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Zhou J, Liu F, He M, Gao J, Wu C, Gan Y, Bian Y, Wei J, Zhang W, Zhang W, Han X, Dai J, Sun L. Detection and Analysis of Antidiarrheal Genes and Immune Factors in Various Shanghai Pig Breeds. Biomolecules 2024; 14:595. [PMID: 38786002 PMCID: PMC11117698 DOI: 10.3390/biom14050595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 05/14/2024] [Accepted: 05/16/2024] [Indexed: 05/25/2024] Open
Abstract
The aim of this study was to identify effective genetic markers for the Antigen Processing Associated Transporter 1 (TAP1), α (1,2) Fucosyltransferase 1 (FUT1), Natural Resistance Associated Macrophage Protein 1 (NRAMP1), Mucin 4 (MUC4) and Mucin 13 (MUC13) diarrhea-resistance genes in the local pig breeds, namely Shanghai white pigs, Fengjing pigs, Shawutou pigs, Meishan pigs and Pudong white pigs, to provide a reference for the characterization of local pig breed resources in Shanghai. Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLR) and sequence sequencing were applied to analyze the polymorphisms of the above genes and to explore the effects on the immunity of Shanghai local pig breeds in conjunction with some immunity factors. The results showed that both TAP1 and MUC4 genes had antidiarrheal genotype GG in the five pig breeds, AG and GG genotypes of the FUT1 gene were detected in Pudong white pigs, AA antidiarrheal genes of the NRAMP1 gene were detected in Meishan pigs, the AB type of the NRAMP1 gene was detected in Pudong white pigs, and antidiarrheal genotype GG of the MUC13 gene was only detected in Shanghai white pigs. The MUC13 antidiarrhea genotype GG was only detected in Shanghai white pigs. The TAP1 gene was moderately polymorphic in Shanghai white pigs, Fengjing pigs, Shawutou pigs, Meishan pigs and Pudong white pigs, among which TAP1 in Shanghai white pigs and Shawutou pigs did not satisfy the Hardy-Weinberg equilibrium. The FUT1 gene of Pudong white pigs was in a state of low polymorphism. NRAMP1 of Meishan pigs and Pudong white pigs was in a state of moderate polymorphism, which did not satisfy the Hardy-Weinberg equilibrium. The MUC4 genes of Shanghai white pigs and Pudong white pigs were in a state of low polymorphism, and the MUC4 genes of Fengjing pigs and Shawutou pigs were in a state of moderate polymorphism, and the MUC4 genes of Fengjing pigs and Pudong white pigs did not satisfy the Hardy-Weinberg equilibrium. The MUC13 gene of Shanghai white pigs and Pudong white pigs was in a state of moderate polymorphism. Meishan pigs had higher levels of IL-2, IL-10, IgG and TNF-α, and Pudong white pigs had higher levels of IL-12 than the other pigs. The level of interleukin 12 (IL-12) was significantly higher in the AA genotype of the MUC13 gene of Shanghai white pigs than in the AG genotype. The indicator of tumor necrosis factor alpha (TNF-α) in the AA genotype of the TAP1 gene of Fengjing pigs was significantly higher than that of the GG and AG genotypes. The indicator of IL-12 in the AG genotype of the Shawutou pig TAP1 gene was significantly higher than that of the GG genotype. The level of TNF-α in the AA genotype of the NRAMP1 gene of Meishan pigs was markedly higher than that of the AB genotype. The IL-2 level of the AG type of the FUT1 gene was obviously higher than that of the GG type of Pudong white pigs, the IL-2 level of the AA type of the MUC4 gene was dramatically higher than that of the AG type, and the IgG level of the GG type of the MUC13 gene was apparently higher than that of the AG type. The results of this study are of great significance in guiding the antidiarrhea breeding and molecular selection of Shanghai white pigs, Fengjing pigs, Shawutou pigs, Meishan pigs and Pudong white pigs and laying the foundation for future antidiarrhea breeding of various local pig breeds in Shanghai.
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Affiliation(s)
- Jinyong Zhou
- Shanghai Municipal Key Laboratory of Agri-Genetics and Breeding, Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China; (J.Z.); (F.L.); (M.H.); (J.G.); (C.W.)
- Key Laboratory of Livestock and Poultry Resources (Pig) Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai 201106, China
| | - Fuqin Liu
- Shanghai Municipal Key Laboratory of Agri-Genetics and Breeding, Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China; (J.Z.); (F.L.); (M.H.); (J.G.); (C.W.)
- Key Laboratory of Livestock and Poultry Resources (Pig) Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai 201106, China
| | - Mengqian He
- Shanghai Municipal Key Laboratory of Agri-Genetics and Breeding, Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China; (J.Z.); (F.L.); (M.H.); (J.G.); (C.W.)
- Key Laboratory of Livestock and Poultry Resources (Pig) Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai 201106, China
| | - Jun Gao
- Shanghai Municipal Key Laboratory of Agri-Genetics and Breeding, Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China; (J.Z.); (F.L.); (M.H.); (J.G.); (C.W.)
- Key Laboratory of Livestock and Poultry Resources (Pig) Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai 201106, China
| | - Caifeng Wu
- Shanghai Municipal Key Laboratory of Agri-Genetics and Breeding, Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China; (J.Z.); (F.L.); (M.H.); (J.G.); (C.W.)
- Key Laboratory of Livestock and Poultry Resources (Pig) Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai 201106, China
| | - Yeqing Gan
- Shanghai Jiading Municipal Centre for Disease Control and Prevention, Shanghai 201899, China; (Y.G.); (Y.B.); (J.W.)
| | - Yi Bian
- Shanghai Jiading Municipal Centre for Disease Control and Prevention, Shanghai 201899, China; (Y.G.); (Y.B.); (J.W.)
| | - Jinliang Wei
- Shanghai Jiading Municipal Centre for Disease Control and Prevention, Shanghai 201899, China; (Y.G.); (Y.B.); (J.W.)
| | - Weijian Zhang
- Shanghai Municipal Centre for Disease Control and Prevention, Shanghai 200051, China; (W.Z.); (W.Z.)
| | - Wengang Zhang
- Shanghai Municipal Centre for Disease Control and Prevention, Shanghai 200051, China; (W.Z.); (W.Z.)
| | - Xuejun Han
- Shanghai Engineering Research Center of Breeding Pig, Shanghai 201106, China;
| | - Jianjun Dai
- Shanghai Municipal Key Laboratory of Agri-Genetics and Breeding, Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China; (J.Z.); (F.L.); (M.H.); (J.G.); (C.W.)
- Shanghai Engineering Research Center of Breeding Pig, Shanghai 201106, China;
| | - Lingwei Sun
- Shanghai Municipal Key Laboratory of Agri-Genetics and Breeding, Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China; (J.Z.); (F.L.); (M.H.); (J.G.); (C.W.)
- Key Laboratory of Livestock and Poultry Resources (Pig) Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai 201106, China
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Huang M, Zhang H, Wu ZP, Wang XP, Li DS, Liu SJ, Zheng SM, Yang LJ, Liu BB, Li GX, Jiang YC, Chen H, Ren J. Whole-genome resequencing reveals genetic structure and introgression in Pudong White pigs. Animal 2021; 15:100354. [PMID: 34543995 DOI: 10.1016/j.animal.2021.100354] [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: 03/28/2021] [Revised: 08/10/2021] [Accepted: 08/13/2021] [Indexed: 10/20/2022] Open
Abstract
Pudong White (PDW) pigs, historically originating from Shanghai, are the only Chinese indigenous pigs characterised by their completely white coats, with the exception of Rongchang pigs. However, there is limited information concerning their overall genetic structure or relationship with other breeds, especially the East Chinese (ECN) and European pigs. To uncover the genetic structure, selection signatures, and potential exotic introgression in PDW pigs, we sampled 15 PDW pigs using whole-genome sequencing (~20×). We then conducted in-depth population genetic analyses in 320 pigs from 27 global pig groups, namely, European wild boars, Chinese wild boars, and outgroup. Neighbour-joining tree and principal component analysis confirmed that PDW pigs belonged to the ecotype of ECN pigs. Both f3, D-statistics, and structure analysis showed that PDW pigs shared apparent alleles with Large White (LW) pigs. Three statistics, rIBD, a haplotype heat map and copy number variation, further indicated that PDW pigs shared apparent alleles with LW pigs at the KIT Proto-Oncogene, Receptor Tyrosine Kinase (KIT) and PARG-MARCHF8 loci, suggesting that the lineage of European pigs in PDW originated from LW pigs. After further detecting the KIT mutations in different pig breeds, PDW was confirmed to have the same duplication region 1, duplication region 2, and the splicing mutation on intron 17 of KIT as LW pigs that determine the white coat colour phenotype in European white pigs. We hypothesised that LW pigs were imported to China ∼110-160 years ago according to the admixture time estimate and then crossed with ECN pigs, resulting in the introgression of the KIT alleles that produce the white coat colour phenotype in the PDW pig breed. To our knowledge, this study presents the first thorough description of the genetic structure of PDW pigs via whole-genome resequencing data; moreover, the results provide a basis for the national project for the conservation of this unique Chinese local population.
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Affiliation(s)
- M Huang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong Province, China
| | - H Zhang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong Province, China
| | - Z P Wu
- Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong Province, China
| | - X P Wang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong Province, China
| | - D S Li
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong Province, China
| | - S J Liu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong Province, China
| | - S M Zheng
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong Province, China
| | - L J Yang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong Province, China
| | - B B Liu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong Province, China
| | - G X Li
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong Province, China
| | - Y C Jiang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong Province, China
| | - H Chen
- College of Life Science, Jiangxi Science & Technology Normal University, Nanchang, Jiangxi Province, China.
| | - J Ren
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong Province, China
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Abstract
Pudong White (PW) pigs are distributed in the Taihu region of China and are characterized by their completely white coats. A heated debate concerning this genetic resource and its relationship to Taihu and western pig breeds has arisen, due to the white coat of the animals. To determine whether PW is a unique genetic resource, we performed a detailed assessment of the genetic relationships among PW, six breeds from the Taihu population and three western pig breeds, based on whole-genome single nucleotide polymorphism (SNP) data. A total of 68 102 SNPs were identified in the genomes of the tested populations by next-generation sequencing technology, of which, 64 were determined as the potentially specific to PW breed. The genetic distance between PW pigs and the Taihu population was shorter than that between PW and western breeds. The genetic distance within the PW population was small and neighbour-joining tree analysis revealed that all PW individuals clustered into a separated group, indicating a close genetic relationship among PW individuals which may result from a small effective population size (N e ) and inbreeding. The results of both principal component analysis and evaluation using fastSTRUCTURE demonstrated that PW was clearly differentiated from other breeds. Together, these results indicate that PW is a distinctive genetic resource with a unique genetic structure separate from other Taihu and western pig breeds. Furthermore, this genome-wide comprehensive survey of the relationships among PW, Taihu and western pig breeds, demonstrates the rationality of the current breed classification of PW. The results also provide evidence about the unique genetic resource of PW, based on genome-wide genetic markers. These data will improve our understanding of the genetic structure and current state of PW breed, and facilitate the development of a national project for the conservation and utilization of these pigs.
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Liu R, Jin L, Long K, Chai J, Ma J, Tang Q, Tian S, Hu Y, Lin L, Wang X, Jiang A, Li X, Li M. Detection of genetic diversity and selection at the coding region of the melanocortin receptor 1 ( MC1R ) gene in Tibetan pigs and Landrace pigs. Gene 2016; 575:537-542. [DOI: 10.1016/j.gene.2015.09.032] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Revised: 08/13/2015] [Accepted: 09/15/2015] [Indexed: 11/30/2022]
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