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Xie X, Shi L, Zhong Z, Wang Z, Pan D, Hou G, Xiao Q. Danzhou chicken: a unique genetic resource revealed by genome-wide resequencing data. Poult Sci 2024; 103:103960. [PMID: 38964270 PMCID: PMC11278292 DOI: 10.1016/j.psj.2024.103960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 05/27/2024] [Accepted: 06/04/2024] [Indexed: 07/06/2024] Open
Abstract
Danzhou chicken (DZ) is a local breed in China noted for its strong adaptability, roughage resistance, strong wildness, and delicious taste, thus containing important genetic resources. In this study, genome re-sequencing data was generated from 200 DZ chickens. Combined with previously generated data from 72 additional chickens across six other exotic and local breeds, these data were used to systematically evaluate the germplasm characteristics of DZ chickens from a genomic perspective. Unlike exotic breeds, both DZ and southern local chicken varieties exhibited high genetic diversity, and the genetic distance between DZ and southern local chickens was smaller than the genetic distance between DZ and exotic chickens. A reconstructed Neighbor-Joining phylogenetic tree indicated that all sampled populations clustered into single independent populations, with DZ chickens showing clear evidence of intra-population differentiation, forming 2 subpopulations. Principal component analysis and ADMIXTURE analysis showed that DZ was significantly different from other breeds. These results indicate that DZ is a unique genetic resource that is different from other southern native and exotic chickens. The results of the study will improve our understanding of the genetic structure and current status of the DZ breed, which is of great significance in promoting the conservation of genetic resources of DZ chickens and fostering breed innovations and genetic improvement.
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Affiliation(s)
- Xinfeng Xie
- School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
| | - Liguang Shi
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan 571101, China
| | - Ziqi Zhong
- School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
| | - Ziyi Wang
- School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
| | - Deyou Pan
- School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
| | - Guanyu Hou
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan 571101, China
| | - Qian Xiao
- School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China.
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2
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Zhong Z, Wang Z, Xie X, Tian S, Wang F, Wang Q, Ni S, Pan Y, Xiao Q. Evaluation of the Genetic Diversity, Population Structure and Selection Signatures of Three Native Chinese Pig Populations. Animals (Basel) 2023; 13:2010. [PMID: 37370521 DOI: 10.3390/ani13122010] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 06/12/2023] [Accepted: 06/15/2023] [Indexed: 06/29/2023] Open
Abstract
Indigenous pig populations in Hainan Province live in tropical climate conditions and a relatively closed geographical environment, which has contributed to the formation of some excellent characteristics, such as heat tolerance, strong disease resistance and excellent meat quality. Over the past few decades, the number of these pig populations has decreased sharply, largely due to a decrease in growth rate and poor lean meat percentage. For effective conservation of these genetic resources (such as heat tolerance, meat quality and disease resistance), the whole-genome sequencing data of 78 individuals from 3 native Chinese pig populations, including Wuzhishan (WZS), Tunchang (TC) and Dingan (DA), were obtained using a 150 bp paired-end platform, and 25 individuals from two foreign breeds, including Landrace (LR) and Large White (LW), were downloaded from a public database. A total of 28,384,282 SNPs were identified, of which 27,134,233 SNPs were identified in native Chinese pig populations. Both genetic diversity statistics and linkage disequilibrium (LD) analysis indicated that indigenous pig populations displayed high genetic diversity. The result of population structure implied the uniqueness of each native Chinese pig population. The selection signatures were detected between indigenous pig populations and foreign breeds by using the population differentiation index (FST) method. A total of 359 candidate genes were identified, and some genes may affect characteristics such as immunity (IL-2, IL-21 and ZFYVE16), adaptability (APBA1), reproduction (FGF2, RNF17, ADAD1 and HIPK4), meat quality (ABCA1, ADIG, TLE4 and IRX5), and heat tolerance (VPS13A, HSPA4). Overall, the findings of this study will provide some valuable insights for the future breeding, conservation and utilization of these three Chinese indigenous pig populations.
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Affiliation(s)
- Ziqi Zhong
- Hainan Key Laboratory of Tropical Animal Reproduction & Breeding and Epidemic Disease Research, College of Animal Science and Technology, Hainan University, Haikou 570228, China
| | - Ziyi Wang
- Hainan Key Laboratory of Tropical Animal Reproduction & Breeding and Epidemic Disease Research, College of Animal Science and Technology, Hainan University, Haikou 570228, China
| | - Xinfeng Xie
- Hainan Key Laboratory of Tropical Animal Reproduction & Breeding and Epidemic Disease Research, College of Animal Science and Technology, Hainan University, Haikou 570228, China
| | - Shuaishuai Tian
- Hainan Key Laboratory of Tropical Animal Reproduction & Breeding and Epidemic Disease Research, College of Animal Science and Technology, Hainan University, Haikou 570228, China
| | - Feifan Wang
- Hainan Key Laboratory of Tropical Animal Reproduction & Breeding and Epidemic Disease Research, College of Animal Science and Technology, Hainan University, Haikou 570228, China
| | - Qishan Wang
- Hainan Yazhou Bay Seed Laboratory, Yongyou Industrial Park, Yazhou Bay Sci-Tech City, Sanya 572025, China
- Department of Animal Science, College of Animal Science, Zhejiang University, Hangzhou 310058, China
| | - Shiheng Ni
- Animal Husbandry Technology Extending Stations of Hainan Province, Haikou 570203, China
| | - Yuchun Pan
- Hainan Yazhou Bay Seed Laboratory, Yongyou Industrial Park, Yazhou Bay Sci-Tech City, Sanya 572025, China
- Department of Animal Science, College of Animal Science, Zhejiang University, Hangzhou 310058, China
| | - Qian Xiao
- Hainan Key Laboratory of Tropical Animal Reproduction & Breeding and Epidemic Disease Research, College of Animal Science and Technology, Hainan University, Haikou 570228, China
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3
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Yuan J, Zhou X, Xu G, Xu S, Liu B. Genetic diversity and population structure of Tongcheng pigs in China using whole-genome SNP chip. Front Genet 2022; 13:910521. [PMID: 36092902 PMCID: PMC9455598 DOI: 10.3389/fgene.2022.910521] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 07/29/2022] [Indexed: 11/13/2022] Open
Abstract
Tongcheng (TC) pigs, distinguished by their superior meat quality, are a Chinese indigenous pig breed. Recently, the genetic resources of TC pigs are under tremendous threat due to the introduction of cosmopolitan pig breeds and African swine fever disease. To promote their management and conservation, the present study assessed genetic diversity and population structure of TC pigs using single nucleotide polymorphism (SNP) markers. A total of 26, 999 SNPs were screened from 51, 315 SNPs in 68 TC pigs. The multi-dimensional scaling (MDS) analysis and neighbor-joining tree revealed that all 68 pigs were from a purebred population. The effective population size decreased over time, and it was 96 prior to generation 20. Both linkage disequilibrium (LD) and neutrality test indicated a low selection of TC pigs with average LD value of 0.15 ± 0.23. Genetic diversity results exhibited a minor allele frequency (MAF) of 0.23, observed heterozygosity (HO) of 0.32, expected heterozygosity (He) of 0.31, and nucleotide diversity (Pi) of 0.31. All these parameters indicated a remarkably high genetic diversity of TC pigs. Additionally, 184 runs of homozygosity (ROH) segments were detected from the whole genome of TC pigs with an average ROH length of 23.71Mb, ranging from 11.26Mb to 69.02 Mb. The highest ROH coverage was found on chromosome 1 (10.12%), while the lowest was on chromosome 18 (1.49%). The average inbreeding coefficients based on ROH (FROH) was 0.04%. Fourteen ROH islands containing 240 genes were detected on 9 different autosomes. Some of these 240 genes were overlapped with the genes related to biological processes such as immune function, reproduction, muscular development, and fat deposition, including FFAR2, FFAR4, MAPK8, NPY5R, KISS1, and these genes might be associated with such traits as meat quality and disease resistance in TC pigs. Taken together, population structure and genetic diversity results suggested that the TC pig represented a valuable genetic resource. However, TC pig breed conservation program remains to be further optimized to ensure adequate genetic diversity and avoid inbreeding depression. Our findings provide theoretical basis for formulating management and conservation strategies for TC pigs.
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Affiliation(s)
- Jiao Yuan
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xiang Zhou
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
- The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
- The Engineering Technology Research Center of Local Pig Breed Improvement of Hubei Province, Wuhan, China
| | - Guoqiang Xu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Sanping Xu
- Department of Agricultural and Rural Bureau, Xianning, China
| | - Bang Liu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
- The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
- The Engineering Technology Research Center of Local Pig Breed Improvement of Hubei Province, Wuhan, China
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4
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Chen Z, Zhang Z, Wang Z, Zhang Z, Wang Q, Pan Y. Heterozygosity and homozygosity regions affect reproductive success and the loss of reproduction: a case study with litter traits in pigs. Comput Struct Biotechnol J 2022; 20:4060-4071. [PMID: 35983229 PMCID: PMC9364102 DOI: 10.1016/j.csbj.2022.07.039] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 07/21/2022] [Accepted: 07/22/2022] [Indexed: 12/23/2022] Open
Abstract
Runs of heterozygosity (ROHet) and homozygosity (ROH) harbor useful information related to traits of interest. There is a lack of investigating the effect of ROHet and ROH on reproductive success and the loss of reproduction in mammals. Here, we detected and characterized the ROHet and ROH patterns in the genomes of Chinese indigenous pigs (i.e., Jinhua, Chun’an, Longyou Black, and Shengxian Spotted pigs), revealing the similar genetic characteristics of indigenous pigs. Later, we highlighted the underlying litter traits-related ROHet and ROH using association analysis with linear model in these four indigenous pig breeds. To pinpoint the promising candidate genes associated with litter traits, we further in-depth explore the selection patterns of other five pig breeds (i.e., Erhualian, Meishan, Minzhu, Rongchang, and Diqing pigs) with different levels of reproduction performance at the underlying litter traits-related ROHet and ROH using FST and genetic diversity ratio. Then, we identified a set of known and novel candidate genes associated with reproductive performance in pigs. For the novel candidate genes (i.e., CCDC91, SASH1, SAMD5, MACF1, MFSD2A, EPC2, and MBD5), we obtained public available datasets and performed multi-omics analyses integrating transcriptome-wide association studies and comparative single-cell RNA-seq analyses to uncover the roles of them in mammalian reproductive performance. The genes have not been widely reported to be fertility-related genes and can be complementally considered as prior biological information to modify genomic selections models that benefits pig genetic improvement of litter traits. Besides, our findings provide new insights into the function of ROHet and ROH in mammals.
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5
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Chen Z, Ye X, Zhang Z, Zhao Q, Xiang Y, Xu N, Wang Q, Pan Y, Guo X, Wang Z. Genetic diversity and selection signatures of four indigenous pig breeds from eastern China. Anim Genet 2022; 53:506-509. [PMID: 35489815 DOI: 10.1111/age.13208] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 03/24/2022] [Accepted: 04/11/2022] [Indexed: 12/01/2022]
Abstract
Chinese indigenous pig breeds have been undergoing selection for thousands of years, and have become invaluable genetic sources over the world. To investigate the population structure and genetic diversity of Jinhua (JH), Longyou Black (LYW), Shengxian Spotted (SXH), and Lanxi Spotted (LXH) breeds, a total of 200 pigs belonging to 10 diverse population were genotyped using SNP chips. The results showed that LYW pigs exhibited higher level of heterozygosity than the other indigenous pigs. In addition, gene introgression from intensively reared commercial pig breeds to LYW pigs was detected. Moreover, selection signature analysis revealed the possibility of differences between Chinese indigenous and intensively reared commercial pig breeds were mainly present for meat and carcass traits. Furthermore, we found that ANXA13, DISP1, and SRSF6 were the nearest genes located around the common selection signatures detected between each indigenous pig breed and Chinese wild boars. Our findings provide new insights into the selection signatures of Chinese indigenous pigs, and may contribute to future pig breeding.
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Affiliation(s)
- Zitao Chen
- Department of Animal Science, College of Animal Science, Zhejiang University, Hangzhou, China
| | - Xiaowei Ye
- Department of Animal Science, College of Animal Science, Zhejiang University, Hangzhou, China
| | - Zhe Zhang
- Department of Animal Science, College of Animal Science, Zhejiang University, Hangzhou, China
| | - Qingbo Zhao
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Yun Xiang
- Jinhua Academy of Agricultural Sciences, Jinhua, China
| | - Ningying Xu
- Department of Animal Science, College of Animal Science, Zhejiang University, Hangzhou, China
| | - Qishan Wang
- Department of Animal Science, College of Animal Science, Zhejiang University, Hangzhou, China
| | - Yuchun Pan
- Department of Animal Science, College of Animal Science, Zhejiang University, Hangzhou, China.,Hainan Institute, Zhejiang University, Sanya, China
| | - Xiaoling Guo
- Department of Animal Science, College of Animal Science, Zhejiang University, Hangzhou, China
| | - Zhen Wang
- Department of Animal Science, College of Animal Science, Zhejiang University, Hangzhou, China
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6
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Wang Y, Dong R, Li X, Cui C, Yu G. Analysis of the Genetic Diversity and Family Structure of the Licha Black Pig Population on Jiaodong Peninsula, Shandong Province, China. Animals (Basel) 2022; 12:ani12081045. [PMID: 35454291 PMCID: PMC9026534 DOI: 10.3390/ani12081045] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 04/14/2022] [Accepted: 04/16/2022] [Indexed: 12/31/2022] Open
Abstract
Simple Summary This study investigated the current conservation status, including the genetic diversity, the family structure, and inbreeding, of the Licha black pig population on Jiaodong Peninsula (Shandong Province, China). The results provide insights into the management and conservation of a local pig breed. Breeders are encouraged to utilize genomic data to improve mating schemes based on the family information obtained in this study, such as keeping an equivalent number of boars and sows in each family and selecting individuals with a kinship coefficient of less than 0.1 for mating. Abstract The Licha black pig, a popular indigenous Chinese pig breed, is known for its multi-vertebral trait and higher lean meat rate. Understanding the current conservation status, family structure, and degree of inbreeding of the Licha black pig population will be useful to maintain a sufficient level of genetic diversity in these animal resources. In the present study, the genetic diversity, population structure, and inbreeding coefficient of this conserved population were analyzed using SNP genotyping data from 209 Licha black pigs. Based on the genomic information, this population was divided into eight different families with boars. The effective population size (Ne), polymorphic marker ratio (PN), expected heterozygosity (He), and observed heterozygosity (Ho) of this population were 8.7, 0.827, 0.3576, and 0.3512, respectively. In addition, a total of 5976 runs of homozygosity (ROHs) were identified, and most of the ROHs (54.9%) were greater than 5 Mb. The genomic inbreeding coefficient of each individual was estimated based on ROHs (FROH) with an average inbreeding coefficient of 0.11 for the population. Five statistics (Ne, PN, Ho, He, and FROH) showed a decrease in the level of genetic diversity and a high degree of inbreeding in this population. Thus, special preservation programs need to be implemented in the future, such as introducing new individuals or improving the mating plan. Altogether, our study provides the first genomic overview of the genetic diversity and population structure of Licha black pigs, which will be useful for the management and long-term preservation of this breed.
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Affiliation(s)
- Yuan Wang
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao 266109, China; (Y.W.); (R.D.); (X.L.)
| | - Ruilan Dong
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao 266109, China; (Y.W.); (R.D.); (X.L.)
| | - Xiao Li
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao 266109, China; (Y.W.); (R.D.); (X.L.)
| | - Chao Cui
- Bureau of Agriculture and Rural Affairs of Jiaozhou, Jiaozhou 266300, China;
| | - Guanghui Yu
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao 266109, China; (Y.W.); (R.D.); (X.L.)
- Correspondence:
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7
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Zhao Q, Liu H, Qadri QR, Wang Q, Pan Y, Su G. Long-term impact of conventional and optimal contribution conservation methods on genetic diversity and genetic gain in local pig breeds. Heredity (Edinb) 2021; 127:546-553. [PMID: 34750534 PMCID: PMC8626428 DOI: 10.1038/s41437-021-00484-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 10/25/2021] [Accepted: 10/25/2021] [Indexed: 11/09/2022] Open
Abstract
There are rich and vast genetic resources of indigenous pig breeds in the world. Currently, great attention is paid to either crossbreeding or conservation of these indigenous pig breeds, and insufficient attention is paid to the combination of conservation and breeding along with their long-term effects on genetic diversity. Therefore, the objective of this study is to compare the long-term effects of using conventional conservation and optimal contribution selection methods on genetic diversity and genetic gain. A total of 11 different methods including conventional conservation and optimal contribution selection methods were investigated using stochastic simulations. The long-term effects of using these methods were evaluated in terms of genetic diversity metrices such as expected heterozygosity (He) and the rate of genetic gain. The results indicated that the rates of true inbreeding in these conventional conservation methods were maintained at around 0.01. The optimal contribution selection methods based either on the pedigree (POCS) or genome (GOCS) information showed more genetic gain than conventional methods, and POCS achieved the largest genetic gain. Furthermore, the effect of using GOCS methods on most of the genetic diversity metrics was slightly better than the conventional conservation methods when the rate of true inbreeding was the same, but this also required more sires used in OCS methods. According to the rate of true inbreeding, there was no significant difference among these conventional methods. In conclusion, there is no significant difference in different ways of selecting sows on inbreeding when we use different conventional conservation methods. Compared with conventional methods, POCS method could achieve the most genetic gain. However, GOCS methods can not only achieve higher genetic gain, but also maintain a relatively high level of genetic diversity. Therefore, GOCS is a better choice if we want to combine conservation and breeding in actual production in the conservation farms.
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Affiliation(s)
- Qingbo Zhao
- grid.16821.3c0000 0004 0368 8293School of Agriculture and Biology, Department of Animal Science, Shanghai Jiao Tong University, Shanghai, 200240 PR China ,grid.7048.b0000 0001 1956 2722Center for Quantitative Genetics and Genomics, Faculty of Science and Technology, Aarhus University, Tjele, 8830 Denmark
| | - Huiming Liu
- grid.7048.b0000 0001 1956 2722Center for Quantitative Genetics and Genomics, Faculty of Science and Technology, Aarhus University, Tjele, 8830 Denmark
| | - Qamar Raza Qadri
- grid.16821.3c0000 0004 0368 8293School of Agriculture and Biology, Department of Animal Science, Shanghai Jiao Tong University, Shanghai, 200240 PR China
| | - Qishan Wang
- grid.13402.340000 0004 1759 700XDepartment of Animal Breeding and Reproduction, College of Animal Science, Zhejiang University, Hangzhou, 310030 PR China
| | - Yuchun Pan
- Department of Animal Breeding and Reproduction, College of Animal Science, Zhejiang University, Hangzhou, 310030, PR China.
| | - Guosheng Su
- Center for Quantitative Genetics and Genomics, Faculty of Science and Technology, Aarhus University, Tjele, 8830, Denmark.
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An Overview of the Use of Genotyping Techniques for Assessing Genetic Diversity in Local Farm Animal Breeds. Animals (Basel) 2021; 11:ani11072016. [PMID: 34359144 PMCID: PMC8300386 DOI: 10.3390/ani11072016] [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: 06/10/2021] [Revised: 06/30/2021] [Accepted: 07/01/2021] [Indexed: 12/18/2022] Open
Abstract
Simple Summary The number of local farm animal breeds is declining worldwide. However, these breeds have different degrees of genetic diversity. Measuring genetic diversity is important for the development of conservation strategies and, therefore, various genomic analysis techniques are available. The aim of the present work was to shed light on the use of these techniques in diversity studies of local breeds. In summary, a total of 133 worldwide studies that examined genetic diversity in local cattle, sheep, goat, chicken and pig breeds were reviewed. The results show that over time, almost all available genomic techniques were used and various diversity parameters were calculated. Therefore, the present results provide a comprehensive overview of the application of these techniques in the field of local breeds. This can provide helpful insights into the advancement of the conservation of breeds with high genetic diversity. Abstract Globally, many local farm animal breeds are threatened with extinction. However, these breeds contribute to the high amount of genetic diversity required to combat unforeseen future challenges of livestock production systems. To assess genetic diversity, various genotyping techniques have been developed. Based on the respective genomic information, different parameters, e.g., heterozygosity, allele frequencies and inbreeding coefficient, can be measured in order to reveal genetic diversity between and within breeds. The aim of the present work was to shed light on the use of genotyping techniques in the field of local farm animal breeds. Therefore, a total of 133 studies across the world that examined genetic diversity in local cattle, sheep, goat, chicken and pig breeds were reviewed. The results show that diversity of cattle was most often investigated with microsatellite use as the main technique. Furthermore, a large variety of diversity parameters that were calculated with different programs were identified. For 15% of the included studies, the used genotypes are publicly available, and, in 6%, phenotypes were recorded. In conclusion, the present results provide a comprehensive overview of the application of genotyping techniques in the field of local breeds. This can provide helpful insights to advance the conservation of breeds.
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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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10
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Liu B, Shen L, Guo Z, Gan M, Chen Y, Yang R, Niu L, Jiang D, Zhong Z, Li X, Zhang S, Zhu L. Single nucleotide polymorphism-based analysis of the genetic structure of Liangshan pig population. Anim Biosci 2020; 34:1105-1115. [PMID: 32777894 PMCID: PMC8255872 DOI: 10.5713/ajas.19.0884] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 04/14/2020] [Indexed: 11/27/2022] Open
Abstract
Objective To conserve and utilize the genetic resources of a traditional Chinese indigenous pig breed, Liangshan pig, we assessed the genetic diversity, genetic structure, and genetic distance in this study. Methods We used 50K single nucleotide polymorphism (SNP) chip for SNP detection of 139 individuals in the Liangshan Pig Conservation Farm. Results The genetically closed conserved population consisted of five overlapping generations, and the total effective content of the population (Ne) was 15. The whole population was divided into five boar families and one non-boar family. Among them, the effective size of each generation subpopulation continuously decreased. However, the proportion of polymorphic markers (PN) first decreased and then increased. The average genetic distance of these 139 Liangshan pigs was 0.2823±0.0259, and the average genetic distance of the 14 boars was 0.2723±0.0384. Thus, it can be deduced that the genetic distance changed from generation to generation. In the conserved population, 983 runs of homozygosity (ROH) were detected, and the majority of ROH (80%) were within 100 Mb. The inbreeding coefficient calculated based on ROH showed an average value of 0.026 for the whole population. In addition, the inbreeding coefficient of each generation subpopulation initially increased and then decreased. In the pedigree of the whole conserved population, the error rate of paternal information was more than 11.35% while the maternal information was more than 2.13%. Conclusion This molecular study of the population genetic structure of Liangshan pig showed loss of genetic diversity during the closed cross-generation reproduction process. It is necessary to improve the mating plan or introduce new outside blood to ensure long-term preservation of Liangshan pig.
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Affiliation(s)
- Bin Liu
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Linyuan Shen
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Zhixian Guo
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Mailing Gan
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Ying Chen
- Sichuan Province General Station of Animal Husbandry, Chengdu 610066, China
| | - Runling Yang
- Agriculture and Rural Bureau of Mabian Yi Autonomous County, Mabian, 614600, China
| | - Lili Niu
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Dongmei Jiang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Zhijun Zhong
- Sichuan Academy of Animal Sciences, Chengdu 610066, China
| | - Xuewei Li
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Shunhua Zhang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Li Zhu
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
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11
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Huang M, Yang B, Chen H, Zhang H, Wu Z, Ai H, Ren J, Huang L. The fine-scale genetic structure and selection signals of Chinese indigenous pigs. Evol Appl 2020; 13:458-475. [PMID: 31993089 PMCID: PMC6976964 DOI: 10.1111/eva.12887] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 10/14/2019] [Accepted: 10/17/2019] [Indexed: 01/24/2023] Open
Abstract
Genome-wide SNP profiling has yielded insights into the genetic structure of China indigenous pigs, but has focused on a limited number of populations. Here, we present an analysis of population structure and signals of positive selection in 42 Chinese pig populations that represent the most extensive pig phenotypic diversity in China, using genotype data of 1.1 million SNPs on customized Beadchips. This unravels the fine-scale genetic diversity, phylogenic relationships, and population structure of these populations, which shows remarkably concordance between genetic clusters and geography with few exceptions. We also reveal the genetic contribution to North Chinese pigs from European modern pigs. Furthermore, we identify possible targets of selection in the Tibetan pig, including the well-characterized hypoxia gene (EPAS1) and several previously unrecognized candidates. Intriguingly, the selected haplotype in the EPAS1 gene is associated with higher hemoglobin contents in Tibetan pigs, which is different from the protective role of EPAS1 in the high-altitude adaptation in Tibetan dogs and their owners. Additionally, we present evidence for the causality between EDNRB variants and the two-end-black (TEB) coat color phenotype in all Chinese pig populations except the Jinhua pig. We hypothesize that distinct targets have been independently selected for the formation of the TEB phenotype in Chinese pigs of different geographic origins. This highlights the importance of characterizing population-specific genetic determinants for heritable phenotype in diverse pig populations.
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Affiliation(s)
- Min Huang
- State Key Laboratory of Pig Genetic Improvement and Production TechnologyJiangxi Agricultural UniversityNanchangChina
| | - Bin Yang
- State Key Laboratory of Pig Genetic Improvement and Production TechnologyJiangxi Agricultural UniversityNanchangChina
| | - Hao Chen
- State Key Laboratory of Pig Genetic Improvement and Production TechnologyJiangxi Agricultural UniversityNanchangChina
| | - Hui Zhang
- State Key Laboratory of Pig Genetic Improvement and Production TechnologyJiangxi Agricultural UniversityNanchangChina
| | - Zhongping Wu
- State Key Laboratory of Pig Genetic Improvement and Production TechnologyJiangxi Agricultural UniversityNanchangChina
| | - Huashui Ai
- State Key Laboratory of Pig Genetic Improvement and Production TechnologyJiangxi Agricultural UniversityNanchangChina
| | - Jun Ren
- State Key Laboratory of Pig Genetic Improvement and Production TechnologyJiangxi Agricultural UniversityNanchangChina
- Present address:
College of Animal ScienceSouth China Agricultural UniversityGuangzhouChina
| | - Lusheng Huang
- State Key Laboratory of Pig Genetic Improvement and Production TechnologyJiangxi Agricultural UniversityNanchangChina
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12
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Xu Z, Sun H, Zhang Z, Zhao Q, Olasege BS, Li Q, Yue Y, Ma P, Zhang X, Wang Q, Pan Y. Assessment of Autozygosity Derived From Runs of Homozygosity in Jinhua Pigs Disclosed by Sequencing Data. Front Genet 2019; 10:274. [PMID: 30984245 PMCID: PMC6448551 DOI: 10.3389/fgene.2019.00274] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 03/12/2019] [Indexed: 12/21/2022] Open
Abstract
Jinhua pig, a well-known Chinese indigenous breed, has evolved as a pig breed with excellent meat quality, greater disease resistance, and higher prolificacy. The reduction in the number of Jinhua pigs over the past years has raised concerns about inbreeding. Runs of homozygosity (ROH) along the genome have been applied to quantify individual autozygosity to improve the understanding of inbreeding depression and identify genes associated with traits of interest. Here, we investigated the occurrence and distribution of ROH using next-generation sequencing data to characterize autozygosity in 202 Jinhua pigs, as well as to identify the genomic regions with high ROH frequencies within individuals. The average inbreeding coefficient, based on ROH longer than 1 Mb, was 0.168 ± 0.052. In total, 18,690 ROH were identified in all individuals, among which shorter segments (1-5 Mb) predominated. Individual ROH autosome coverage ranged from 5.32 to 29.14% in the Jinhua population. On average, approximately 16.8% of the whole genome was covered by ROH segments, with the lowest coverage on SSC11 and the highest coverage on SSC17. A total of 824 SNPs (about 0.5%) and 11 ROH island regions were identified (occurring in over 45% of the samples). Genes associated with reproduction (HOXA3, HOXA7, HOXA10, and HOXA11), meat quality (MYOD1, LPIN3, and CTNNBL1), appetite (NUCB2) and disease resistance traits (MUC4, MUC13, MUC20, LMLN, ITGB5, HEG1, SLC12A8, and MYLK) were identified in ROH islands. Moreover, several quantitative trait loci for ham weight and ham fat thickness were detected. Genes in ROH islands suggested, at least partially, a selection for economic traits and environmental adaptation, and should be subject of future investigation. These findings contribute to the understanding of the effects of environmental and artificial selection in shaping the distribution of functional variants in the pig genome.
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Affiliation(s)
- Zhong Xu
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Hao Sun
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Zhe Zhang
- 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
| | - Babatunde Shittu Olasege
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Qiumeng Li
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Yang Yue
- 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
| | - Xiangzhe Zhang
- 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
| | - Yuchun Pan
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Key Laboratory of Veterinary Biotechnology, Shanghai, China
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13
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Qiao R, Li X, Han X, Wang K, Lv G, Ren G, Li X. Population structure and genetic diversity of four Henan pig populations. Anim Genet 2019; 50:262-265. [PMID: 30883844 DOI: 10.1111/age.12775] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/09/2019] [Indexed: 12/22/2022]
Abstract
To investigate the population structure and genetic diversity of Henan indigenous pig breeds, samples from a total of 78 pigs of 11 breeds were collected, including four pig populations from Henan Province, three Western commercial breeds, three Chinese native pig breeds from other provinces and one Asian wild boar. The genotyping datasets were obtained by genotyping-by-sequencing technology. We found a high degree of polymorphism and rapid linkage disequilibrium decay in Henan pigs. A neighbor-joining tree, principal component analysis and structure analysis revealed that the Huainan and Erhualian pigs were clustered together and that the Queshan black pigs were clearly grouped together but that the Nanyang and Yuxi pigs were extensively admixed with Western pigs. In addition, heterozygosity values might indicate that Henan indigenous pigs, especially the Queshan black and Huainan pigs, were subjected to little selection during domestication. The results presented here indicate that Henan pig breeds were admixed from Western breeds, especially Nanyang and Yuxi pigs. Therefore, establishment of purification and rejuvenation systems to implement conservation strategies is urgent. In addition, it is also necessary to accelerate genetic resources improvement and utilization using modern breeding technologies, such as genomic selection and genome-wide association studies.
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Affiliation(s)
- R Qiao
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - X Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - X Han
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - K Wang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - G Lv
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - G Ren
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - X Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
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14
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Zhao QB, Sun H, Zhang Z, Xu Z, Olasege BS, Ma PP, Zhang XZ, Wang QS, Pan YC. Exploring the Structure of Haplotype Blocks and Genetic Diversity in Chinese Indigenous Pig Populations for Conservation Purpose. Evol Bioinform Online 2019; 15:1176934318825082. [PMID: 30718942 PMCID: PMC6348539 DOI: 10.1177/1176934318825082] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 12/07/2018] [Indexed: 11/16/2022] Open
Abstract
Chinese indigenous pigs in the Taihu Lake region are well known for their high
fecundity and other excellent characteristics. To better understand the
characteristics of these breeds in this area as well as to provide the
government and breeders the molecular basis for formulating a reasonable
conservation policy, we explored the structure of haplotype blocks and genetic
diversity of the 7 populations which is relevant for the management and
conservation of these important genetic resources using next-generation
sequencing data. In this study, a total of 131 300 single-nucleotide
polymorphisms with minor allele frequencies ⩾0.05 were obtained for further
analysis. In general, there are similar within-breed genetic diversities (He,
Ho, Pn, Ar) among these 7 pig populations in the Taihu
Lake region. Average values for the inbreeding coefficients estimates in the 7
populations are 0.110 (F1), 0.056 (F2), and 0.078 (F3). All the breeds have seen
a continuous decline in Ne estimates over time with FJ and SW populations having
a very similar curve. Moreover, the Ne of SMS pig breeds were smaller than other
Chinese pig breeds, indicating that SMS pig breeds underwent stronger selection
pressure than other Chinese pig breeds. The average genetic distances among the
7 populations in the Taihu Lake region were 0.235 (MMS), 0.240 (SMS), 0.269
(EH), 0.248 (MI), 0.221 (FJ), 0.254 (JX), and 0.212 (SW). A summary of the
number of haplotype blocks and haplotype diversity was also presented. This
study provide a deep understanding of the current situation of conservation in
this region, thereby uncovering the pertinent insight to better formulate more
reasonable preservation policies for the government departments and breeding
planners to follow-up.
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Affiliation(s)
- Qing-Bo Zhao
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, P.R. China
| | - Hao Sun
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, P.R. China
| | - Zhe Zhang
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, P.R. China
| | - Zhong Xu
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, P.R. China
| | - Babatunde Shittu Olasege
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, P.R. China
| | - Pei-Pei Ma
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, P.R. China.,Shanghai Key Laboratory of Veterinary Biotechnology, Shanghai Jiao Tong University, Shanghai, P.R. China
| | - Xiang-Zhe Zhang
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, P.R. China.,Shanghai Key Laboratory of Veterinary Biotechnology, Shanghai Jiao Tong University, Shanghai, P.R. China
| | - Qi-Shan Wang
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, P.R. China.,Shanghai Key Laboratory of Veterinary Biotechnology, Shanghai Jiao Tong University, Shanghai, P.R. China
| | - Yu-Chun Pan
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, P.R. China.,Shanghai Key Laboratory of Veterinary Biotechnology, Shanghai Jiao Tong University, Shanghai, P.R. China
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