Genetic diversity and population structure of Tongcheng pigs in China using whole-genome SNP chip
Tongcheng (TC) pigs, distinguished by their superior meat quality, are a Chinese indigenous pig breed. Recently, the genetic resources of TC pigs are under tremendous threat due to the introduction of cosmopolitan pig breeds and African swine fever disease. To promote their management and conservati...
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Frontiers Media S.A.
2022-08-01
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| Series: | Frontiers in Genetics |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fgene.2022.910521/full |
| _version_ | 1828453215951126528 |
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| author | Jiao Yuan Xiang Zhou Xiang Zhou Xiang Zhou Guoqiang Xu Sanping Xu Bang Liu Bang Liu Bang Liu |
| author_facet | Jiao Yuan Xiang Zhou Xiang Zhou Xiang Zhou Guoqiang Xu Sanping Xu Bang Liu Bang Liu Bang Liu |
| author_sort | Jiao Yuan |
| collection | DOAJ |
| description | Tongcheng (TC) pigs, distinguished by their superior meat quality, are a Chinese indigenous pig breed. Recently, the genetic resources of TC pigs are under tremendous threat due to the introduction of cosmopolitan pig breeds and African swine fever disease. To promote their management and conservation, the present study assessed genetic diversity and population structure of TC pigs using single nucleotide polymorphism (SNP) markers. A total of 26, 999 SNPs were screened from 51, 315 SNPs in 68 TC pigs. The multi-dimensional scaling (MDS) analysis and neighbor-joining tree revealed that all 68 pigs were from a purebred population. The effective population size decreased over time, and it was 96 prior to generation 20. Both linkage disequilibrium (LD) and neutrality test indicated a low selection of TC pigs with average LD value of 0.15 ± 0.23. Genetic diversity results exhibited a minor allele frequency (MAF) of 0.23, observed heterozygosity (HO) of 0.32, expected heterozygosity (He) of 0.31, and nucleotide diversity (Pi) of 0.31. All these parameters indicated a remarkably high genetic diversity of TC pigs. Additionally, 184 runs of homozygosity (ROH) segments were detected from the whole genome of TC pigs with an average ROH length of 23.71Mb, ranging from 11.26Mb to 69.02 Mb. The highest ROH coverage was found on chromosome 1 (10.12%), while the lowest was on chromosome 18 (1.49%). The average inbreeding coefficients based on ROH (FROH) was 0.04%. Fourteen ROH islands containing 240 genes were detected on 9 different autosomes. Some of these 240 genes were overlapped with the genes related to biological processes such as immune function, reproduction, muscular development, and fat deposition, including FFAR2, FFAR4, MAPK8, NPY5R, KISS1, and these genes might be associated with such traits as meat quality and disease resistance in TC pigs. Taken together, population structure and genetic diversity results suggested that the TC pig represented a valuable genetic resource. However, TC pig breed conservation program remains to be further optimized to ensure adequate genetic diversity and avoid inbreeding depression. Our findings provide theoretical basis for formulating management and conservation strategies for TC pigs. |
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| language | English |
| last_indexed | 2024-12-11T00:04:15Z |
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| spelling | doaj.art-8d11ae7a6623414baa4cd87a82f3855e2022-12-22T01:28:22ZengFrontiers Media S.A.Frontiers in Genetics1664-80212022-08-011310.3389/fgene.2022.910521910521Genetic diversity and population structure of Tongcheng pigs in China using whole-genome SNP chipJiao Yuan0Xiang Zhou1Xiang Zhou2Xiang Zhou3Guoqiang Xu4Sanping Xu5Bang Liu6Bang Liu7Bang Liu8Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, ChinaKey Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, ChinaThe Cooperative Innovation Center for Sustainable Pig Production, Wuhan, ChinaThe Engineering Technology Research Center of Local Pig Breed Improvement of Hubei Province, Wuhan, ChinaKey Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, ChinaDepartment of Agricultural and Rural Bureau, Xianning, ChinaKey Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, ChinaThe Cooperative Innovation Center for Sustainable Pig Production, Wuhan, ChinaThe Engineering Technology Research Center of Local Pig Breed Improvement of Hubei Province, Wuhan, ChinaTongcheng (TC) pigs, distinguished by their superior meat quality, are a Chinese indigenous pig breed. Recently, the genetic resources of TC pigs are under tremendous threat due to the introduction of cosmopolitan pig breeds and African swine fever disease. To promote their management and conservation, the present study assessed genetic diversity and population structure of TC pigs using single nucleotide polymorphism (SNP) markers. A total of 26, 999 SNPs were screened from 51, 315 SNPs in 68 TC pigs. The multi-dimensional scaling (MDS) analysis and neighbor-joining tree revealed that all 68 pigs were from a purebred population. The effective population size decreased over time, and it was 96 prior to generation 20. Both linkage disequilibrium (LD) and neutrality test indicated a low selection of TC pigs with average LD value of 0.15 ± 0.23. Genetic diversity results exhibited a minor allele frequency (MAF) of 0.23, observed heterozygosity (HO) of 0.32, expected heterozygosity (He) of 0.31, and nucleotide diversity (Pi) of 0.31. All these parameters indicated a remarkably high genetic diversity of TC pigs. Additionally, 184 runs of homozygosity (ROH) segments were detected from the whole genome of TC pigs with an average ROH length of 23.71Mb, ranging from 11.26Mb to 69.02 Mb. The highest ROH coverage was found on chromosome 1 (10.12%), while the lowest was on chromosome 18 (1.49%). The average inbreeding coefficients based on ROH (FROH) was 0.04%. Fourteen ROH islands containing 240 genes were detected on 9 different autosomes. Some of these 240 genes were overlapped with the genes related to biological processes such as immune function, reproduction, muscular development, and fat deposition, including FFAR2, FFAR4, MAPK8, NPY5R, KISS1, and these genes might be associated with such traits as meat quality and disease resistance in TC pigs. Taken together, population structure and genetic diversity results suggested that the TC pig represented a valuable genetic resource. However, TC pig breed conservation program remains to be further optimized to ensure adequate genetic diversity and avoid inbreeding depression. Our findings provide theoretical basis for formulating management and conservation strategies for TC pigs.https://www.frontiersin.org/articles/10.3389/fgene.2022.910521/fulltongcheng pigpopulation structuregenetic diversityruns of homozygositySNP chip |
| spellingShingle | Jiao Yuan Xiang Zhou Xiang Zhou Xiang Zhou Guoqiang Xu Sanping Xu Bang Liu Bang Liu Bang Liu Genetic diversity and population structure of Tongcheng pigs in China using whole-genome SNP chip Frontiers in Genetics tongcheng pig population structure genetic diversity runs of homozygosity SNP chip |
| title | Genetic diversity and population structure of Tongcheng pigs in China using whole-genome SNP chip |
| title_full | Genetic diversity and population structure of Tongcheng pigs in China using whole-genome SNP chip |
| title_fullStr | Genetic diversity and population structure of Tongcheng pigs in China using whole-genome SNP chip |
| title_full_unstemmed | Genetic diversity and population structure of Tongcheng pigs in China using whole-genome SNP chip |
| title_short | Genetic diversity and population structure of Tongcheng pigs in China using whole-genome SNP chip |
| title_sort | genetic diversity and population structure of tongcheng pigs in china using whole genome snp chip |
| topic | tongcheng pig population structure genetic diversity runs of homozygosity SNP chip |
| url | https://www.frontiersin.org/articles/10.3389/fgene.2022.910521/full |
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