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Li G, Liu Y, Feng X, Diao S, Zhong Z, Li B, Teng J, Zhang W, Zeng H, Cai X, Gao Y, Liu X, Yuan X, Li J, Zhang Z. Integrating Multiple Database Resources to Elucidate the Gene Flow in Southeast Asian Pig Populations. Int J Mol Sci 2024; 25:5689. [PMID: 38891877 PMCID: PMC11171535 DOI: 10.3390/ijms25115689] [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: 04/17/2024] [Revised: 05/16/2024] [Accepted: 05/18/2024] [Indexed: 06/21/2024] Open
Abstract
The domestic pig (Sus scrofa) and its subfamilies have experienced long-term and extensive gene flow, particularly in Southeast Asia. Here, we analyzed 236 pigs, focusing on Yunnan indigenous, European commercial, East Asian, and Southeast Asian breeds, using the Pig Genomics Reference Panel (PGRP v1) of Pig Genotype-Tissue Expression (PigGTEx) to investigate gene flow and associated complex traits by integrating multiple database resources. In this study, we discovered evidence of admixtures from European pigs into the genome of Yunnan indigenous pigs. Additionally, we hypothesized that a potential conceptual gene flow route that may have contributed to the genetic composition of the Diannan small-ear pig is a gene exchange from the Vietnamese pig. Based on the most stringent gene introgression scan using the fd statistic, we identified three specific loci on chromosome 8, ranging from 51.65 to 52.45 Mb, which exhibited strong signatures of selection and harbored the NAF1, NPY1R, and NPY5R genes. These genes are associated with complex traits, such as fat mass, immunity, and litter weight, in pigs, as supported by multiple bio-functionalization databases. We utilized multiple databases to explore the potential dynamics of genetic exchange in Southeast Asian pig populations and elucidated specific gene functionalities.
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Affiliation(s)
- Guangzhen Li
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (G.L.); (Y.L.); (X.F.); (S.D.); (Z.Z.); (B.L.); (J.T.); (W.Z.); (H.Z.); (X.C.); (Y.G.); (X.Y.)
| | - Yuqiang Liu
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (G.L.); (Y.L.); (X.F.); (S.D.); (Z.Z.); (B.L.); (J.T.); (W.Z.); (H.Z.); (X.C.); (Y.G.); (X.Y.)
| | - Xueyan Feng
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (G.L.); (Y.L.); (X.F.); (S.D.); (Z.Z.); (B.L.); (J.T.); (W.Z.); (H.Z.); (X.C.); (Y.G.); (X.Y.)
| | - Shuqi Diao
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (G.L.); (Y.L.); (X.F.); (S.D.); (Z.Z.); (B.L.); (J.T.); (W.Z.); (H.Z.); (X.C.); (Y.G.); (X.Y.)
| | - Zhanming Zhong
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (G.L.); (Y.L.); (X.F.); (S.D.); (Z.Z.); (B.L.); (J.T.); (W.Z.); (H.Z.); (X.C.); (Y.G.); (X.Y.)
| | - Bolang Li
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (G.L.); (Y.L.); (X.F.); (S.D.); (Z.Z.); (B.L.); (J.T.); (W.Z.); (H.Z.); (X.C.); (Y.G.); (X.Y.)
| | - Jinyan Teng
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (G.L.); (Y.L.); (X.F.); (S.D.); (Z.Z.); (B.L.); (J.T.); (W.Z.); (H.Z.); (X.C.); (Y.G.); (X.Y.)
| | - Wenjing Zhang
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (G.L.); (Y.L.); (X.F.); (S.D.); (Z.Z.); (B.L.); (J.T.); (W.Z.); (H.Z.); (X.C.); (Y.G.); (X.Y.)
| | - Haonan Zeng
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (G.L.); (Y.L.); (X.F.); (S.D.); (Z.Z.); (B.L.); (J.T.); (W.Z.); (H.Z.); (X.C.); (Y.G.); (X.Y.)
| | - Xiaodian Cai
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (G.L.); (Y.L.); (X.F.); (S.D.); (Z.Z.); (B.L.); (J.T.); (W.Z.); (H.Z.); (X.C.); (Y.G.); (X.Y.)
| | - Yahui Gao
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (G.L.); (Y.L.); (X.F.); (S.D.); (Z.Z.); (B.L.); (J.T.); (W.Z.); (H.Z.); (X.C.); (Y.G.); (X.Y.)
| | - Xiaohong Liu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China;
| | - Xiaolong Yuan
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (G.L.); (Y.L.); (X.F.); (S.D.); (Z.Z.); (B.L.); (J.T.); (W.Z.); (H.Z.); (X.C.); (Y.G.); (X.Y.)
| | - Jiaqi Li
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (G.L.); (Y.L.); (X.F.); (S.D.); (Z.Z.); (B.L.); (J.T.); (W.Z.); (H.Z.); (X.C.); (Y.G.); (X.Y.)
| | - Zhe Zhang
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (G.L.); (Y.L.); (X.F.); (S.D.); (Z.Z.); (B.L.); (J.T.); (W.Z.); (H.Z.); (X.C.); (Y.G.); (X.Y.)
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Song Y, Xue M, Wang F, Tang Q, Luo Y, Zheng M, Wang Y, Xue P, Dong N, Sun R, Fang M. Study on the Characteristics of Coarse Feeding Tolerance of Ding'an Pigs: Phenotypic and Candidate Genes Identification. Genes (Basel) 2024; 15:599. [PMID: 38790227 PMCID: PMC11121715 DOI: 10.3390/genes15050599] [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: 03/25/2024] [Revised: 04/28/2024] [Accepted: 05/03/2024] [Indexed: 05/26/2024] Open
Abstract
Ding'an (DA) pig, a prominent local breed in Hainan Province, exhibits notable advantages in coarse feeding tolerance and high-quality meat. To explore the potential genetic mechanism of coarse feeding tolerance in DA pigs, 60-day-old full sibling pairs of DA and DLY (Duroc-Landrace-Yorkshire) pigs were subjected to fed normal (5%) and high (10%) crude fiber diets for 56 days, respectively. The findings showed that increasing the crude fiber level had no impact on the apparent digestibility of crude fiber, intramuscular fat, and marbling scores in DA pigs, whereas these factors were significantly reduced in DLY pigs (p < 0.05). Through differential expression analysis and Weighted Gene Co-expression Network Analysis (WGCNA) of the colonic mucosal transcriptome data, 65 and 482 candidate genes with coarse feeding tolerance in DA pigs were identified, respectively. Joint analysis screened four key candidate genes, including LDHB, MLC1, LSG1, and ESM1, potentially serving as key regulated genes for coarse feeding tolerance. Functional analysis revealed that the most significant pathway enriched in differential genes associated with coarse feeding tolerance in Ding'an pigs was the signaling receptor binding. The results hold substantial significance for advancing our understanding of the genetic mechanisms governing coarse feeding tolerance in Ding'an pigs.
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Affiliation(s)
- Yanxia Song
- Sanya Institute of China Agricultural University, Sanya 572024, China; (Y.S.); (Y.W.); (N.D.)
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, MOA Key Laboratory of Animal Genetics and Breeding, Beijing Key Laboratory for Animal Genetic Improvement, State Key Laboratory of Animal Biotech Breeding, Frontiers Science Center for Molecular Design Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (M.X.); (Q.T.); (Y.L.); (P.X.)
| | - Mingming Xue
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, MOA Key Laboratory of Animal Genetics and Breeding, Beijing Key Laboratory for Animal Genetic Improvement, State Key Laboratory of Animal Biotech Breeding, Frontiers Science Center for Molecular Design Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (M.X.); (Q.T.); (Y.L.); (P.X.)
| | - Feng Wang
- Institute of Animal Science and Veterinary Medicine, Hainan Academy of Agricultural Science, Haikou 571100, China; (F.W.); (R.S.)
| | - Qiguo Tang
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, MOA Key Laboratory of Animal Genetics and Breeding, Beijing Key Laboratory for Animal Genetic Improvement, State Key Laboratory of Animal Biotech Breeding, Frontiers Science Center for Molecular Design Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (M.X.); (Q.T.); (Y.L.); (P.X.)
| | - Yabiao Luo
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, MOA Key Laboratory of Animal Genetics and Breeding, Beijing Key Laboratory for Animal Genetic Improvement, State Key Laboratory of Animal Biotech Breeding, Frontiers Science Center for Molecular Design Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (M.X.); (Q.T.); (Y.L.); (P.X.)
| | - Meili Zheng
- Beijing General Station of Animal Husbandry, Beijing 100107, China;
| | - Yubei Wang
- Sanya Institute of China Agricultural University, Sanya 572024, China; (Y.S.); (Y.W.); (N.D.)
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, MOA Key Laboratory of Animal Genetics and Breeding, Beijing Key Laboratory for Animal Genetic Improvement, State Key Laboratory of Animal Biotech Breeding, Frontiers Science Center for Molecular Design Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (M.X.); (Q.T.); (Y.L.); (P.X.)
| | - Pengxiang Xue
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, MOA Key Laboratory of Animal Genetics and Breeding, Beijing Key Laboratory for Animal Genetic Improvement, State Key Laboratory of Animal Biotech Breeding, Frontiers Science Center for Molecular Design Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (M.X.); (Q.T.); (Y.L.); (P.X.)
| | - Ningqi Dong
- Sanya Institute of China Agricultural University, Sanya 572024, China; (Y.S.); (Y.W.); (N.D.)
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, MOA Key Laboratory of Animal Genetics and Breeding, Beijing Key Laboratory for Animal Genetic Improvement, State Key Laboratory of Animal Biotech Breeding, Frontiers Science Center for Molecular Design Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (M.X.); (Q.T.); (Y.L.); (P.X.)
| | - Ruiping Sun
- Institute of Animal Science and Veterinary Medicine, Hainan Academy of Agricultural Science, Haikou 571100, China; (F.W.); (R.S.)
| | - Meiying Fang
- Sanya Institute of China Agricultural University, Sanya 572024, China; (Y.S.); (Y.W.); (N.D.)
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, MOA Key Laboratory of Animal Genetics and Breeding, Beijing Key Laboratory for Animal Genetic Improvement, State Key Laboratory of Animal Biotech Breeding, Frontiers Science Center for Molecular Design Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (M.X.); (Q.T.); (Y.L.); (P.X.)
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Tan Z, Li J, He Y, Wang F, Xiao Q. Characteristics of gut microbiota and metabolomic of Hainan Tunchang pigs at various growth stages. Gene 2024; 900:148161. [PMID: 38219876 DOI: 10.1016/j.gene.2024.148161] [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: 09/18/2023] [Revised: 01/03/2024] [Accepted: 01/11/2024] [Indexed: 01/16/2024]
Abstract
Numerous gut microorganisms residing in the gut tract and their metabolites play an important role in animal growth. Diet, as the main factor, affects the changes of gut microbiota, and host genetics also have a significant impact on gut microbiota, including growth stages. However, the differences of gut microbiota and its metabolites at various growth stages in local pig breed remains unclear. We used 16S rRNA gene sequencing and untargeted metabolomics to investigate the fecal microbiota and metabolites in different developmental stages of Hainan Tunchang pigs. The relative proportions of dominant bacteria Firmicutes and Spirochaetes increased, Bacteroidetes and Proteobacteria decreased with the development. As age increased, different physiological states led to structural and functional changes in animal nutrition metabolism and immune needs, as well as changes in gut microbiota and its metabolites. We have detected several statistically different microbial and metabolic biomarkers at different growth stages. Meanwhile, through correlation analysis between differential bacteria and metabolites, it was found that the bacteria forming networks with their significant related metabolites were different at various growth stages, Holdemanella, Sharpea, Subdoligranulum, and uncultured_bacterium_o_Bacteroidales were enriched between preweaning piglets and weaning piglets, and they all positive correlated with related metabolites. We also found that the differential bacteria were significantly related to short-chain fatty acid. These findings might provide new insights into the developmental changes of gut microbiota in local pig breeds and the interaction mechanism between the body, and improve pig growth performance and efficiency by regulating the composition of gut microbiota and metabolites.
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Affiliation(s)
- Zhen Tan
- School of Tropical Agriculture and Forestry, Hainan University, 571737 Danzhou, PR China.
| | - Jie Li
- School of Tropical Agriculture and Forestry, Hainan University, 571737 Danzhou, PR China
| | - Yingzhi He
- School of Tropical Agriculture and Forestry, Hainan University, 571737 Danzhou, PR China
| | - Feifan Wang
- School of Tropical Agriculture and Forestry, Hainan University, 571737 Danzhou, PR China
| | - Qian Xiao
- School of Tropical Agriculture and Forestry, Hainan University, 571737 Danzhou, PR China.
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Li W, Wu X, Xiang D, Zhang W, Wu L, Meng X, Huo J, Yin Z, Fu G, Zhao G. Genome-Wide Detection for Runs of Homozygosity in Baoshan Pigs Using Whole Genome Resequencing. Genes (Basel) 2024; 15:233. [PMID: 38397222 PMCID: PMC10887577 DOI: 10.3390/genes15020233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 02/08/2024] [Accepted: 02/09/2024] [Indexed: 02/25/2024] Open
Abstract
Baoshan pigs (BS) are a local breed in Yunnan Province that may face inbreeding owing to its limited population size. To accurately evaluate the inbreeding level of the BS pig population, we used whole-genome resequencing to identify runs of homozygosity (ROH) regions in BS pigs, calculated the inbreeding coefficient based on pedigree and ROH, and screened candidate genes with important economic traits from ROH islands. A total of 22,633,391 SNPS were obtained from the whole genome of BS pigs, and 201 ROHs were detected from 532,450 SNPS after quality control. The number of medium-length ROH (1-5 Mb) was the highest (98.43%), the number of long ROH (>5 Mb) was the lowest (1.57%), and the inbreeding of BS pigs mainly occurred in distant generations. The inbreeding coefficient FROH, calculated based on ROH, was 0.018 ± 0.016, and the FPED, calculated based on the pedigree, was 0.027 ± 0.028, which were positively correlated. Forty ROH islands were identified, containing 507 genes and 891 QTLs. Several genes were associated with growth and development (IGFALS, PTN, DLX5, DKK1, WNT2), meat quality traits (MC3R, ACSM3, ECI1, CD36, ROCK1, CACNA2D1), and reproductive traits (NPW, TSHR, BMP7). This study provides a reference for the protection and utilization of BS pigs.
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Affiliation(s)
- Wenjun Li
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (W.L.); (L.W.); (X.M.); (J.H.); (G.F.)
| | - Xudong Wu
- Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230036, China; (X.W.); (W.Z.)
| | - Decai Xiang
- Institute of Pig and Animal Research, Yunnan Academy of Animal Husbandry and Veterinary Science, Kunming 650201, China;
| | - Wei Zhang
- Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230036, China; (X.W.); (W.Z.)
| | - Lingxiang Wu
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (W.L.); (L.W.); (X.M.); (J.H.); (G.F.)
| | - Xintong Meng
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (W.L.); (L.W.); (X.M.); (J.H.); (G.F.)
| | - Jinlong Huo
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (W.L.); (L.W.); (X.M.); (J.H.); (G.F.)
| | - Zongjun Yin
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China;
| | - Guowen Fu
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (W.L.); (L.W.); (X.M.); (J.H.); (G.F.)
| | - Guiying Zhao
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (W.L.); (L.W.); (X.M.); (J.H.); (G.F.)
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Wang Z, Zhong Z, Xie X, Wang F, Pan D, Wang Q, Pan Y, Xiao Q, Tan Z. Detection of Runs of Homozygosity and Identification of Candidate Genes in the Whole Genome of Tunchang Pigs. Animals (Basel) 2024; 14:201. [PMID: 38254370 PMCID: PMC10812771 DOI: 10.3390/ani14020201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 12/23/2023] [Accepted: 01/03/2024] [Indexed: 01/24/2024] Open
Abstract
Tunchang pigs are an indigenous pig population in China known for their high tolerance to roughage, delicious meat, and fecundity. However, the number of Tunchang pigs has been declining due to the influence of commercial breeds and African swine fever, which could potentially lead to inbreeding. To assess the inbreeding level and the genetic basis of important traits in Tunchang pigs, our research investigated the patterns in "runs of homozygosity" (ROHs) using whole genome resequencing data from 32 Tunchang pigs. The study aimed to determine the length, number, coverage, and distribution model of ROHs in Tunchang pigs, as well as genomic regions with high ROH frequencies. The results of the study revealed that a total of 20,499,374 single-nucleotide polymorphisms (SNPs) and 1953 ROH fragments were recognized in 32 individuals. The ROH fragments in Tunchang pigs were predominantly short, ranging from 0.5 to 1 megabases (Mb) in length. Furthermore, the coverage of ROHs varied across chromosomes, with chromosome 3 having the highest coverage and chromosome 11 having the lowest coverage. The genetic diversity of Tunchang pigs was found to be relatively high based on the values of HE (expected heterozygosity), HO (observed heterozygosity), pi (nucleotide diversity), Ne (effective population size), and MAF (minor allele frequency). The average inbreeding coefficients of Tunchang pigs, as determined by three different methods (FHOM, FGRM, and FROH), were 0.019, 0.0138, and 0.0304, respectively. These values indicate that the level of inbreeding in Tunchang pigs is currently low. Additionally, the study identified a total of 13 ROH islands on all chromosomes, which in total contained 38,913 SNPs and 120 genes. These ROH islands included genes associated with economically important traits, including meat quality (GYS1, PHLPP1, SLC27A5, and CRTC1), growth and development (ANKS1A, TAF11, SPDEF, LHB, and PACSIN1), and environmental adaptation (SLC26A7). The findings of this research offer valuable perspectives on the present status of Tunchang pig resources and offer a reference for breeding conservation plans and the efficient utilization of Tunchang pigs in the future. By understanding the inbreeding level and genetic basis of important traits in Tunchang pigs, conservation efforts can be targeted towards maintaining genetic diversity and promoting the sustainable development of this indigenous pig population.
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Affiliation(s)
- Ziyi Wang
- Hainan Key Laboratory of Tropical Animal Reproduction & Breeding and Epidemic Disease Research, School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China; (Z.W.)
| | - Ziqi Zhong
- Hainan Key Laboratory of Tropical Animal Reproduction & Breeding and Epidemic Disease Research, School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China; (Z.W.)
| | - Xinfeng Xie
- Hainan Key Laboratory of Tropical Animal Reproduction & Breeding and Epidemic Disease Research, School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China; (Z.W.)
| | - Feifan Wang
- Hainan Key Laboratory of Tropical Animal Reproduction & Breeding and Epidemic Disease Research, School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China; (Z.W.)
| | - Deyou Pan
- Hainan Key Laboratory of Tropical Animal Reproduction & Breeding and Epidemic Disease Research, School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China; (Z.W.)
| | - 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
| | - 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, School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China; (Z.W.)
| | - Zhen Tan
- Hainan Key Laboratory of Tropical Animal Reproduction & Breeding and Epidemic Disease Research, School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China; (Z.W.)
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Feng X, Diao S, Liu Y, Xu Z, Li G, Ma Y, Su Z, Liu X, Li J, Zhang Z. Exploring the mechanism of artificial selection signature in Chinese indigenous pigs by leveraging multiple bioinformatics database tools. BMC Genomics 2023; 24:743. [PMID: 38053015 DOI: 10.1186/s12864-023-09848-7] [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: 02/23/2023] [Accepted: 11/27/2023] [Indexed: 12/07/2023] Open
Abstract
BACKGROUND Chinese indigenous pigs in Yunnan exhibit considerable phenotypic diversity, but their population structure and the biological interpretation of signatures of artificial selection require further investigation. To uncover population genetic diversity, migration events, and artificial selection signatures in Chinese domestic pigs, we sampled 111 Yunnan pigs from four breeds in Yunnan which is considered to be one of the centres of livestock domestication in China, and genotyped them using Illumina Porcine SNP60K BeadChip. We then leveraged multiple bioinformatics database tools to further investigate the signatures and associated complex traits. RESULTS Population structure and migration analyses showed that Diannanxiaoer pigs had different genetic backgrounds from other Yunnan pigs, and Gaoligongshan may undergone the migration events from Baoshan and Saba pigs. Intriguingly, we identified a possible common target of sharing artificial selection on a 265.09 kb region on chromosome 5 in Yunnan indigenous pigs, and the genes on this region were associated with cardiovascular and immune systems. We also detected several candidate genes correlated with dietary adaptation, body size (e.g., PASCIN1, GRM4, ITPR2), and reproductive performance. In addition, the breed-sharing gene MMP16 was identified to be a human-mediated gene. Multiple lines of evidence at the mammalian genome, transcriptome, and phenome levels further supported the evidence for the causality between MMP16 variants and the metabolic diseases, brain development, and cartilage tissues in Chinese pigs. Our results suggested that the suppression of MMP16 would directly lead to inactivity and insensitivity of neuronal activity and skeletal development in Chinese indigenous pigs. CONCLUSION In this study, the population genetic analyses and identification of artificial selection signatures of Yunnan indigenous pigs help to build an understanding of the effect of human-mediated selection mechanisms on phenotypic traits in Chinese indigenous pigs. Further studies are needed to fully characterize the process of human-mediated genes and biological mechanisms.
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Affiliation(s)
- Xueyan Feng
- State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
| | - Shuqi Diao
- State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
| | - Yuqiang Liu
- State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
| | - Zhiting Xu
- State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
| | - Guangzhen Li
- State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
| | - Ye Ma
- State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
| | - Zhanqin Su
- State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
| | - Xiaohong Liu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Jiaqi Li
- State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China.
| | - Zhe Zhang
- State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China.
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Giovannini S, Strillacci MG, Bagnato A, Albertini E, Sarti FM. Genetic and Phenotypic Characteristics of Belted Pig Breeds: A Review. Animals (Basel) 2023; 13:3072. [PMID: 37835678 PMCID: PMC10571877 DOI: 10.3390/ani13193072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 09/26/2023] [Accepted: 09/27/2023] [Indexed: 10/15/2023] Open
Abstract
Belted pig breeds have unique, distinguishing phenotypic characteristics. This review summarises the current knowledge on pig breeds displaying a belted coat pattern. Belts of different widths and positions around the animal's trunk characterise specific pig breeds from all around the world. All the breeds included in the present paper have been searched through the FAO domestic animal diversity information system (DAD-IS), Every country was checked to identify all breeds described as having black or red piebald coat pattern variations. Advances in genomic technologies have made it possible to identify the specific genes and genetic markers associated with the belted phenotype and explore the genetic relationships between different local breeds. Thus, the origin, history, and production traits of these breeds, together with all the genomic information related to the mechanism of skin pigmentation, are discussed. By increasing our understanding of these breeds, we can appreciate the richness of our biological and cultural heritage and work to preserve the biodiversity of the world's animals.
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Affiliation(s)
- Samira Giovannini
- Department of Agricultural, Food and Environmental Sciences, Università degli Studi di Perugia, Borgo XX Giugno 74, 06121 Perugia, Italy; (E.A.); (F.M.S.)
| | - Maria Giuseppina Strillacci
- Department of Veterinary and Animal Science, Università degli Studi di Milano, Via Dell’Università 6, 26900 Lodi, Italy; (M.G.S.); (A.B.)
| | - Alessandro Bagnato
- Department of Veterinary and Animal Science, Università degli Studi di Milano, Via Dell’Università 6, 26900 Lodi, Italy; (M.G.S.); (A.B.)
| | - Emidio Albertini
- Department of Agricultural, Food and Environmental Sciences, Università degli Studi di Perugia, Borgo XX Giugno 74, 06121 Perugia, Italy; (E.A.); (F.M.S.)
| | - Francesca Maria Sarti
- Department of Agricultural, Food and Environmental Sciences, Università degli Studi di Perugia, Borgo XX Giugno 74, 06121 Perugia, Italy; (E.A.); (F.M.S.)
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8
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Wu F, Chen Z, Zhang Z, Wang Z, Zhang Z, Wang Q, Pan Y. The Role of SOCS3 in Regulating Meat Quality in Jinhua Pigs. Int J Mol Sci 2023; 24:10593. [PMID: 37445769 DOI: 10.3390/ijms241310593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 06/15/2023] [Accepted: 06/20/2023] [Indexed: 07/15/2023] Open
Abstract
Meat quality is an important economic trait that influences the development of the pig industry. Skeletal muscle development and glycolytic potential (GP) are two crucial aspects that significantly impact meat quality. It has been reported that abnormal skeletal muscle development and high glycogen content results in low meat quality. However, the genetic mechanisms underlying these factors are still unclear. Compared with intensive pig breeds, Chinese indigenous pig breeds, such as the Jinhua pig, express superior meat quality characteristics. The differences in the meat quality traits between Jinhua and intensive pig breeds make them suitable for uncovering the genetic mechanisms that regulate meat quality traits. In this study, the Jinhua pig breed and five intensive pig breeds, including Duroc, Landrace, Yorkshire, Berkshire, and Pietrain pig breeds, were selected as experimental materials. First, the FST and XP-EHH methods were used to screen the selective signatures on the genome in the Jinhua population. Then, combined with RNA-Seq data, the study further confirmed that SOCS3 could be a key candidate gene that influences meat quality by mediating myoblast proliferation and glycometabolism because of the down-regulated expression of SOCS3 in Jinhua pigs compared with Landrace pigs. Finally, through SOCS3 knockout (KO) and overexpression (OE) experiments in mouse C2C12 cells, the results showed that SOCS3 regulated the cell proliferation of myoblasts. Moreover, SOCS3 is involved in regulating glucose uptake by the IRS1/PI3K/AKT signaling pathway. Overall, these findings provide a basis for the genetic improvement of meat quality traits in the pig industry.
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Affiliation(s)
- Fen Wu
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Zitao Chen
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Zhenyang Zhang
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Zhen Wang
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Zhe Zhang
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Qishan Wang
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
- Key Laboratory of Livestock and Poultry Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Hangzhou 310058, China
| | - Yuchun Pan
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
- Key Laboratory of Livestock and Poultry Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Hangzhou 310058, China
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9
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Wang F, Zha Z, He Y, Li J, Zhong Z, Xiao Q, Tan Z. Genome-Wide Re-Sequencing Data Reveals the Population Structure and Selection Signatures of Tunchang Pigs in China. Animals (Basel) 2023; 13:1835. [PMID: 37889708 PMCID: PMC10252034 DOI: 10.3390/ani13111835] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 05/26/2023] [Accepted: 05/30/2023] [Indexed: 09/29/2023] Open
Abstract
Tunchang pig is one population of Hainan pig in the Hainan Province of China, with the characteristics of delicious meat, strong adaptability, and high resistance to diseases. To explore the genetic diversity and population structure of Tunchang pigs and uncover their germplasm characteristics, 10 unrelated Tunchang pigs were re-sequenced using the Illumina NovaSeq 150 bp paired-end platform with an average depth of 10×. Sequencing data from 36 individuals of 7 other pig breeds (including 4 local Chinese pig breeds (5 Jinhua, 5 Meishan, 5 Rongchang, and 6 Wuzhishan), and 3 commonly used commercial pig breeds (5 Duorc, 5 Landrace, and 5 Large White)) were downloaded from the NCBI public database. After analysis of genetic diversity and population structure, it has been found that compared to commercial pigs, Tunchang pigs have higher genetic diversity and are genetically close to native Chinese breeds. Three methods, FST, θπ, and XP-EHH, were used to detect selection signals for three breeds of pigs: Tunchang, Duroc, and Landrace. A total of 2117 significantly selected regions and 201 candidate genes were screened. Gene enrichment analysis showed that candidate genes were mainly associated with good adaptability, disease resistance, and lipid metabolism traits. Finally, further screening was conducted to identify potential candidate genes related to phenotypic traits, including meat quality (SELENOV, CBR4, TNNT1, TNNT3, VPS13A, PLD3, SRFBP1, and SSPN), immune regulation (CD48, FBL, PTPRH, GNA14, LOX, SLAMF6, CALCOCO1, IRGC, and ZNF667), growth and development (SYT5, PRX, PPP1R12C, and SMG9), reproduction (LGALS13 and EPG5), vision (SLC9A8 and KCNV2), energy metabolism (ATP5G2), cell migration (EPS8L1), and olfaction (GRK3). In summary, our research results provide a genomic overview of the genetic variation, genetic diversity, and population structure of the Tunchang pig population, which will be valuable for breeding and conservation of Tunchang pigs in the future.
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Affiliation(s)
| | | | | | | | | | - Qian Xiao
- School of Animal Science and Technology, Hainan University, Haikou 570228, China; (F.W.)
| | - Zhen Tan
- School of Animal Science and Technology, Hainan University, Haikou 570228, China; (F.W.)
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10
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Zhang L, Zhang S, Zhan F, Song M, Shang P, Zhu F, Li J, Yang F, Li X, Qiao R, Han X, Li X, Liu G, Wang K. Population Genetic Analysis of Six Chinese Indigenous Pig Meta-Populations Based on Geographically Isolated Regions. Animals (Basel) 2023; 13:ani13081396. [PMID: 37106959 PMCID: PMC10135051 DOI: 10.3390/ani13081396] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 03/28/2023] [Accepted: 04/12/2023] [Indexed: 04/29/2023] Open
Abstract
The diversification of indigenous pig breeds in China has resulted from multiple climate, topographic, and human cultural influences. The numerous indigenous pig breeds can be geographically divided into six meta-populations; however, their genetic relationships, contributions to genetic diversity, and genetic signatures remain unclear. Whole-genome SNP data for 613 indigenous pigs from the six Chinese meta-populations were obtained and analyzed. Population genetic analyses confirmed significant genetic differentiation and a moderate mixture among the Chinese indigenous pig meta-populations. The North China (NC) meta-population had the largest contribution to genetic and allelic diversity. Evidence from selective sweep signatures revealed that genes related to fat deposition and heat stress response (EPAS1, NFE2L2, VPS13A, SPRY1, PLA2G4A, and UBE3D) were potentially involved in adaptations to cold and heat. These findings from population genetic analyses provide a better understanding of indigenous pig characteristics in different environments and a theoretical basis for future work on the conservation and breeding of Chinese indigenous pigs.
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Affiliation(s)
- Lige Zhang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China
| | - Songyuan Zhang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China
| | - Fengting Zhan
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China
| | - Mingkun Song
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China
| | - Peng Shang
- Animal Science College, Tibet Agriculture and Animal Husbandry University, Linzhi 860000, China
| | - Fangxian Zhu
- National Animal Husbandry Service, Beijing 100193, China
| | - Jiang Li
- National Supercomputing Center in Zhengzhou, Zhengzhou 450001, China
| | - Feng Yang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China
| | - Xiuling Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China
| | - Ruimin Qiao
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China
| | - Xuelei Han
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China
| | - Xinjian Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China
| | - Gang Liu
- National Animal Husbandry Service, Beijing 100193, China
| | - Kejun Wang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China
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11
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Miao J, Chen Z, Zhang Z, Wang Z, Wang Q, Zhang Z, Pan Y. A web tool for the global identification of pig breeds. Genet Sel Evol 2023; 55:18. [PMID: 36944938 PMCID: PMC10029154 DOI: 10.1186/s12711-023-00788-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 02/14/2023] [Indexed: 03/23/2023] Open
Abstract
BACKGROUND Natural and artificial selection for more than 9000 years have led to a variety of domestic pig breeds. Accurate identification of pig breeds is important for breed conservation, sustainable breeding, pork traceability, and local resource registration. RESULTS We evaluated the performance of four selectors and six classifiers for breed identification using a wide range of pig breeds (N = 91). The internal cross-validation and external independent testing showed that partial least squares regression (PLSR) was the most effective selector and partial least squares-discriminant analysis (PLS-DA) was the most powerful classifier for breed identification among many breeds. Five-fold cross-validation indicated that using PLSR as the selector and PLS-DA as the classifier to discriminate 91 pig breeds yielded 98.4% accuracy with only 3K single nucleotide polymorphisms (SNPs). We also constructed a reference dataset with 124 pig breeds and used it to develop the web tool iDIGs ( http://alphaindex.zju.edu.cn/iDIGs_en/ ) as a comprehensive application for global pig breed identification. iDIGs allows users to (1) identify pig breeds without a reference population and (2) design small panels to discriminate several specific pig breeds. CONCLUSIONS In this study, we proved that breed identification among a wide range of pig breeds is feasible and we developed a web tool for such pig breed identification.
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Affiliation(s)
- Jian Miao
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Zitao Chen
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Zhenyang Zhang
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Zhen Wang
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Qishan Wang
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
- Hainan Institute of Zhejiang University, Building 11, Yongyou Industrial Park, Yazhou Bay Science and Technology City, Yazhou District, Sanya, 572025, Hainan, China
| | - Zhe Zhang
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China.
| | - Yuchun Pan
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China.
- Hainan Institute of Zhejiang University, Building 11, Yongyou Industrial Park, Yazhou Bay Science and Technology City, Yazhou District, Sanya, 572025, Hainan, China.
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12
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He Y, Li Y, Pan Y, Li A, Huang Y, Mi Q, Zhao S, Zhang C, Ran J, Hu H, Pan H. Correlation analysis between jejunum metabolites and immune function in Saba and Landrace piglets. Front Vet Sci 2023; 10:1069809. [PMID: 37008364 PMCID: PMC10060822 DOI: 10.3389/fvets.2023.1069809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 02/28/2023] [Indexed: 03/18/2023] Open
Abstract
The immune function of the intestinal mucosa plays a crucial role in the intestinal health of hosts. As signaling molecules and precursors of metabolic reactions, intestinal chyme metabolites are instrumental in maintaining host immune homeostasis. Saba (SB) pigs, a unique local pig species in central Yunnan Province, China. However, research on jejunal metabolites in this species is limited. Here, we used immunohistochemistry and untargeted metabolomics by liquid chromatography mass spectrometry (LC-MS/MS) to study differences in jejunal immunophenotypes and metabolites between six Landrace (LA) and six SB piglets (35 days old). The results showed that the levels of the anti-inflammatory factor interleukin 10 (IL-10) were markedly higher in SB piglets than in LA piglets (P < 0.01), while the levels of the proinflammatory factors IL-6, IL-1β, and Toll-like receptor 2 (TLR-2) were markedly lower (P < 0.01). Furthermore, the levels of mucin 2 (MUC2) and zona occludens (ZO-1), which are related to mucosal barrier function, were significantly higher in SB piglets than in LA piglets (P < 0.01), as were villus height, villus height/crypt depth ratio, and goblet cell number (P < 0.05). Differences in jejunal chyme metabolic patterns were observed between the two piglets. In the negative ion mode, cholic acid metabolites ranked in the top 20 and represented 25% of the total. Taurodeoxycholic acid (TDCA) content was significantly higher in SB piglets than in LA piglets (P < 0.01). TDCA positively correlated with ZO-1, villus height, villus height/crypt depth ratio, and goblet cell number. These results suggest that SB pigs have a strong jejunal immune function and that TDCA was positively regulates jejunal immunity and mucosal barrier function. Our findings provide a reference for understanding intestinal immune function in different pig breeds and for the discovery of potential biomarkers to help solve health issues related to pig production.
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Affiliation(s)
- Yang He
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed Science, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Yongxiang Li
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed Science, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Yangsu Pan
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed Science, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Anjian Li
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed Science, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Ying Huang
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed Science, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Qianhui Mi
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed Science, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Sumei Zhao
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed Science, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Chunyong Zhang
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed Science, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Jinming Ran
- College of Modern Agriculture, Dazhou Vocational and Technical College, Dazhou, China
| | - Hong Hu
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed Science, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
- Hong Hu
| | - Hongbin Pan
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed Science, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
- *Correspondence: Hongbin Pan
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13
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Han Y, Tan T, Li Z, Ma Z, Lan G, Liang J, Li K, Bai L. Identification of Selection Signatures and Loci Associated with Important Economic Traits in Yunan Black and Huainan Pigs. Genes (Basel) 2023; 14:genes14030655. [PMID: 36980926 PMCID: PMC10048629 DOI: 10.3390/genes14030655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 02/26/2023] [Accepted: 03/01/2023] [Indexed: 03/08/2023] Open
Abstract
Henan Province is located in central China and rich in domestic pig populations; Huainan (HN) pigs are one of three Henan indigenous breeds with great performance, including early maturation, strong disease resistance and high meat quality. Yunan (YN) black pigs are a typical, newly cultivated breed, synthesized between HN pigs and American Duroc, and are subjected to selection for important traits, such as fast growth and excellent meat quality. However, the genomic differences, selection signatures and loci associated with important economic traits in YN black pigs and HN pigs are still not well understood. In this study, based on high-density SNP chip analysis of 159 samples covering commercial DLY (Duroc × Landrace × Large White) pigs, HN pigs and YN black pigs, we performed a comprehensive analysis of phylogenetic relationships and genetic diversity among the three breeds. Furthermore, we used composite likelihood ratio tests (CLR) and F-statistics (Fst) to identify specific signatures of selection associated with important economic traits and potential candidate genes. We found 147 selected regions (top 1%) harboring 90 genes based on genetic differentiation (Fst) in the YN-DLY group. In the HN-DLY group, 169 selected regions harbored 58 genes. In the YN-HN group, 179 selected regions harbored 77 genes. In addition, the QTLs database with the most overlapping regions was associated with triglyceride level, number of mummified pigs, hemoglobin and loin muscle depth for YN black pigs, litter size and intramuscular fat content for HN pigs, and humerus length, linolenic acid content and feed conversion ratio mainly in DLY pigs. Of note, overlapping 14 tissue-specific promoters’ annotation with the top Fst 1% selective regions systematically demonstrated the muscle-specific and hypothalamus-specific regulatory elements in YN black pigs. Taken together, these results contribute to an accurate knowledge of crossbreeding, thus benefitting the evaluation of production performance and improving the genome-assisted breeding of other important indigenous pig in the future.
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Affiliation(s)
- Yachun Han
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Tao Tan
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Zixin Li
- College of Animal Science & Technology, Guangxi University, Nanning 530003, China
| | - Zheng Ma
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Ganqiu Lan
- College of Animal Science & Technology, Guangxi University, Nanning 530003, China
| | - Jing Liang
- College of Animal Science & Technology, Guangxi University, Nanning 530003, China
| | - Kui Li
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Lijing Bai
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
- Correspondence: ; Tel./Fax: +86-0755-2325-0160
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14
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Wang H, Wang X, Li M, Sun H, Chen Q, Yan D, Dong X, Pan Y, Lu S. Genome-wide association study reveals genetic loci and candidate genes for meat quality traits in a four-way crossbred pig population. Front Genet 2023; 14:1001352. [PMID: 36814900 PMCID: PMC9939654 DOI: 10.3389/fgene.2023.1001352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Accepted: 01/24/2023] [Indexed: 02/08/2023] Open
Abstract
Meat quality traits (MQTs) have gained more attention from breeders due to their increasing economic value in the commercial pig industry. In this genome-wide association study (GWAS), 223 four-way intercross pigs were genotyped using the specific-locus amplified fragment sequencing (SLAF-seq) and phenotyped for PH at 45 min post mortem (PH45), meat color score (MC), marbling score (MA), water loss rate (WL), drip loss (DL) in the longissimus muscle, and cooking loss (CL) in the psoas major muscle. A total of 227, 921 filtered single nucleotide polymorphisms (SNPs) evenly distributed across the entire genome were detected to perform GWAS. A total of 64 SNPs were identified for six meat quality traits using the mixed linear model (MLM), of which 24 SNPs were located in previously reported QTL regions. The phenotypic variation explained (PVE) by the significant SNPs was from 2.43% to 16.32%. The genomic heritability estimates based on SNP for six meat-quality traits were low to moderate (0.07-0.47) being the lowest for CL and the highest for DL. A total of 30 genes located within 10 kb upstream or downstream of these significant SNPs were found. Furthermore, several candidate genes for MQTs were detected, including pH45 (GRM8), MC (ANKRD6), MA (MACROD2 and ABCG1), WL (TMEM50A), CL (PIP4K2A) and DL (CDYL2, CHL1, ABCA4, ZAG and SLC1A2). This study provided substantial new evidence for several candidate genes to participate in different pork quality traits. The identification of these SNPs and candidate genes provided a basis for molecular marker-assisted breeding and improvement of pork quality traits.
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Affiliation(s)
- Huiyu Wang
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, China,Faculty of Animal Science, Xichang University, Xichang, Sichuan, China
| | - Xiaoyi Wang
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Mingli Li
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Hao Sun
- Faculty of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Qiang Chen
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Dawei Yan
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Xinxing Dong
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Yuchun Pan
- Faculty of Animal Science, Zhejiang University, Hangzhou, Zhejiang, China,*Correspondence: Yuchun Pan, ; Shaoxiong Lu,
| | - Shaoxiong Lu
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, China,*Correspondence: Yuchun Pan, ; Shaoxiong Lu,
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15
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Tian S, Li W, Zhong Z, Wang F, Xiao Q. Genome-wide re-sequencing data reveals the genetic diversity and population structure of Wenchang chicken in China. Anim Genet 2023; 54:328-337. [PMID: 36639920 DOI: 10.1111/age.13293] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 11/14/2022] [Accepted: 12/31/2022] [Indexed: 01/15/2023]
Abstract
Wenchang (WC) chicken, the only indigenous chicken breed listed in Chinese genetic resources in Hainan province, is well known for its excellent meat quality and is sold all over southeast Asia. In recent years, the number of WC has decreased sharply with considerable variability in the quality at market. To explore the genetic diversity and population structure of WC chickens, the whole-genome data of 235 WC individuals from three conservation farms were obtained using the Illumina 150 bp paired-end platform and used in conjunction with the sequencing data from 123 individuals from other chicken breeds (including eight Chinese indigenous chicken breeds and three foreign or commercial breeds) downloaded from a public database. A total of 12 111 532 SNPs were identified, of which 11 541 878 SNPs were identified in WC. The results of gene enrichment analyses revealed that the SNPs harbored in WC genomes are mainly related to environmental adaptation, disease resistance and meat quality traits. Genetic diversity statistics, quantified by expected heterozygosity, observed heterozygosity, linkage disequilibrium, nucleotide diversity and fixation statistics, indicated that WC displays high genetic diversity compared with other Chinese indigenous chicken breeds. Genetic structure analyses showed that each population displayed great differentiation between WC and the other breeds, indicating the uniqueness of WC. In conclusion, the results of our study provide the first genomic overview of genetic variants, genetic diversity and population structure of WC from three conservation farms. This information will be valuable for the future breeding and conservation of WC and other surveyed populations.
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Affiliation(s)
- Shuaishuai Tian
- Hainan Key Laboratory of Tropical Animal Reproduction and Breeding and Epidemic Disease Research, College of Animal Science and Technology, Hainan University, Haikou, China
| | - Wei Li
- Department of Animal Science, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Ziqi Zhong
- Hainan Key Laboratory of Tropical Animal Reproduction and Breeding and Epidemic Disease Research, College of Animal Science and Technology, Hainan University, Haikou, China
| | - Feifan Wang
- Hainan Key Laboratory of Tropical Animal Reproduction and Breeding and Epidemic Disease Research, College of Animal Science and Technology, Hainan University, Haikou, China
| | - Qian Xiao
- Hainan Key Laboratory of Tropical Animal Reproduction and Breeding and Epidemic Disease Research, College of Animal Science and Technology, Hainan University, Haikou, China
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16
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Abbasi-Moshaii B, Moradi MH, Yin T, Rahimi-Mianji G, Nejati-Javaremi A, König S. Genome-wide scan for selective sweeps identifies novel loci associated with resistance to mastitis in German Holstein cattle. J Anim Breed Genet 2023; 140:92-105. [PMID: 35988016 DOI: 10.1111/jbg.12737] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 08/02/2022] [Indexed: 12/13/2022]
Abstract
Domestication and selection significantly changed phenotypic and behavioural traits in modern domestic animals. In this study, to identify the genomic regions associated with mastitis, genomic data of German Holstein dairy cattle were analysed. The samples were genotyped using the Bovine 50 K SNP chip. For each defined healthy and sick group, 133 samples from 13,276 genotyped dairy cows were selected based on mastitis random residual effects. Grouping was done to infer selection signatures based on XP-EHH statistic. The results revealed that for the top 0.01 percentile of the obtained XP-EHH values, five genomic regions on chromosomes 8, 11, 12, 14 and 26 of the control group, and four regions on chromosomes 3, 4 (two regions) and 22 of the case group, have been under selection. Also, consideration of the top 0.1 percentile of the XP-EHH values, clarified 21 and 15 selective sweeps in the control and case group, respectively. This study identified some genomic regions containing potential candidate genes associated with resistance and susceptibility to mastitis, immune system and inflammation, milk traits, udder morphology and different types of cancers. In addition, these regions overlap with some quantitative trait loci linked to clinical mastitis, immunoglobulin levels, somatic cell score, udder traits, milk fat and protein, milk yield, milking speed and veterinary treatments. It is noteworthy that we found two regions in the healthy group (on chromosomes 12 and 14) with strong signals, which were not described previously. It is likely that future research could link these identified genomic regions to mastitis. The results of the current study contribute to the identification of causal mutations, genomic regions and genes affecting mastitis incidence in dairy cows.
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Affiliation(s)
- Bita Abbasi-Moshaii
- Institute of Animal Breeding and Genetics, Justus-Liebig University Giessen, Giessen, Germany.,Department of Animal Science and Fisheries, Sari Agricultural Science and Natural Resources University, Sari, Iran
| | | | - Tong Yin
- Institute of Animal Breeding and Genetics, Justus-Liebig University Giessen, Giessen, Germany
| | - Ghodratollah Rahimi-Mianji
- Department of Animal Science and Fisheries, Sari Agricultural Science and Natural Resources University, Sari, Iran
| | - Ardeshir Nejati-Javaremi
- Department of Animal Science, University College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
| | - Sven König
- Institute of Animal Breeding and Genetics, Justus-Liebig University Giessen, Giessen, Germany
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17
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Li Y, He Y, Ran J, Huang Y, Li X, Jiang H, Li X, Pan Y, Zhao S, Song C, Pan H, Hu H. Comparison of meat quality and glycolysis potential of two hybrid pigs in three-way hybrid model. Front Vet Sci 2023; 10:1136485. [PMID: 36875993 PMCID: PMC9981941 DOI: 10.3389/fvets.2023.1136485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 02/01/2023] [Indexed: 02/19/2023] Open
Abstract
With the improvement of consumers' requirements for pork quality, the method of crossbreeding with excellent local pig breeds to improve meat quality is popular. Saba pig has high reproduction rate, good meat quality and high utilization rate of roughage, but its excellent characteristics have not been fully developed and utilized. To promote the development and utilization of Saba pigs and production of high-quality pork, the meat quality traits and glycolysis potential of Duroc × (Landrace × Yorkshire) (DLY), Berkshire × (Duroc × Saba) (BDS), and Duroc × (Berkshire × Saba) (DBS) three-way crossbred pigs were compared. The results showed that DLY had the highest live weight, carcass weight, lean meat percentage, drip loss, glycolysis potential, muscle diameter, and relative mRNA expression levels of type IIb muscle fibers as well as the lowest ultimate pH (p < 0.05). The lightness value of DBS was the highest (p < 0.05). Among the three crossbred pigs, myristic, arachidic, palmitoleic, and eicosenoic acids were the highest in BDS. These results indicated that the carcass traits of local crossbred pigs were worse than those of DLY pigs, but meat quality was markedly higher, with BDS showing the best meat quality.
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Affiliation(s)
- Yongxiang Li
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed Science, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Yang He
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed Science, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Jinming Ran
- College of Modern Agriculture, Dazhou Vocational and Technical College, Dazhou, China
| | - Ying Huang
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed Science, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Xian Li
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed Science, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Hengxin Jiang
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed Science, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Xueyan Li
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed Science, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Yangsu Pan
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed Science, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Sumei Zhao
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed Science, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Chunlian Song
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming, China
| | - Hongbin Pan
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed Science, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Hong Hu
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed Science, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
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18
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Genome-Wide Association Study of Growth Traits in a Four-Way Crossbred Pig Population. Genes (Basel) 2022; 13:genes13111990. [DOI: 10.3390/genes13111990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Revised: 10/28/2022] [Accepted: 10/28/2022] [Indexed: 11/04/2022] Open
Abstract
Growth traits are crucial economic traits in the commercial pig industry and have a substantial impact on pig production. However, the genetic mechanism of growth traits is not very clear. In this study, we performed a genome-wide association study (GWAS) based on the specific-locus amplified fragment sequencing (SLAF-seq) to analyze ten growth traits on 223 four-way intercross pigs. A total of 227,921 highly consistent single nucleotide polymorphisms (SNPs) uniformly dispersed throughout the entire genome were used to conduct GWAS. A total of 53 SNPs were identified for ten growth traits using the mixed linear model (MLM), of which 18 SNPs were located in previously reported quantitative trait loci (QTL) regions. Two novel QTLs on SSC4 and SSC7 were related to average daily gain from 30 to 60 kg (ADG30–60) and body length (BL), respectively. Furthermore, 13 candidate genes (ATP5O, GHRHR, TRIM55, EIF2AK1, PLEKHA1, BRAP, COL11A2, HMGA1, NHLRC1, SGSM1, NFATC2, MAML1, and PSD3) were found to be associated with growth traits in pigs. The GWAS findings will enhance our comprehension of the genetic architecture of growth traits. We suggested that these detected SNPs and corresponding candidate genes might provide a biological foundation for improving the growth and production performance of pigs in swine breeding.
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19
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Chen Z, Teng J, Diao S, Xu Z, Ye S, Qiu D, Zhang Z, Pan Y, Li J, Zhang Q, Zhang Z. Insights into the architecture of human-induced polygenic selection in Duroc pigs. J Anim Sci Biotechnol 2022; 13:99. [PMID: 36127741 PMCID: PMC9490910 DOI: 10.1186/s40104-022-00751-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 07/03/2022] [Indexed: 11/10/2022] Open
Abstract
Background As one of the most utilized commercial composite boar lines, Duroc pigs have been introduced to China and undergone strongly human-induced selection over the past decades. However, the efficiencies and limitations of previous breeding of Chinese Duroc pigs are largely understudied. The objective of this study was to uncover directional polygenic selection in the Duroc pig genome, and investigate points overlooked in the past breeding process. Results Here, we utilized the Generation Proxy Selection Mapping (GPSM) on a dataset of 1067 Duroc pigs with 8,766,074 imputed SNPs. GPSM detected a total of 5649 putative SNPs actively under selection in the Chinese Duroc pig population, and the potential functions of the selection regions were mainly related to production, meat and carcass traits. Meanwhile, we observed that the allele frequency of variants related to teat number (NT) relevant traits was also changed, which might be influenced by genes that had pleiotropic effects. First, we identified the direction of selection on NT traits by \documentclass[12pt]{minimal}
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\begin{document}$$\hat{G}$$\end{document}G^, and further pinpointed large-effect genomic regions associated with NT relevant traits by selection signature and GWAS. Combining results of NT relevant traits-specific selection signatures and GWAS, we found three common genome regions, which were overlapped with QTLs related to production, meat and carcass traits besides “teat number” QTLs. This implied that there were some pleiotropic variants underlying NT and economic traits. We further found that rs346331089 has pleiotropic effects on NT and economic traits, e.g., litter size at weaning (LSW), litter weight at weaning (LWW), days to 100 kg (D100), backfat thickness at 100 kg (B100), and loin muscle area at 100 kg (L100) traits. Conclusions The selected loci that we identified across methods displayed the past breeding process of Chinese Duroc pigs, and our findings could be used to inform future breeding decision. Supplementary Information The online version contains supplementary material available at 10.1186/s40104-022-00751-x.
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Affiliation(s)
- Zitao Chen
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, P.R. China.,Department of Animal Science, College of Animal Science, Zhejiang University, 866# Yuhangtang Road, Hangzhou, 310058, P.R. China
| | - Jinyan Teng
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, P.R. China
| | - Shuqi Diao
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, P.R. China
| | - Zhiting Xu
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, P.R. China
| | - Shaopan Ye
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, P.R. China.,Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, 243 Daxue Road, Shantou, 515063, P.R. China
| | - Dingjie Qiu
- Fujian Yongcheng Agricultural & Animal Husbandry Sci-Tech Group Co., Ltd., Fuqing, 350399, P.R. China
| | - Zhe Zhang
- Department of Animal Science, College of Animal Science, Zhejiang University, 866# Yuhangtang Road, Hangzhou, 310058, P.R. China
| | - Yuchun Pan
- Department of Animal Science, College of Animal Science, Zhejiang University, 866# Yuhangtang Road, Hangzhou, 310058, P.R. China
| | - Jiaqi Li
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, P.R. China
| | - Qin Zhang
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, Shandong Agricultural University, Tai'an, 271018, P.R. China
| | - Zhe Zhang
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, P.R. China.
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20
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Shi S, Shao D, Yang L, Liang Q, Han W, Xue Q, Qu L, Leng L, Li Y, Zhao X, Dong P, Walugembe M, Kayang BB, Muhairwa AP, Zhou H, Tong H. Whole Genome Analyses Reveal Novel Genes Associated with Chicken Adaptation to Tropical and Frigid Environments. J Adv Res 2022; 47:13-25. [PMID: 35907630 PMCID: PMC10173185 DOI: 10.1016/j.jare.2022.07.005] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 07/01/2022] [Accepted: 07/17/2022] [Indexed: 01/25/2023] Open
Abstract
INTRODUCTION Investigating the genetic footprints of historical temperature selection can get insights to the local adaptation and feasible influences of climate change on long-term population dynamics. OBJECT Chicken is a significative species to study genetic adaptation on account of its similar domestication track related to human activity with the most diversified varieties. Yet, few studies have demonstrated the genetic signatures of its adaptation to naturally tropical and frigid environments. METHOD Here, we generated whole genome resequencing of 119 domesticated chickens in China including the following breeds which are in order of breeding environmental temperature from more tropical to more frigid: Wenchang chicken (WCC), green-shell chicken (GSC), Tibetan chicken (TBC), and Lindian chicken (LDC). RESULTS Our results showed WCC branched off earlier than LDC with an evident genetic admixture between WCC and LDC, suggesting their closer genetic relationship. Further comparative genomic analyses solute carrier family 33 member 1 (SLC33A1) and thyroid stimulating hormone receptor (TSHR) genes exhibited stronger signatures for positive selection in the genome of the more tropical WCC. Furthermore, genotype data from about 3,000 African local ecotypes confirmed that allele frequencies of single nucleotide polymorphisms (SNPs) in these 2 genes appeared strongly associated with tropical environment adaptation. In addition, the NADH:ubiquinone oxidoreductase subunit S4 (NDUFS4) gene exhibited a strong signature for positive selection in the LDC genome, and SNPs with marked allele frequency differences indicated a significant relationship with frigid environment adaptation. CONCLUSION Our findings partially clarify how selection footprints from environmental temperature stress can lead to advantageous genomic adaptions to tropical and frigid environments in poultry and provide a valuable resource for selective breeding of chickens.
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Affiliation(s)
- Shourong Shi
- Poultry Institute, Chinese Academy of Agriculture Science, Yangzhou, Jiangsu 225125, China
| | - Dan Shao
- Poultry Institute, Chinese Academy of Agriculture Science, Yangzhou, Jiangsu 225125, China
| | - Lingyun Yang
- Novogene Bioinformatics Institute, Beijing 10089, China
| | - Qiqi Liang
- Novogene Bioinformatics Institute, Beijing 10089, China
| | - Wei Han
- Poultry Institute, Chinese Academy of Agriculture Science, Yangzhou, Jiangsu 225125, China
| | - Qian Xue
- Poultry Institute, Chinese Academy of Agriculture Science, Yangzhou, Jiangsu 225125, China
| | - Liang Qu
- Poultry Institute, Chinese Academy of Agriculture Science, Yangzhou, Jiangsu 225125, China
| | - Li Leng
- College of Animal Science and technology, Northeast Agricultural University, Harbin, Heilongjiang, 150038, China
| | - Yishu Li
- Tropical Crop Germplasm Research Institute, Haikou, Hainan, 571101, China
| | - Xiaogang Zhao
- Agriculture and Animal Husbandry Rural and Science and Technology Bureau, Xiangcheng County, Ganzi Tibetan Autonomous Prefecture, Sichuan, 626000, China
| | - Ping Dong
- Agriculture and Animal Husbandry Rural and Science and Technology Bureau, Xiangcheng County, Ganzi Tibetan Autonomous Prefecture, Sichuan, 626000, China
| | - Muhammed Walugembe
- Department of Animal Science, Iowa State University, 2255 Kildee Hall, Ames, IA 50011, USA
| | - Boniface B Kayang
- Department of Animal Science, University of Ghana, Legon, Accra 233, Ghana
| | - Amandus P Muhairwa
- Department of Veterinary Medicine and Public Health, College of Veterinary Medicine and Biomedical Sciences, Sokoine University of Agriculture, P.O. Box 3000 Chuo Kikuu, Morogoro, Tanzania
| | - Huaijun Zhou
- Department of Animal Science, College of Agricultural and Environmental Sciences, University of California, Davis, CA 95616, USA
| | - Haibing Tong
- Poultry Institute, Chinese Academy of Agriculture Science, Yangzhou, Jiangsu 225125, China.
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21
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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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22
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Zheng Z, Li Y, Li M, Li G, Du X, Hongyin H, Yin M, Lu Z, Zhang X, Shrestha N, Liu J, Yang Y. Whole-Genome Diversification Analysis of the Hornbeam Species Reveals Speciation and Adaptation Among Closely Related Species. FRONTIERS IN PLANT SCIENCE 2021; 12:581704. [PMID: 33643339 PMCID: PMC7902934 DOI: 10.3389/fpls.2021.581704] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 01/04/2021] [Indexed: 06/12/2023]
Abstract
Speciation is the key evolutionary process for generating biological diversity and has a central place in evolutionary and ecological research. How species diverge and adapt to different habitats is one of the most exciting areas in speciation studies. Here, we sequenced 55 individuals from three closely related species in the genus Carpinus: Carpinus tibetana, Carpinus monbeigiana, and Carpinus mollicoma to understand the strength and direction of gene flow and selection during the speciation process. We found low genetic diversity in C. tibetana, which reflects its extremely small effective population size. The speciation analysis between C. monbeigiana and C. mollicoma revealed that both species diverged ∼1.2 Mya with bidirectional gene flow. A total of 291 highly diverged genes, 223 copy number variants genes, and 269 positive selected genes were recovered from the two species. Genes associated with the diverged and positively selected regions were mainly involved in thermoregulation, plant development, and response to stress, which included adaptations to their habitats. We also found a great population decline and a low genetic divergence of C. tibetana, which suggests that this species is extremely vulnerable. We believe that the current diversification and adaption study and the important genomic resource sequenced herein will facilitate the speciation studies and serve as an important methodological reference for future research.
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Affiliation(s)
- Zeyu Zheng
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology and School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Ying Li
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology and School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Minjie Li
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology and School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Guiting Li
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology and School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Xin Du
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology and School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Hu Hongyin
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology and School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Mou Yin
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology and School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Zhiqiang Lu
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, China
| | - Xu Zhang
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology and School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Nawal Shrestha
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology and School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Jianquan Liu
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology and School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Yongzhi Yang
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology and School of Life Sciences, Lanzhou University, Lanzhou, China
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23
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Yang Y, Shen L, Gao H, Ran J, Li X, Jiang H, Li X, Cao Z, Huang Y, Zhao S, Song C, Pan H. Comparison of cecal microbiota composition in hybrid pigs from two separate three-way crosses. Anim Biosci 2020; 34:1202-1209. [PMID: 33332946 PMCID: PMC8255879 DOI: 10.5713/ab.20.0681] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 11/26/2020] [Indexed: 11/27/2022] Open
Abstract
Objective The intestinal microbiota plays an important role in host physiology, metabolism, immunity, and behavior. And host genetics could influence the gut microbiota of hybrid animals. The three-way cross model is commonly utilized in commercial pig production; however, the use of this model to analyse the gut microbial composition is rarely reported. Methods Two three-way hybrid pigs were selected, with Saba pigs as the starting maternal pig: Duroc× (Berkshire×Saba) (DBS) pig, Berkshire×(Duroc×Saba) (BDS) pig. One hundred pigs of each model were reared from 35 days (d) to 210 d. The body weight or feed consumption of all pigs were recorded and their feed/gain (F/G) ratio was calculated. On day 210, 10 pigs from each three-way cross were selected for slaughter, and cecal chyme samples were collected for 16S rRNA gene sequencing. Results The final body weight (FBW) and average daily gain (ADG) of DBS pigs were significantly higher than those of BDS pigs (p<0.05), while the F/G ratios of DBS pigs were significantly lower than those of BDS pigs (p<0.05). The dominant phyla in DBS and BDS pigs were Bacteroidetes (55.23% vs 59%, respectively) and Firmicutes (36.65% vs 34.86%, respectively) (p>0.05). At the genus level, the abundance of Prevotella, Roseburia, and Anaerovibrio in DBS pigs was significantly lower than in BDS pigs (p<0.01). The abundance of Eubacterium, Clostridium XI, Bacteroides, Methanomassiliicoccus, and Parabacteroides in DBS pigs was significantly higher than in BDS pigs (p<0.05). The FBWs and ADGs were positively correlated with Bacteroides, ClostridiumXI, and Parabacteroides but negatively correlated with the Prevotella, Prevotella/Bacteroides (P/B) ratio, Roseburia, and Anaerovibrio. Conclusion These results indicated that host genetics affect the cecal microbiota composition and the porcine gut microbiota is associated with growth performance, thereby suggesting that gut microbiota composition may be a useful biomarker in porcine genetics and breeding.
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Affiliation(s)
- Yuting Yang
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed Science, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Liyan Shen
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed Science, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Huan Gao
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed Science, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Jinming Ran
- Dazhou Vocational and Technical College, Dazhou 635000, China
| | - Xian Li
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed Science, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Hengxin Jiang
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed Science, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Xueyan Li
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed Science, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Zhenhui Cao
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed Science, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Ying Huang
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed Science, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Sumei Zhao
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed Science, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Chunlian Song
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed Science, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China.,Collge of Veterinary Medicine, Yunnan Agricultural University, Kunming 650201, China
| | - Hongbin Pan
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed Science, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
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Genetic Signatures of Selection for Cashmere Traits in Chinese Goats. Animals (Basel) 2020; 10:ani10101905. [PMID: 33080940 PMCID: PMC7603090 DOI: 10.3390/ani10101905] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 10/12/2020] [Accepted: 10/16/2020] [Indexed: 12/12/2022] Open
Abstract
Simple Summary Cashmere goats are a unique husbandry resource in China. These goats are well known for producing the highest cashmere yield and best fiber quality in the world. Although cashmere is highly valued and also known as “fiber gem” and “soft gold”, few studies have examined the genetic basis of cashmere traits in cashmere goats. Here, we identified selection signals by comparing Fst and XP-EHH (the cross population extend haplotype homozygosity test) of a non-cashmere breed (Huanghuai goat) with those of two cashmere breeds (Inner Mongolia and Liaoning cashmere goats). Two genes (WNT10A and CSN3) were potentially associated with cashmere traits. This information may be valuable for studying the genetic uniqueness of cashmere goats and elucidating the mechanisms underlying cashmere traits in cashmere goats. Abstract Inner Mongolia and Liaoning cashmere goats in China are well-known for their cashmere quality and yield. Thus, they are great models for identifying genomic regions associated with cashmere traits. Herein, 53 Inner Mongolia cashmere goats, Liaoning cashmere goats and Huanghuai goats were genotyped, and 53,347 single-nucleotide polymorphisms (SNPs) were produced using the Illumina Caprine 50K SNP chip. Additionally, we identified some positively selected SNPs by analyzing Fst and XP-EHH. The top 5% of SNPs had selection signatures. After gene annotation, 222 and 173 candidate genes were identified in Inner Mongolia and Liaoning cashmere goats, respectively. Several genes were related to hair follicle development, such as TRPS1, WDR74, LRRC14, SPTLC3, IGF1R, PADI2, FOXP1, WNT10A and CSN3. Gene enrichment analysis of these cashmere trait-associated genes related 67 enriched signaling pathways that mainly participate in hair follicle development and stem cell pluripotency regulation. Furthermore, we identified 20 overlapping genes that were selected in both cashmere goat breeds. Among these overlapping genes, WNT10A and CSN3, which are associated with hair follicle development, are potentially involved in cashmere production. These findings may improve molecular breeding of cashmere goats in the future.
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Gao H, Yang Y, Cao Z, Ran J, Zhang C, Huang Y, Yang M, Zhao S, An Q, Pan H. Characteristics of the Jejunal Microbiota in 35-Day-Old Saba and Landrace Piglets. Pol J Microbiol 2020; 69:367-378. [PMID: 33574866 PMCID: PMC7810115 DOI: 10.33073/pjm-2020-041] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 08/17/2020] [Accepted: 08/19/2020] [Indexed: 12/18/2022] Open
Abstract
The balanced microbiological system is a significant hallmark of piglet health. One of the crucial factors affecting intestinal microbiota is the host’s genetics. This study explored the difference in the diversity of jejunal microbiota between Saba (SB) and Landrace (LA) piglets. Nine Saba and nine Landrace piglets were fed with sow’s milk until day 35. Jejunal contents were harvested for 16S rRNA sequencing. The birth weight, body weight, and average daily gain of Saba piglets were lower than those of Landrace piglets (p < 0.01). Firmicutes were the main phylum in Saba and Landrace piglets, and the Saba piglets had a higher (p < 0.05) abundance of Bacteroidetes compared with Landrace piglets. The two most abundant genera were Lactobacilli and Clostridium XI in the jejunum of Landrace and Saba piglets. Compared with Landrace piglets, the Saba piglets had significantly lower (p < 0.05) abundance of Veillonella, Streptococcus, and Saccharibacteria genera incertae sedis. The functional prediction showed that “d-glutamine and d-glutamate metabolism” and “one carbon pool by folate” pathways were enriched in Saba piglets, while “limonene and pinene degradation”, “tryptophan metabolism”, and “sulfur relay system” pathways were enriched in Landrace piglets. In summary, the growth performance was higher for Landrace piglets compared with Saba piglets due to their genetic characteristics. The rich diversity and fewer infection-associated taxa were observed in Saba piglets, partially accounting for their higher adaptability to environmental perturbations than Landrace piglets. Furthermore, different pig breeds may regulate their health through different metabolic pathways.
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Affiliation(s)
- Huan Gao
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed Science, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Yuting Yang
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed Science, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Zhenhui Cao
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed Science, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Jinming Ran
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed Science, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Chunyong Zhang
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed Science, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Ying Huang
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed Science, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Minghua Yang
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed Science, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Sumei Zhao
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed Science, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Qingcong An
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed Science, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Hongbin Pan
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed Science, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
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