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Zhao QB, Oyelami FO, Qadri QR, Sun H, Xu Z, Wang QS, Pan YC. Identifying the unique characteristics of the Chinese indigenous pig breeds in the Yangtze River Delta region for precise conservation. BMC Genomics 2021; 22:151. [PMID: 33653278 PMCID: PMC7927379 DOI: 10.1186/s12864-021-07476-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Accepted: 02/24/2021] [Indexed: 02/08/2023] Open
Abstract
Background China is the country with the most abundant swine genetic resources in the world. Through thousands of years of domestication and natural selection, most of pigs in China have developed unique genetic characteristics. Finding the unique genetic characteristics and modules of each breed is an essential part of their precise conservation. Results In this study, we used the partial least squares method to identify the significant specific SNPs of 19 local Chinese pig breeds and 5 Western pig breeds. A total of 37,514 significant specific SNPs (p < 0.01) were obtained from these breeds, and the Chinese local pig breed with the most significant SNPs was Hongdenglong (HD), followed by Jiaxing black (JX), Huaibei (HB), Bihu (BH), small Meishan (SMS), Shengxian Hua (SH), Jiangquhai (JQ), Mi (MI), Chunan (CA), Chalu (CL), Jinhualiangtouwu (JHL), Fengjing (FJ), middle Meishan (MMS), Shanzhu (SZ), Pudong white (PD), Dongchuan (DC), Erhualian (EH), Shawutou (SW) and Lanxi Hua (LX) pig. Furthermore, we identified the breeds with the most significant genes, GO terms, pathways, and networks using KOBAS and IPA and then ranked them separately. The results showed that the breeds with the highest number of interaction networks were Hongdenglong (12) and Huaibei (12) pigs. In contrast, the breeds with the lowest interaction networks were Shawutou (4) and Lanxi Hua pigs (3), indicating that Hongdenglong and Huaibei pigs might have the most significant genetic modules in their genome, whereas Shawutou and Lanxi Hua pigs may have the least unique characteristics. To some degree, the identified specific pathways and networks are related to the number of genes and SNPs linked to the specific breeds, but they do not appear to be the same. Most importantly, more significant modules were found to be related to the development and function of the digestive system, regulation of diseases, and metabolism of amino acids in the local Chinese pig breeds, whereas more significant modules were found to be related to the growth rate in the Western pig breeds. Conclusion Our results show that each breed has some relatively unique structural modules and functional characteristics. These modules allow us to better understand the genetic differences among local Chinese and Western pig breeds and therefore implement precise conservation methods. This study could provide a basis for formulating more effective strategies for managing and protecting these genetic resources in the future. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07476-7.
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Affiliation(s)
- Qing-Bo Zhao
- School of Agriculture and Biology, Department of Animal Science, Shanghai Jiao Tong University, Shanghai, 200240, P.R. China
| | - Favour Oluwapelumi Oyelami
- School of Agriculture and Biology, Department of Animal Science, Shanghai Jiao Tong University, Shanghai, 200240, P.R. China
| | - Qamar Raza Qadri
- School of Agriculture and Biology, Department of Animal Science, Shanghai Jiao Tong University, Shanghai, 200240, P.R. China
| | - Hao Sun
- School of Agriculture and Biology, Department of Animal Science, Shanghai Jiao Tong University, Shanghai, 200240, P.R. China
| | - Zhong Xu
- School of Agriculture and Biology, Department of Animal Science, Shanghai Jiao Tong University, Shanghai, 200240, P.R. China
| | - Qi-Shan Wang
- Department of Animal Breeding and Reproduction, College of Animal Science, Zhejiang University, Hangzhou, 310030, P.R. China.
| | - Yu-Chun Pan
- Department of Animal Breeding and Reproduction, College of Animal Science, Zhejiang University, Hangzhou, 310030, P.R. China.
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Oyelami FO, Zhao Q, Xu Z, Zhang Z, Sun H, Zhang Z, Ma P, Wang Q, Pan Y. Haplotype Block Analysis Reveals Candidate Genes and QTLs for Meat Quality and Disease Resistance in Chinese Jiangquhai Pig Breed. Front Genet 2020; 11:752. [PMID: 33101353 PMCID: PMC7498712 DOI: 10.3389/fgene.2020.00752] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Accepted: 06/23/2020] [Indexed: 11/19/2022] Open
Abstract
The Jiangquhai (JQ) pig breed is one of the most widely recognized pig populations in China due to its unique and dominant characteristics. In this study, we examined the extent of Linkage disequilibrium (LD) and haplotype block structure of the JQ pig breed, and scanned the blocks for possible genes underlying important QTLs that could either be responsible for some adaptive features in these pigs or might have undergone some selection pressure. We compared some of our results with other Chinese and Western pig breeds. The results show that the JQ breed had the highest total block length (349.73 Mb ≈ 15% of its genome), and the coverage rate of blocks in most of its chromosomes was larger than those of other breeds except for Sus scrofa chromosome 4 (SSC4), SSC6, SSC7, SSC8, SSC10, SSC12, SSC13, SSC14, SSC17, SSC18, and SSCX. Moreover, the JQ breed had more SNPs that were clustered into haplotype blocks than the other breeds examined in this study. Our shared and unique haplotype block analysis revealed that the Hongdenglong (HD) breed had the lowest percentage of shared haplotype blocks while the Shanzhu (SZ) breed had the highest. We found that the JQ breed had an average r2 > 0.2 at SNPs distances 10–20 kb and concluded that about 120,000–240,000 SNPs would be needed for a successful GWAS in the breed. Finally, we detected a total of 88 genes harbored by selected haplotype blocks in the JQ breed, of which only 4 were significantly enriched (p-value ≤ 0.05). These genes were significantly enriched in 2 GO terms (p-value < 0.01), and 2 KEGG pathways (p-value < 0.02). Most of these enriched genes were related to health. Also, most of the overlapping QTLs detected in the haplotype blocks were related to meat and carcass quality, as well as health, with a few of them relating to reproduction and production. These results provide insights into the genetic architecture of some adaptive and meat quality traits observed in the JQ pig breed and also revealed the pattern of LD in the genome of the pig. Our result provides significant guidance for improving the statistical power of GWAS and optimizing the conservation strategy for this JQ pig breed.
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Affiliation(s)
- Favour Oluwapelumi Oyelami
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Qingbo Zhao
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Zhong Xu
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Zhe Zhang
- Department of Animal Breeding and Reproduction, College of Animal Science, Zhejiang University, Hangzhou, China
| | - Hao Sun
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Zhenyang Zhang
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Peipei Ma
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Qishan Wang
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China.,Department of Animal Breeding and Reproduction, College of Animal Science, Zhejiang University, Hangzhou, China
| | - Yuchun Pan
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China.,Department of Animal Breeding and Reproduction, College of Animal Science, Zhejiang University, Hangzhou, China
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Liu C, Li P, Zhou W, Ma X, Wang X, Xu Y, Jiang N, Zhao M, Zhou T, Yin Y, Ren J, Huang R. Genome Data Uncover Conservation Status, Historical Relatedness and Candidate Genes Under Selection in Chinese Indigenous Pigs in the Taihu Lake Region. Front Genet 2020; 11:591. [PMID: 32582299 PMCID: PMC7296076 DOI: 10.3389/fgene.2020.00591] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 05/15/2020] [Indexed: 12/17/2022] Open
Abstract
Chinese indigenous pig breeds in the Taihu Lake (TL) region of Eastern China are well documented by their exceptional prolificacy. There are seven breeds in this region including Meishan (MS), Erhualian (EHL), Jiaxing Black (JXB), Fengjing (FJ), Shawutou (SWT), Mi (MI), and Hongdenglong (HDL). At present, these breeds are facing a great threat of population decline, inbreeding depression and lineage admixture since Western commercial pigs have dominated in Chinese pig industry. To provide better conservation strategies and identify candidate genes under selection for these breeds, we explored genome-wide single nucleotide polymorphism (SNP) markers to uncover genetic variability and relatedness, population structure, historical admixture and genomic signature of selection of 440 pigs representing the most comprehensive lineages of these breeds in TL region in a context of 1228 pigs from 45 Eurasian breeds. We showed that these breeds were more closely related to each other as compared to other Eurasian breeds, defining one of the main ancestral lineages of Chinese indigenous pigs. These breeds can be divided into two subgroups, one including JXB and FJ, and the other comprising of EHL, MI, HDL, MS, and SWT. In addition, HDL was highly inbred whereas EHL and MS had more abundant genetic diversity owing to their multiple conservation populations. Moreover, we identified a list of candidate genes under selection for body size and prolificacy. Our results would benefit the conservation of these valuable breeds and improve our understanding of the genetic mechanisms of body size and fecundity in pigs.
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Affiliation(s)
- Chenxi Liu
- Institute of Swine Science, Nanjing Agricultural University, Nanjing, China
| | - Pinghua Li
- Institute of Swine Science, Nanjing Agricultural University, Nanjing, China.,Huaian Academy, Nanjing Agricultural University, Huaian, China
| | - Wuduo Zhou
- Institute of Swine Science, Nanjing Agricultural University, Nanjing, China
| | - Xiang Ma
- Institute of Swine Science, Nanjing Agricultural University, Nanjing, China
| | - Xiaopeng Wang
- College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Yan Xu
- Jiangsu Provincial Station of Animal Husbandry, Nanjing, China
| | - Nengjing Jiang
- Institute of Swine Science, Nanjing Agricultural University, Nanjing, China
| | - Moran Zhao
- Institute of Swine Science, Nanjing Agricultural University, Nanjing, China
| | - Tianwei Zhou
- Institute of Swine Science, Nanjing Agricultural University, Nanjing, China
| | - Yanzhen Yin
- Institute of Swine Science, Nanjing Agricultural University, Nanjing, China
| | - Jun Ren
- College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Ruihua Huang
- Institute of Swine Science, Nanjing Agricultural University, Nanjing, China.,Huaian Academy, Nanjing Agricultural University, Huaian, China
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Zhao P, Yu Y, Feng W, Du H, Yu J, Kang H, Zheng X, Wang Z, Liu GE, Ernst CW, Ran X, Wang J, Liu JF. Evidence of evolutionary history and selective sweeps in the genome of Meishan pig reveals its genetic and phenotypic characterization. Gigascience 2018; 7:5001425. [PMID: 29790964 PMCID: PMC6007440 DOI: 10.1093/gigascience/giy058] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2018] [Accepted: 05/11/2018] [Indexed: 12/18/2022] Open
Abstract
Background Meishan is a pig breed indigenous to China and famous for its high fecundity. The traits of Meishan are strongly associated with its distinct evolutionary history and domestication. However, the genomic evidence linking the domestication of Meishan pigs with its unique features is still poorly understood. The goal of this study is to investigate the genomic signatures and evolutionary evidence related to the phenotypic traits of Meishan via large-scale sequencing. Results We found that the unique domestication of Meishan pigs occurred in the Taihu Basin area between the Majiabang and Liangzhu Cultures, during which 300 protein-coding genes have underwent positive selection. Notably, enrichment of the FoxO signaling pathway with significant enrichment signal and the harbored gene IGF1R were likely associated with the high fertility of Meishan pigs. Moreover, NFKB1 exhibited strong selective sweep signals and positively participated in hyaluronan biosynthesis as the key gene of NF-kB signaling, which may have resulted in the wrinkled skin and face of Meishan pigs. Particularly, three population-specific synonymous single-nucleotide variants occurred in PYROXD1, MC1R, and FAM83G genes; the T305C substitution in the MCIR gene explained the black coat of the Meishan pigs well. In addition, the shared haplotypes between Meishan and Duroc breeds confirmed the previous Asian-derived introgression and demonstrated the specific contribution of Meishan pigs. Conclusions These findings will help us explain the unique genetic and phenotypic characteristics of Meishan pigs and offer a plausible method for their utilization of Meishan pigs as valuable genetic resources in pig breeding and as an animal model for human wrinkled skin disease research.
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Affiliation(s)
- Pengju Zhao
- National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding, and Reproduction, Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Ying Yu
- National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding, and Reproduction, Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Wen Feng
- National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding, and Reproduction, Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Heng Du
- National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding, and Reproduction, Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Jian Yu
- National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding, and Reproduction, Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Huimin Kang
- National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding, and Reproduction, Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Xianrui Zheng
- National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding, and Reproduction, Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Zhiquan Wang
- Department of Agricultural, Food & Nutritional Science, University of Alberta, Edmonton, T6G 2C8, Canada
| | - George E Liu
- Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Beltsville, MD 20705-2350, USA
| | | | - Xueqin Ran
- School of Animal Science, Guizhou University, Guiyang, 550025, China
| | - Jiafu Wang
- School of Animal Science, Guizhou University, Guiyang, 550025, China
| | - Jian-Feng Liu
- National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding, and Reproduction, Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
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Zhang Z, Zhang Q, Xiao Q, Sun H, Gao H, Yang Y, Chen J, Li Z, Xue M, Ma P, Yang H, Xu N, Wang Q, Pan Y. Distribution of runs of homozygosity in Chinese and Western pig breeds evaluated by reduced-representation sequencing data. Anim Genet 2018; 49:579-591. [DOI: 10.1111/age.12730] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/28/2018] [Indexed: 02/02/2023]
Affiliation(s)
- Zhe Zhang
- Department of Animal Science; School of Agriculture and Biology; Shanghai Jiao Tong University; Shanghai 200240 China
- Shanghai Key Laboratory of Veterinary Biotechnology; Shanghai 200240 China
| | - Qianqian Zhang
- Animal Genetics, Bioinformatics and Breeding; University of Copenhagen; Frederiksberg 1870 Denmark
| | - Qian Xiao
- Department of Animal Science; School of Agriculture and Biology; Shanghai Jiao Tong University; Shanghai 200240 China
- Shanghai Key Laboratory of Veterinary Biotechnology; Shanghai 200240 China
| | - Hao Sun
- Department of Animal Science; School of Agriculture and Biology; Shanghai Jiao Tong University; Shanghai 200240 China
- Shanghai Key Laboratory of Veterinary Biotechnology; Shanghai 200240 China
| | - Hongding Gao
- Center for Quantitative Genetics and Genomics; Department of Molecular Biology and Genetics; Aarhus University; 8830 Tjele Denmark
| | - Yumei Yang
- Department of Animal Science; School of Agriculture and Biology; Shanghai Jiao Tong University; Shanghai 200240 China
- Shanghai Key Laboratory of Veterinary Biotechnology; Shanghai 200240 China
| | - Jiucheng Chen
- College of Animal Sciences; Zhejiang University; Hangzhou 310058 China
| | - Zhengcao Li
- College of Animal Sciences; Zhejiang University; Hangzhou 310058 China
| | - Ming Xue
- National Station of Animal Husbandry; Beijing 100125 China
| | - Peipei Ma
- Department of Animal Science; School of Agriculture and Biology; Shanghai Jiao Tong University; Shanghai 200240 China
- Shanghai Key Laboratory of Veterinary Biotechnology; Shanghai 200240 China
| | - Hongjie Yang
- National Station of Animal Husbandry; Beijing 100125 China
| | - Ningying Xu
- College of Animal Sciences; Zhejiang University; Hangzhou 310058 China
| | - Qishan Wang
- Department of Animal Science; School of Agriculture and Biology; Shanghai Jiao Tong University; Shanghai 200240 China
- Shanghai Key Laboratory of Veterinary Biotechnology; Shanghai 200240 China
| | - Yuchun Pan
- Department of Animal Science; School of Agriculture and Biology; Shanghai Jiao Tong University; Shanghai 200240 China
- Shanghai Key Laboratory of Veterinary Biotechnology; Shanghai 200240 China
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6
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Genomic analysis reveals genes affecting distinct phenotypes among different Chinese and western pig breeds. Sci Rep 2018; 8:13352. [PMID: 30190566 PMCID: PMC6127261 DOI: 10.1038/s41598-018-31802-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 08/21/2018] [Indexed: 01/04/2023] Open
Abstract
The differences in artificial and natural selection have been some of the factors contributing to phenotypic diversity between Chinese and western pigs. Here, 830 individuals from western and Chinese pig breeds were genotyped using the reduced-representation genotyping method. First, we identified the selection signatures for different pig breeds. By comparing Chinese pigs and western pigs along the first principal component, the growth gene IGF1R; the immune genes IL1R1, IL1RL1, DUSP10, RAC3 and SWAP70; the meat quality-related gene SNORA50 and the olfactory gene OR1F1 were identified as candidate differentiated targets. Further, along a principal component separating Pudong White pigs from others, a potential causal gene for coat colour (EDNRB) was discovered. In addition, the divergent signatures evaluated by Fst within Chinese pig breeds found genes associated with the phenotypic features of coat colour, meat quality and feed efficiency among these indigenous pigs. Second, admixture and genomic introgression analysis were performed. Shan pigs have introgressed genes from Berkshire, Yorkshire and Hongdenglong pigs. The results of introgression mapping showed that this introgression conferred adaption to the local environment and coat colour of Chinese pigs and the superior productivity of western pigs.
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