMC11527789 DOI: 10.3389/fvets.2024.1488782] [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: 08/30/2024] [Accepted: 10/09/2024] [Indexed: 11/05/2024] Open
Abstract
Introduction The CDO1 gene is an important gene in the taurine synthesis pathway and has been observed to have high expression in ovaries of female mammals. This study aims to explore the conservation of CDO1 gene in domestic yaks, as well as to examine the fundamental characteristics of CDO1 gene and its expression in female yaks. Methods Ovarian samples were collected from yaks in the follicular phase, luteal phase and gestation period in this experiment, and their total RNA and protein were extracted. Then Polymerase Chain Reaction (PCR) and bioinformatics online software were used to clone and analyze the CDO1 gene. The relative expression of CDO1 in yak ovaries was detected by Quantitative Real-time PCR (RT-qPCR) and Western blotting. The distribution and localization of CDO1 protein in ovary were detected by immunohistochemistry. Results We have successfully cloned the coding region of CDO1 gene in yak. The results showed that the CDS region of CDO1 gene was 603 bp, encoding 200 amino acids, and was a relatively stable hydrophilic protein. CDO1 is relatively conservative in species evolution. The protein encoded by CDO1 gene does not have a signaling peptide or a transmembrane structure. It is a protein that is not involved in transmembrane transport and is mainly located in the cytoplasm. The secondary structure of the protein is dominated by the random coil. CDO1 is estimated to interact with 10 proteins. The results of RT-qPCR and Western blotting showed that the CDO1 gene exhibited the highest expression in the ovary during the luteal phase and the lowest expression in the ovary during the follicular phase (P < 0.01). The results of immunohistochemistry showed that CDO1 was mainly expressed in granular cells, theca cells and lutein cells of ovarian tissue. Conclusion These results suggest that the CDO1 gene has undergone minimal evolutionary changes during the course of animal evolution. The results provide a reference for further investigation of the function of CDO1 gene in reproduction and production in yaks.
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Affiliation(s)
- Yuxin Fu
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Ministry of Education, Chengdu, China
- Key Laboratory of Animal Medicine at Southwest Minzu University of Sichuan Province, Chengdu, China
- College of Animal and Veterinary Sciences, Southwest Minzu University, Chengdu, China
| | - Jiuru Yan
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Ministry of Education, Chengdu, China
- Key Laboratory of Animal Medicine at Southwest Minzu University of Sichuan Province, Chengdu, China
- College of Animal and Veterinary Sciences, Southwest Minzu University, Chengdu, China
| | - Lan Lan
- Animal Husbandry Science Institute of Ganzi Tibetan Autonomous Prefecture, Kangding, China
| | - Huizhu Zhang
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Ministry of Education, Chengdu, China
- Key Laboratory of Animal Medicine at Southwest Minzu University of Sichuan Province, Chengdu, China
- College of Animal and Veterinary Sciences, Southwest Minzu University, Chengdu, China
| | - Peng Wang
- Animal Husbandry Science Institute of Ganzi Tibetan Autonomous Prefecture, Kangding, China
| | - Yaying Wang
- Key Laboratory of Animal Medicine at Southwest Minzu University of Sichuan Province, Chengdu, China
- College of Animal and Veterinary Sciences, Southwest Minzu University, Chengdu, China
| | - Xianrong Xiong
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Ministry of Education, Chengdu, China
- Key Laboratory of Animal Medicine at Southwest Minzu University of Sichuan Province, Chengdu, China
- College of Animal and Veterinary Sciences, Southwest Minzu University, Chengdu, China
| | - Jian Li
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Ministry of Education, Chengdu, China
- Key Laboratory of Animal Medicine at Southwest Minzu University of Sichuan Province, Chengdu, China
- College of Animal and Veterinary Sciences, Southwest Minzu University, Chengdu, China
| | - Honghong He
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Ministry of Education, Chengdu, China
- Key Laboratory of Animal Medicine at Southwest Minzu University of Sichuan Province, Chengdu, China
- College of Animal and Veterinary Sciences, Southwest Minzu University, Chengdu, China
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13
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Li H, Xi B, Lin S, Tang D, Gao Y, Zhao X, Liang J, Yang W, Li J. Volatile Flavor Analysis in Yak Meat: Effects of Different Breeds, Feeding Methods, and Parts Using GC-IMS and Multivariate Analyses. Foods 2024; 13:3130. [PMID: 39410166 PMCID: PMC11476270 DOI: 10.3390/foods13193130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2024] [Revised: 09/23/2024] [Accepted: 09/24/2024] [Indexed: 10/20/2024] Open
Abstract
This study investigates the effects of breeds, feeding methods, and parts on the volatile flavor of yak meat. Gas chromatography-ion mobility spectrometry (GC-IMS) and multivariate analysis were used to analyze the volatile organic components (VOCs) in yak meat from various sources. A total of 71 volatile compounds were identified, 53 of which were annotated based on the GC-IMS database. These include 20 alcohols, 16 ketones, 10 aldehydes, four alkenes, one ester, one acid, and one furan. Using VOC fingerprinting and multivariate analysis, yak meats from different sources were distinctly categorized. Breed had the most significant impact on yak meat VOCs, followed by feeding method and then part. Six volatiles with a variable importance in projection value greater than one were identified as potential markers for distinguishing yak meat. This study offers insights into the flavor profile of yak meat from different sources and demonstrates the efficacy of GC-IMS and multivariate analysis in characterizing and discriminating meats.
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Affiliation(s)
- Hongqiang Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (H.L.); (S.L.); (D.T.); (X.Z.); (J.L.); (W.Y.)
| | - Bin Xi
- Laboratory of Quality & Safety Risk Assessment for Livestock Products of Ministry of Agriculture, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (B.X.); (Y.G.)
| | - Shuqin Lin
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (H.L.); (S.L.); (D.T.); (X.Z.); (J.L.); (W.Y.)
| | - Defu Tang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (H.L.); (S.L.); (D.T.); (X.Z.); (J.L.); (W.Y.)
| | - Yaqin Gao
- Laboratory of Quality & Safety Risk Assessment for Livestock Products of Ministry of Agriculture, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (B.X.); (Y.G.)
| | - Xiangmin Zhao
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (H.L.); (S.L.); (D.T.); (X.Z.); (J.L.); (W.Y.)
| | - Jing Liang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (H.L.); (S.L.); (D.T.); (X.Z.); (J.L.); (W.Y.)
| | - Wanyun Yang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (H.L.); (S.L.); (D.T.); (X.Z.); (J.L.); (W.Y.)
| | - Jinlu Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (H.L.); (S.L.); (D.T.); (X.Z.); (J.L.); (W.Y.)
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14
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Zheng Q, Wu X, Ma X, Zhou X, Wang T, Ma C, Zhang M, Chu M, Guo X, Liang C, Bao P, Yan P. Genetic structure analysis of yak breeds and their response to adaptive evolution. Genomics 2024; 116:110933. [PMID: 39218165 DOI: 10.1016/j.ygeno.2024.110933] [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: 06/25/2024] [Revised: 08/14/2024] [Accepted: 08/29/2024] [Indexed: 09/04/2024]
Abstract
Yaks are crucial genetic resources in the Tibetan Plateau and surrounding regions. Throughout the long process of domestication, natural and artificial selection pressures have enabled yaks to demonstrate adaptive characteristics to the environment in terms of physiological structure and genetic molecules, but no systematic cell analysis has been carried out on this phenomenon of yaks. Here, the population structure and genetic diversity of yak were studied by WGRS, and the genes related to yak adaptability were excavated. Combined with scRNA-seq method, the transcription map of yak lung tissue and skin tissue was constructed, which provided a new comprehensive insight into yak adaptability. The analysis of yak population structure showed that there was obvious genetic differentiation between TZ _ yak and other seven yak populations, while there was significant genetic exchange between PL _ yak and SB _ yak at high altitude. WGRS and scRNA-seq analysis revealed that the gene HIF1A related to high altitude adaptation was expressed in various cell types, while EPAS1 was predominantly expressed in epithelial and endothelial cells of yak lung tissue. Endothelial cells play a critical role in hypoxia-adapted VEGF signaling, which correlates closely with the high expression of KDR and VEGFA genes in endothelial cells and monocytes. Furthermore, in the selection signal of High _ yak vs Low _ yak, 19.8 % of the genes overlapped with the genes screened by skin scRNA-seq, including genes related to coat color such as RORA, BNC2, and KIT. Notably, BNC2 is a gene associated with melanin deposition and shows high expression levels in HS cells. Additionally, GRN in melanocytes and SORT1 in IRS play an important role in cell communication between melanocytes and IRS. These findings offer new insights into the natural polymorphism of yaks and provide a valuable reference for future research on high-altitude mammals, and potentially even human genetics.
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Affiliation(s)
- Qingbo Zheng
- 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
| | - 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
| | - 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
| | - Xuelan Zhou
- 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
| | - Tong Wang
- 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
| | - Chaofan 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
| | - Minghao Zhang
- 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
| | - Min Chu
- 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
| | - 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
| | - Pengjia Bao
- 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.
| | - 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; Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji 831100, China.
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Wang Y, Lv Y, Wang G, Liu F, Ji Y, Liu Z, Zhao W, Liu W, Dun Zhu PB, Jin K. Identification of Individuals of Two Takin Subspecies Using Biological and Ecological Criteria in Eastern Himalayas of China. Animals (Basel) 2024; 14:2426. [PMID: 39199959 PMCID: PMC11350688 DOI: 10.3390/ani14162426] [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: 07/21/2024] [Revised: 08/09/2024] [Accepted: 08/20/2024] [Indexed: 09/01/2024] Open
Abstract
Limited background data are available on the Mishmi takin (Budorcas taxicolor taxicolor) and Bhutan takin (Budorcas taxicolor whitei) subspecies in the Eastern Himalayas of China because of the lack of systematic field investigations and research. Therefore, mature-animal ecological methods were used to evaluate these takin subspecies' phenotypic characteristics, distribution range, activity rhythm, and population size. From 2013 to 2022, 214 camera traps were installed for wild ungulate monitoring and investigation in all human-accessible areas of the Eastern Himalayas, resulting in 4837 distinguishable takin photographs. The external morphological characteristics were described and compared using visual data. Artificial image correction and related technologies were used to establish physical image models based on the differences between subspecies. MaxEnt niche and random encounter models obtained distribution ranges and population densities. Mishmi takins have a distribution area of 17,314 km2, population density of 0.1729 ± 0.0134 takins/km2, and population size of 2995 ± 232. Bhutan takins have a distribution area of 25,006 km2, population density of 0.1359 ± 0.0264 takins/km2, and population size of 3398 ± 660. Long-term monitoring data confirmed that the vertical migration within the mountain ecosystems is influenced by climate. Mishmi takins are active at 500-4500 m, whereas Bhutan takins are active at 1500-4500 m. The two subspecies were active at >3500 m from May to October yearly (rainy season). In addition, surveying combined with model simulation shows that the Yarlung Zangbo River is not an obstacle to migration. This study provides basic data that contribute to animal diversity knowledge in biodiversity hotspots of the Eastern Himalayas and detailed information and references for species identification, distribution range, and population characteristics.
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Affiliation(s)
- Yuan Wang
- Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing 100091, China;
- Tibet Autonomous Region Research Institute of Forestry Inventory and Planning, Lhasa 850000, China; (Y.L.); (G.W.); (F.L.); (W.L.); (P.B.D.Z.)
- Research Institute of Natural Protected Area, Chinese Academy of Forestry, Beijing 100091, China
- Key Laboratory of Biodiversity Conservation of National Forestry and Grassland Administration, Beijing 100091, China
| | - Yonglei Lv
- Tibet Autonomous Region Research Institute of Forestry Inventory and Planning, Lhasa 850000, China; (Y.L.); (G.W.); (F.L.); (W.L.); (P.B.D.Z.)
- University of Chinese Academy of Sciences, Beijing 100000, China
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100083, China
| | - Guanglong Wang
- Tibet Autonomous Region Research Institute of Forestry Inventory and Planning, Lhasa 850000, China; (Y.L.); (G.W.); (F.L.); (W.L.); (P.B.D.Z.)
| | - Feng Liu
- Tibet Autonomous Region Research Institute of Forestry Inventory and Planning, Lhasa 850000, China; (Y.L.); (G.W.); (F.L.); (W.L.); (P.B.D.Z.)
| | - Yingxun Ji
- Forestry and Grassland Bureau of Linzhi City, Tibet Autonomous Region, Linzhi 860010, China;
| | - Zheng Liu
- Forestry and Grassland Bureau of Medog County, Tibet Autonomous Region, Medog 860799, China;
| | - Wanglin Zhao
- Medog Earth Landscape and Earth System Comprehensive Observation and Research Center, Chinese Academy of Sciences, Medog 860799, China;
| | - Wulin Liu
- Tibet Autonomous Region Research Institute of Forestry Inventory and Planning, Lhasa 850000, China; (Y.L.); (G.W.); (F.L.); (W.L.); (P.B.D.Z.)
| | - Pu Bu Dun Zhu
- Tibet Autonomous Region Research Institute of Forestry Inventory and Planning, Lhasa 850000, China; (Y.L.); (G.W.); (F.L.); (W.L.); (P.B.D.Z.)
| | - Kun Jin
- Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing 100091, China;
- Research Institute of Natural Protected Area, Chinese Academy of Forestry, Beijing 100091, China
- Key Laboratory of Biodiversity Conservation of National Forestry and Grassland Administration, Beijing 100091, China
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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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17
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Liang X, Duan Q, Li B, Wang Y, Bu Y, Zhang Y, Kuang Z, Mao L, An X, Wang H, Yang X, Wan N, Feng Z, Shen W, Miao W, Chen J, Liu S, Storz JF, Liu J, Nevo E, Li K. Genomic structural variation contributes to evolved changes in gene expression in high-altitude Tibetan sheep. Proc Natl Acad Sci U S A 2024; 121:e2322291121. [PMID: 38913905 PMCID: PMC11228492 DOI: 10.1073/pnas.2322291121] [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: 01/10/2024] [Accepted: 05/06/2024] [Indexed: 06/26/2024] Open
Abstract
Tibetan sheep were introduced to the Qinghai Tibet plateau roughly 3,000 B.P., making this species a good model for investigating genetic mechanisms of high-altitude adaptation over a relatively short timescale. Here, we characterize genomic structural variants (SVs) that distinguish Tibetan sheep from closely related, low-altitude Hu sheep, and we examine associated changes in tissue-specific gene expression. We document differentiation between the two sheep breeds in frequencies of SVs associated with genes involved in cardiac function and circulation. In Tibetan sheep, we identified high-frequency SVs in a total of 462 genes, including EPAS1, PAPSS2, and PTPRD. Single-cell RNA-Seq data and luciferase reporter assays revealed that the SVs had cis-acting effects on the expression levels of these three genes in specific tissues and cell types. In Tibetan sheep, we identified a high-frequency chromosomal inversion that exhibited modified chromatin architectures relative to the noninverted allele that predominates in Hu sheep. The inversion harbors several genes with altered expression patterns related to heart protection, brown adipocyte proliferation, angiogenesis, and DNA repair. These findings indicate that SVs represent an important source of genetic variation in gene expression and may have contributed to high-altitude adaptation in Tibetan sheep.
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Affiliation(s)
- Xiaolong Liang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou730000, China
| | - Qijiao Duan
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou730000, China
| | - Bowen Li
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou730000, China
| | - Yinjia Wang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou730000, China
| | - Yueting Bu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou730000, China
| | - Yonglu Zhang
- Fengjia Town Health Center, Rushan City, Weihai City264200, China
| | - Zhuoran Kuang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou730000, China
| | - Leyan Mao
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou730000, China
| | - Xuan An
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou730000, China
| | - Huihua Wang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing100193, China
| | - Xiaojie Yang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou730000, China
| | - Na Wan
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou730000, China
| | - Zhilong Feng
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou730000, China
| | - Wei Shen
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou730000, China
| | - Weilan Miao
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou730000, China
| | - Jiaqi Chen
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou730000, China
| | - Sanyuan Liu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou730000, China
| | - Jay F. Storz
- School of Biological Sciences, University of Nebraska, Lincoln, NE68588
| | - Jianquan Liu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou730000, China
| | - Eviatar Nevo
- Institute of Evolution, University of Haifa, Haifa3498838, Israel
| | - Kexin Li
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou730000, China
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Ding Y, Zhao F, Hu J, Zhao Z, Shi B, Li S. A conjoint analysis of renal structure and omics characteristics reveal new insight to yak high-altitude hypoxia adaptation. Genomics 2024; 116:110857. [PMID: 38729453 DOI: 10.1016/j.ygeno.2024.110857] [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: 01/23/2024] [Revised: 04/17/2024] [Accepted: 05/05/2024] [Indexed: 05/12/2024]
Abstract
BACKGROUND Yaks have unique adaptive mechanisms to the hypoxic environment, in which the kidney plays an important role. The aim of this study was to explore the histological changes of yak kidney at different altitudes and the metabolites and genes associated with adaptation to the hypoxic environment. METHODS We analyzed the tissue structure and transcriptomic metabolomic data of yak kidney tissue at two altitudes, 2600 and 4400 m. We compared and identified the morphological adaptations of the kidney and the metabolites and genes associated with hypoxia adaptation in yaks. Changes in renal morphological adaptations, differential metabolites and genes were compared and identified, combining the two in a joint analysis. RESULTS High-altitude yak kidneys showed significant adaptive changes: increased mitochondria, increased glomerular thylakoid area, and decreased localized ribosomes. Transcriptomics and metabolomics identified 69 DAMs (Differential metabolites) and 594 DEGs (differential genes). Functional enrichment analysis showed that the DAMs were associated with protein digestion and absorption, ABC transporter, and MTOR signaling pathway; the DEGs were significantly enriched in Cholesterol metabolism and P53 signaling pathway. The joint analysis indicated that metabolites such as lysine and arginine, as well as key genes such as ABCB5 and COL1A2, were particularly affected under hypoxic conditions, whereas changes in mitochondria in the tissue structure may be related to the expression of MFN1 and OPA1, and changes in glomerular thylakoid membranes are related to VEGFA and TGFB3. CONCLUSION The kidney regulates metabolites and gene expression related to hormone synthesis, protein metabolism, and angiogenesis by adjusting the mitochondrial and glomerular thylakoid membrane structure to support the survival of yaks in high-altitude environments.
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Affiliation(s)
- Yuan Ding
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Fangfang Zhao
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China.
| | - Jiang Hu
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Zhidong Zhao
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Bingang Shi
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Shaobin Li
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China.
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Yan Z, Yang J, Wei WT, Zhou ML, Mo DX, Wan X, Ma R, Wu MM, Huang JH, Liu YJ, Lv FH, Li MH. A time-resolved multi-omics atlas of transcriptional regulation in response to high-altitude hypoxia across whole-body tissues. Nat Commun 2024; 15:3970. [PMID: 38730227 PMCID: PMC11087590 DOI: 10.1038/s41467-024-48261-w] [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: 08/23/2023] [Accepted: 04/23/2024] [Indexed: 05/12/2024] Open
Abstract
High-altitude hypoxia acclimatization requires whole-body physiological regulation in highland immigrants, but the underlying genetic mechanism has not been clarified. Here we use sheep as an animal model for low-to-high altitude translocation. We generate multi-omics data including whole-genome sequences, time-resolved bulk RNA-Seq, ATAC-Seq and single-cell RNA-Seq from multiple tissues as well as phenotypic data from 20 bio-indicators. We characterize transcriptional changes of all genes in each tissue, and examine multi-tissue temporal dynamics and transcriptional interactions among genes. Particularly, we identify critical functional genes regulating the short response to hypoxia in each tissue (e.g., PARG in the cerebellum and HMOX1 in the colon). We further identify TAD-constrained cis-regulatory elements, which suppress the transcriptional activity of most genes under hypoxia. Phenotypic and transcriptional evidence indicate that antenatal hypoxia could improve hypoxia tolerance in offspring. Furthermore, we provide time-series expression data of candidate genes associated with human mountain sickness (e.g., BMPR2) and high-altitude adaptation (e.g., HIF1A). Our study provides valuable resources and insights for future hypoxia-related studies in mammals.
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Affiliation(s)
- Ze Yan
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Ji Yang
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Wen-Tian Wei
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Ming-Liang Zhou
- Sichuan Academy of Grassland Science, Chengdu, 611743, China
| | - Dong-Xin Mo
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Xing Wan
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Rui Ma
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Mei-Ming Wu
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Jia-Hui Huang
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Ya-Jing Liu
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Feng-Hua Lv
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Meng-Hua Li
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China.
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
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Chen Q, Wu B, Li C, Ding L, Huang S, Wang J, Zhao J. Deciphering male influence in gynogenetic Pengze crucian carp ( Carassius auratus var. pengsenensis): insights from Nanopore sequencing of structural variations. Front Genet 2024; 15:1392110. [PMID: 38784042 PMCID: PMC11111978 DOI: 10.3389/fgene.2024.1392110] [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: 02/27/2024] [Accepted: 04/11/2024] [Indexed: 05/25/2024] Open
Abstract
In this study, we investigate gynogenetic reproduction in Pengze Crucian Carp (Carassius auratus var. pengsenensis) using third-generation Nanopore sequencing to uncover structural variations (SVs) in offspring. Our objective was to understand the role of male genetic material in gynogenesis by examining the genomes of both parents and their offspring. We discovered a notable number of male-specific structural variations (MSSVs): 1,195 to 1,709 MSSVs in homologous offspring, accounting for approximately 0.52%-0.60% of their detected SVs, and 236 to 350 MSSVs in heterologous offspring, making up about 0.10%-0.13%. These results highlight the significant influence of male genetic material on the genetic composition of offspring, particularly in homologous pairs, challenging the traditional view of asexual reproduction. The gene annotation of MSSVs revealed their presence in critical gene regions, indicating potential functional impacts. Specifically, we found 5 MSSVs in the exonic regions of protein-coding genes in homologous offspring, suggesting possible direct effects on protein structure and function. Validation of an MSSV in the exonic region of the polyunsaturated fatty acid 5-lipoxygenase gene confirmed male genetic material transmission in some offspring. This study underscores the importance of further research on the genetic diversity and gynogenesis mechanisms, providing valuable insights for reproductive biology, aquaculture, and fostering innovation in biological research and aquaculture practices.
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Affiliation(s)
- Qianhui Chen
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Biyu Wu
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Chao Li
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Liyun Ding
- Jiangxi Fisheries Research Institute, Nanchang, China
| | - Shiting Huang
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Junjie Wang
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Jun Zhao
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Sciences, South China Normal University, Guangzhou, China
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A panoply of pangenomes. Nat Ecol Evol 2024; 8:833. [PMID: 38741009 DOI: 10.1038/s41559-024-02421-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
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Liu X, Zheng J, Ding J, Wu J, Zuo F, Zhang G. When Livestock Genomes Meet Third-Generation Sequencing Technology: From Opportunities to Applications. Genes (Basel) 2024; 15:245. [PMID: 38397234 PMCID: PMC10888458 DOI: 10.3390/genes15020245] [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: 12/23/2023] [Revised: 01/30/2024] [Accepted: 02/10/2024] [Indexed: 02/25/2024] Open
Abstract
Third-generation sequencing technology has found widespread application in the genomic, transcriptomic, and epigenetic research of both human and livestock genetics. This technology offers significant advantages in the sequencing of complex genomic regions, the identification of intricate structural variations, and the production of high-quality genomes. Its attributes, including long sequencing reads, obviation of PCR amplification, and direct determination of DNA/RNA, contribute to its efficacy. This review presents a comprehensive overview of third-generation sequencing technologies, exemplified by single-molecule real-time sequencing (SMRT) and Oxford Nanopore Technology (ONT). Emphasizing the research advancements in livestock genomics, the review delves into genome assembly, structural variation detection, transcriptome sequencing, and epigenetic investigations enabled by third-generation sequencing. A comprehensive analysis is conducted on the application and potential challenges of third-generation sequencing technology for genome detection in livestock. Beyond providing valuable insights into genome structure analysis and the identification of rare genes in livestock, the review ventures into an exploration of the genetic mechanisms underpinning exemplary traits. This review not only contributes to our understanding of the genomic landscape in livestock but also provides fresh perspectives for the advancement of research in this domain.
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Affiliation(s)
- Xinyue Liu
- College of Animal Science and Technology, Southwest University, Rongchang, Chongqing 402460, China; (X.L.); (J.Z.); (J.D.); (J.W.); (F.Z.)
| | - Junyuan Zheng
- College of Animal Science and Technology, Southwest University, Rongchang, Chongqing 402460, China; (X.L.); (J.Z.); (J.D.); (J.W.); (F.Z.)
| | - Jialan Ding
- College of Animal Science and Technology, Southwest University, Rongchang, Chongqing 402460, China; (X.L.); (J.Z.); (J.D.); (J.W.); (F.Z.)
| | - Jiaxin Wu
- College of Animal Science and Technology, Southwest University, Rongchang, Chongqing 402460, China; (X.L.); (J.Z.); (J.D.); (J.W.); (F.Z.)
| | - Fuyuan Zuo
- College of Animal Science and Technology, Southwest University, Rongchang, Chongqing 402460, China; (X.L.); (J.Z.); (J.D.); (J.W.); (F.Z.)
- Beef Cattle Engineering and Technology Research Center of Chongqing, Southwest University, Rongchang, Chongqing 402460, China
| | - Gongwei Zhang
- College of Animal Science and Technology, Southwest University, Rongchang, Chongqing 402460, China; (X.L.); (J.Z.); (J.D.); (J.W.); (F.Z.)
- Beef Cattle Engineering and Technology Research Center of Chongqing, Southwest University, Rongchang, Chongqing 402460, China
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Wang YL, Li L, Paudel BR, Zhao JL. Genomic Insights into High-Altitude Adaptation: A Comparative Analysis of Roscoea alpina and R. purpurea in the Himalayas. Int J Mol Sci 2024; 25:2265. [PMID: 38396942 PMCID: PMC10889555 DOI: 10.3390/ijms25042265] [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: 12/22/2023] [Revised: 02/05/2024] [Accepted: 02/09/2024] [Indexed: 02/25/2024] Open
Abstract
Environmental stress at high altitudes drives the development of distinct adaptive mechanisms in plants. However, studies exploring the genetic adaptive mechanisms of high-altitude plant species are scarce. In the present study, we explored the high-altitude adaptive mechanisms of plants in the Himalayas through whole-genome resequencing. We studied two widespread members of the Himalayan endemic alpine genus Roscoea (Zingiberaceae): R. alpina (a selfing species) and R. purpurea (an outcrossing species). These species are distributed widely in the Himalayas with distinct non-overlapping altitude distributions; R. alpina is distributed at higher elevations, and R. purpurea occurs at lower elevations. Compared to R. purpurea, R. alpina exhibited higher levels of linkage disequilibrium, Tajima's D, and inbreeding coefficient, as well as lower recombination rates and genetic diversity. Approximately 96.3% of the genes in the reference genome underwent significant genetic divergence (FST ≥ 0.25). We reported 58 completely divergent genes (FST = 1), of which only 17 genes were annotated with specific functions. The functions of these genes were primarily related to adapting to the specific characteristics of high-altitude environments. Our findings provide novel insights into how evolutionary innovations promote the adaptation of mountain alpine species to high altitudes and harsh habitats.
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Affiliation(s)
- Ya-Li Wang
- Ministry of Education Key Laboratory for Transboundary Ecosecurity of Southwest China, Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology and Centre for Invasion Biology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming 650504, China; (Y.-L.W.); (L.L.)
| | - Li Li
- Ministry of Education Key Laboratory for Transboundary Ecosecurity of Southwest China, Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology and Centre for Invasion Biology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming 650504, China; (Y.-L.W.); (L.L.)
| | - Babu Ram Paudel
- Research Centre for Applied Science and Technology, Tribhuvan University, Kirtipur 44613, Nepal
| | - Jian-Li Zhao
- Ministry of Education Key Laboratory for Transboundary Ecosecurity of Southwest China, Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology and Centre for Invasion Biology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming 650504, China; (Y.-L.W.); (L.L.)
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Feng S, Zhang Y, He Z, Xi E, Ru D, Liang J, Yang Y. Chromosome-scale genome assembly of Lepus oiostolus (Lepus, Leporidae). Sci Data 2024; 11:183. [PMID: 38341484 PMCID: PMC10858874 DOI: 10.1038/s41597-024-03024-6] [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: 11/14/2023] [Accepted: 01/30/2024] [Indexed: 02/12/2024] Open
Abstract
Lepus oiostolus (L. oiostolus) is a species endemic to the Qinghai-Tibet Plateau. However, the absence of a reference genome limits genetic studies. Here, we reported a high-quality L. oiostolus genome assembly, with scaffolds anchored to 24 chromosomes and a total assembled length of 2.80 Gb (contig N50 = 64.25 Mb). Genomic annotation uncovered 22,295 protein-coding genes and identified 49.84% of the sequences as transposable elements. Long interspersed nuclear elements (LINEs) constitute a high proportion of the genome. Our study is at the first time to report the chromosome-scale genome for the species of the L. oiostolus. It provides a valuable genomic resource for future research on the evolution of the Leporidae.
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Affiliation(s)
- Shuo Feng
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810016, China.
| | - Yaying Zhang
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810016, China
| | - Zhaotong He
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810016, China
| | - Erning Xi
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810016, China
| | - Dafu Ru
- State Key Laboratory of Grassland Agro-Ecosystems, and College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Jian Liang
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810016, China
| | - Yongzhi Yang
- State Key Laboratory of Grassland Agro-Ecosystems, and College of Ecology, Lanzhou University, Lanzhou, 730000, China
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