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Hu Z, Su Y, Zong W, Niu N, Zhao R, Liang R, Wang L, Zhang Y, Zhang L. Unveiling the Genetic Secrets of Chinese Indigenous Pigs from Guizhou Province: Diversity, Evolution and Candidate Genes Affecting Pig Coat Color. Animals (Basel) 2024; 14:699. [PMID: 38473084 DOI: 10.3390/ani14050699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 01/27/2024] [Accepted: 02/10/2024] [Indexed: 03/14/2024] Open
Abstract
The local pig breeds in Guizhou possess exceptional meat quality, robust adaptability, and resilience to harsh feeding conditions, making them ideal for producing high-quality pork. With over 10 local pig breeds in the region, we focused on 7 specific breeds: Baixi pigs (BX), Congjiang Xiang pigs (CJX), Guanling pigs (GL), Jianhe White Xiang pigs (JHBX), Jiangkou Luobo pigs (JKLB), Kele pigs (KL), and Qiandong Hua pigs (QDH). Unfortunately, these breeds face threats such as introduced species and inbreeding, resulting in a decline in population size and numbers. To better protect and utilize these breeds, we employed genome-wide single-nucleotide polymorphism (SNP) markers to investigate the population structure, genetic diversity, and selection characteristics of 283 pigs across these seven breeds. Our findings revealed distinct ancestral sources between Chinese and Western pig breeds, as demonstrated by principal component analysis, adjacent tree analysis, and ADMIXTURE analysis. Notably, JHBX exhibited a distant genetic relationship from the other six local pig breeds in Guizhou province, showcasing unique genetic characteristics. While the genetic diversity of the six Chinese native pig populations, excluding JHBX, was generally moderate in Guizhou province, the JHBX population displayed low genetic diversity. Therefore, it is imperative to intensify selection efforts to prevent inbreeding decline in JHBX while further enhancing the protection measures for the other six pig populations. Additionally, we identified candidate genes influencing the size disparity among pigs in Guizhou province through signal selection. Our study outcomes serve as a reference for developing effective conservation and utilization plans for pig breeds in Guizhou province and deepen our understanding of the genetic mechanisms underlying pig body size.
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Affiliation(s)
- Ziping Hu
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao 266109, China
| | - Yanfang Su
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
| | - Wencheng Zong
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
| | - Naiqi Niu
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
| | - Runze Zhao
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
| | - Ruiping Liang
- Beijing Changping District Center for Animal Disease Prevention and Control, Beijing 102200, China
| | - Lixian Wang
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao 266109, China
| | - Yiyu Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, College of Animal Science, Guizhou University, Guiyang 550025, China
| | - Longchao Zhang
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
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Zou J, Shen G, Qiang W, Zhu YY, Li WX. Study on the polymorphisms of HLA-ABCDQB1DRB1 alleles and haplotypes in Hubei Han population of China. Int J Immunogenet 2020; 48:8-15. [PMID: 32996280 DOI: 10.1111/iji.12516] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 09/02/2020] [Accepted: 09/04/2020] [Indexed: 11/30/2022]
Abstract
The present study aimed to analyse the frequencies of human leukocyte antigen HLA-ABCDQB1 and HLA-DRB1 alleles and haplotypes in a subset of 3,732 Han population from Hubei of China. All samples were typed in the HLA-ABCDQB1 and HLA-DRB1 loci using the sequence-based typing method; subsequently, the HLA polymorphisms were analysed. A total of 47 HLA-A, 89 HLA-B, 43 HLA-C, 49 HLA-DRB1 and 24 HLA-DQB1 alleles were identified in the Hubei Han population. The top three most frequent alleles in the HLA-ABCDQB1 and HLA-DRB1 were A*11:01 (0.2617), A*24:02 (0.1590), A*02:07 (0.1281); B*46:01 (0.1502), B*40:01 (0.1409) and B*58:01 (0.0616); C*01:02 (0.2023), C*07:02 (0.1691) and C*03:04 (0.1175); and DQB1*03:01 (0.2000), DQB1*03:03 (0.1900), DQB1*06:01 (0.1187); DRB1*09:01 (0.1790), DRB1*15:01 (0.1062) and DRB1*12:02 (0.0841), respectively. Meanwhile, the three most frequent two-loci haplotypes were A*02:07-C*01:02 (0.0929), B*46:01-C*01:02 (0.1366) and DQB1*03:03-DRB1*09:01 (0.1766). The three most frequent three-loci haplotypes were A*02:07-B*46:01-C*01:02 (0.0883), B*46:01-DQB1*03:03-DRB1*09:01 (0.0808) and C*01:02-DQB1*03:03-DRB1*09:01 (0.0837). The three most frequent four-loci haplotypes were A*02:07-B*46:01-C*01:02-DQB1*03:03 (0.0494), B*46:01-DRB1*09:01-C*01:02-DQB1*03:03 (0.0729) and A*02:07-B*46:01-DQB1*03:03-DRB1*09:01 (0.0501). The most frequent five-loci haplotype was A*02:07-B*46:01-C*01:02-DQB1*03:03-DRB1*09:01 (0.0487). Heat maps and multiple correspondence analysis based on the frequencies of HLA specificity indicated that the Hubei Han population might be described into Southern Chinese populations. Our results lay a certain foundation for future population studies, disease association studies and donor recruitment strategies.
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Affiliation(s)
- Jie Zou
- HLA Typing Laboratory, Wuhan Blood Center, Wuhan, China
| | - Gang Shen
- HLA Typing Laboratory, Wuhan Blood Center, Wuhan, China
| | - Wen Qiang
- HLA Typing Laboratory, Wuhan Blood Center, Wuhan, China
| | - Yuan Yan Zhu
- HLA Typing Laboratory, Wuhan Blood Center, Wuhan, China
| | - Wang Xia Li
- HLA Typing Laboratory, Wuhan Blood Center, Wuhan, China
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Zou X, Wang Z, He G, Wang M, Su Y, Liu J, Chen P, Wang S, Gao B, Li Z, Hou Y. Population Genetic Diversity and Phylogenetic Characteristics for High-Altitude Adaptive Kham Tibetan Revealed by DNATyper TM 19 Amplification System. Front Genet 2018; 9:630. [PMID: 30619458 PMCID: PMC6304359 DOI: 10.3389/fgene.2018.00630] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 11/26/2018] [Indexed: 11/13/2022] Open
Abstract
Tibetans residing in the high-altitude inhospitable environment have undergone significant natural selection of their genetic architecture. Recently, highly mutational autosomal short tandem repeats were widely used not only in the anthropology and population genetics to investigate the genetic structure and relationships, but also in the medical genetics to explore the pathogenesis of multiple genetic diseases and in the forensic science to identify individual and parentage relatedness. However, genetic variants and forensic efficiency of DNATyperTM 19 amplification system and genetic background of Kham Tibetan remain uncharacterized. Thus, we genotyped 19 forensic genetic markers in 11,402 Kham Tibetans to gain insight into the genetic diversity of Chinese high-altitude adaptive population. Highly discriminating and polymorphic forensic measures were observed, which indicated that this new-developed DNATyper 19 PCR amplification is suitable for routine forensic identification purposes and Chinese national DNA database establishment. Pairwise genetic distances among the comprehensive population comparisons suggested that this high-altitude adaptive Kham Tibetan has genetically closer relationships with lowlanders of Tibeto-Burman-speaking populations (Chengdu Tibetan, Liangshan Tibetan, and Liangshan Yi). Genetic substructure analyses via phylogenetic reconstruction, principal component analysis, and multidimensional scaling analysis in both nationwide and worldwide contexts suggested that the genetic proximity exists along the linguistic, ethnic, and continental geographical boundary. Further studies with whole-genome sequencing of modern or archaic Kham Tibetans would be useful in reconstructing the Tibetan population history.
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Affiliation(s)
- Xing Zou
- Institute of Forensic Medicine, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Zheng Wang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Guanglin He
- Institute of Forensic Medicine, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Mengge Wang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Yongdong Su
- Forensic Identification Center, Public Security Bureau of Tibet Autonomous Region, Lhasa, China
| | - Jing Liu
- Institute of Forensic Medicine, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Pengyu Chen
- Center of Forensic Expertise, Affiliated Hospital of Zunyi Medical University, Zunyi, China.,School of Forensic Medicine, Zunyi Medical University, Zunyi, China
| | - Shouyu Wang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Bo Gao
- Institute of Forensic Science, Yili Public Security Bureau of Xinjiang, Kuytun, China
| | - Zhao Li
- Department of Criminal Investigation, Mianyang Public Security Bureau, Mianyang, China
| | - Yiping Hou
- Institute of Forensic Medicine, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
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Wang X, Wang C, Huang M, Tang J, Fan Y, Li Y, Li X, Ji H, Ren J, Ding N. Genetic diversity, population structure and phylogenetic relationships of three indigenous pig breeds from Jiangxi Province, China, in a worldwide panel of pigs. Anim Genet 2018; 49:275-283. [PMID: 29993136 DOI: 10.1111/age.12687] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/15/2018] [Indexed: 01/08/2023]
Abstract
Dongxiang Spotted, Pingxiang Two-End-Black and Yushan Black pigs are three indigenous breeds in Jiangxi Province, China, that have been listed in the national conservation program for Chinese indigenous livestock germplasm. Here, we investigated the genetic diversity and population structure of the nucleus populations of these three breeds in a worldwide context of European and Chinese pigs using Illumina Porcine 60K chips. Our data indicate that Dongxiang Spotted and Yushan Black pigs have recently experienced severe inbreeding. The two breeds show large runs-of-homozygosity values, long-range extents of linkage disequilibrium and reduced observed heterozygosity. In contrast, Pingxiang Two-End-Black pigs are rich in genetic diversity and have few inbred individuals. Both phylogenetic and admixture analyses illustrate that Dongxiang Spotted and Yushan Black pigs are genetically close to their geographical neighbors in East China and that Pingxiang Two-End-Black pigs have a close relationship with three other Two-End-Black breeds in central China. Finally, we reconstructed the family structures of the three breeds and propose a reliable breeding strategy to better conserve these breeds.
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Affiliation(s)
- X Wang
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, 330045, Nanchang, China
| | - C Wang
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, 330045, Nanchang, China
| | - M Huang
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, 330045, Nanchang, China
| | - J Tang
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, 330045, Nanchang, China
| | - Y Fan
- Department of Animal Science, Jiangxi Biotech Vocational College, 330200, Nanchang, China
| | - Y Li
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, 330045, Nanchang, China
| | - X Li
- Unit of Animal Genetics and Breeding, Institute of Animal Science of Pingxiang, Pingxiang, 347850, China
| | - H Ji
- Institute of Animal Husbandry and Veterinary, Jiangxi Academy of Agricultural Sciences, Nanchang, 330200, China
| | - J Ren
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, 330045, Nanchang, China
| | - N Ding
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, 330045, Nanchang, China
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Shao LN, Zhang ST, Yu WJ, Zhou SH, Duan Y, Pan LZ, Wang N, Liu M. High-resolution HLA-A, -B and -DRB1 allele and haplotype frequencies in 7823 Han marrow donors of Liaoning province, China. HLA 2017; 89:293-300. [PMID: 28296231 DOI: 10.1111/tan.13006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Revised: 01/29/2017] [Accepted: 02/15/2017] [Indexed: 11/28/2022]
Abstract
BACKGROUND The human leukocyte antigen (HLA) system is the most polymorphic gene cluster in humans. High-resolution donor-recipient matching for HLA genes improves patient survival after unrelated hematopoietic stem cell transplantation. MATERIALS AND METHODS In this study, we analyzed the high-resolution allele and haplotype frequencies at the HLA-A, -B and -DRB1 loci in the Liaoning Han population and analyzed its relationships with other populations. RESULTS The 3 most frequent alleles at the HLA-A, -B and -DRB1 loci were A*24:02, A*02:01:01G, A*11:01; B*13:02, B*46:01, B*40:01:01G; DRB1*09:01, DRB1*15:01 and DRB1*07:01, respectively. The most frequent 2-locus haplotypes were A*30:01-B*13:02 and B*13:02-DRB1*07:01. A*30:01-B*13:02-DRB1*07:01 was determined to be the predominant 3-locus haplotype. Hot maps and multiple correspondence analyses based on the frequencies of HLA specificities, which allow statistical visualization of dependent and independent relationships among variables, indicate that the Liaoning Han population is closely related to Northern populations of China and shows relative close relationships with Asian populations. CONCLUSION These data will provide an outline of the HLA characteristics of healthy individuals in our region and help bone marrow transplantation patients find suitable HLA-matched donors.
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Affiliation(s)
- L-N Shao
- Dalian Blood Center, Dalian, Liaoning, China
| | - S-T Zhang
- Dalian Blood Center, Dalian, Liaoning, China
| | - W-J Yu
- Dalian Blood Center, Dalian, Liaoning, China
| | - S-H Zhou
- Dalian Blood Center, Dalian, Liaoning, China
| | - Y Duan
- Dalian Blood Center, Dalian, Liaoning, China
| | - L-Z Pan
- Dalian Blood Center, Dalian, Liaoning, China
| | - N Wang
- Dalian Blood Center, Dalian, Liaoning, China
| | - M Liu
- Department of Cell Biology, Dalian Medical University, Dalian, China
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