High-density single nucleotide polymorphism chip-based conservation genetic analysis of indigenous pig breeds from Shandong Province, China
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초록
Objective: Shandong indigenous pig breeds are important Chinese pig resources. Their progressive population decline in recent decades has attracted attention towards their conservation. Conservation genetics of these indigenous breeds are essential for developing a conservation and utilization scheme. Methods: A high-density single nucleotide polymorphism (HD-SNP) chip-based comparative analysis of genetic characteristics was performed for seven Shandong indigenous pig breeds in the context of five Western commercial breeds. Results: The results showed that Shandong indigenous pig breeds varied greatly in genetic diversity, effective population size, inbreeding level, and genetic distance with the Western commercial breeds. Specifically, Laiwu and Dapulian displayed low genetic diversity, and had a genetically distant relationship with the Western commercial breeds (average F statistics [<i>F</i><sub>ST</sub>] value of 0.3226 and 0.2666, respectively). Contrastingly, the other five breeds (Yantai, Licha, Yimeng, Wulain, and Heigai) displayed high genetic diversity within breed and had some extent of mixture pattern with the Western commercial breeds, especially Duroc and Landrace (<i>F</i><sub>ST</sub> values from 0.1043 to 0.2536). Furthermore, intensive gene flow was discovered among the seven Shandong indigenous breeds, particularly Wulian, Licha, and Heigai, as indicated by the large cluster formed in the principal component analysis scatterplot and small population differentiation (average of 0.1253) among them. Conclusion: Our study advances the understanding of genetic characteristics of Shandong indigenous breeds and provides essential information for developing an appropriate conservation and utilization scheme for these breeds.
Abstract
Objective: Shandong indigenous pig breeds are important Chinese pig resources. Their progressive population decline in recent decades has attracted attention towards their conservation. Conservation genetics of these indigenous breeds are essential for developing a conservation and utilization scheme. Methods: A high-density single nucleotide polymorphism (HD-SNP) chip-based comparative analysis of genetic characteristics was performed for seven Shandong indigenous pig breeds in the context of five Western commercial breeds. Results: The results showed that Shandong indigenous pig breeds varied greatly in genetic diversity, effective population size, inbreeding level, and genetic distance with the Western commercial breeds. Specifically, Laiwu and Dapulian displayed low genetic diversity, and had a genetically distant relationship with the Western commercial breeds (average F statistics [FST] value of 0.3226 and 0.2666, respectively). Contrastingly, the other five breeds (Yantai, Licha, Yimeng, Wulain, and Heigai) displayed high genetic diversity within breed and had some extent of mixture pattern with the Western commercial breeds, especially Duroc and Landrace (FST values from 0.1043 to 0.2536). Furthermore, intensive gene flow was discovered among the seven Shandong indigenous breeds, particularly Wulian, Licha, and Heigai, as indicated by the large cluster formed in the principal component analysis scatterplot and small population differentiation (average of 0.1253) among them. Conclusion: Our study advances the understanding of genetic characteristics of Shandong indigenous breeds and provides essential information for developing an appropriate conservation and utilization scheme for these breeds.
참고문헌 (42)
- Pig report. Understanding agriculture worldwide, "Agri Benchmark", ~ (2018)
- National Commission of Animal Genetic Resources of China, "Animal genetic resources in China: pigs" (2011), China Agriculture Press
- Si J, "Livestock breeds in Shandong province" (1999), Haitian Press
- Hui Wang, "Expression of lipid metabolism genes provides new insights into intramuscular fat deposition in Laiwu pigs", Animal Bioscience, 33(3), pp.390~397 (2020), 아세아·태평양축산학회[DOI]
- Wei Chen, "Longissimus lumborum muscle transcriptome analysis of Laiwu and Yorkshire pigs differing in intramuscular fat content", Genes & Genomics, 39(7), pp.759~766 (2017), 한국유전학회[DOI]
- Xing J, "Genome-wide gene expression profiles in lung tissues of pig breeds differing in resistance to porcine reproductive and respiratory syndrome virus", PLoS One, 9, pp.e86101~ (2014)[DOI]
- Jiang C, "Different expression patterns of PRRSV mediator genes in the lung tissues of PRRSV resistant and susceptible pigs", Dev Comp Immunol, 39, pp.127~131 (2013)[DOI]
- Yang G, "Genetic evidence for the introgression of Western NR6A1 haplotype into Chinese Licha breed associated with increased vertebral number", Anim Genet, 40, pp.247~250 (2009)[DOI]
- Megens HJ, "Biodiversity of pig breeds from China and Europe estimated from pooled DNA samples : differences in microsatellite variation between two areas of domestication", Genet Sel Evol, 40, pp.103~ (2008)[DOI]
- Fenster CB, "Conservation and genetics", Yale J Biol Med, 91, pp.491~501 (2018)
- Frankham R, "Inbreeding leads to extinction", Nature, 392, pp.441~442 (1998)[DOI]
- Lu P, "Flavour differences of cooked longissimus muscle from Chinese indigenous pig breeds and hybrid pig breed(Duroc×Landrace×Large White)", Food Chem, 107, pp.1529~1537 (2008)[DOI]
- J.Y. Wang, "Genetic Diversity of Chinese Indigenous Pig Breeds in Shandong Province Using Microsatellite Markers", Animal Bioscience, 24(1), pp.28~36 (2011), 아세아·태평양축산학회
- Wang J, "Phylogenetic relationships of pig breeds from Shandong province of China and their influence by modern commercial breeds by analysis of mitochondrial DNA sequences", Ital J Anim Sci, 9, pp.e48~ (2010)
- Peripolli E, "Runs of homozygosity : current knowledge and applications in livestock", Anim Genet, 48, pp.255~271 (2017)[DOI]
- Zhan H, "Genome-wide patterns of homozygosity and relevant characterizations on the population structure in Piétrain pigs", Genes, 11, pp.577~ (2020)[DOI]
- Schiavo G, "Comparative evaluation of genomic inbreeding parameters in seven commercial and autochthonous pig breeds", Animal, 14, pp.910~920 (2020)[DOI]
- Herrero-Medrano JM, "Conservation genomic analysis of domestic and wild pig populations from the Iberian Peninsula", BMC Genet, 14, pp.106~ (2013)[DOI]
- Ai H, "Genetic diversity, linkage disequilibrium and selection signatures in Chinese and Western pigs revealed by genome-wide SNP markers", PLoS One, 8, pp.e56001~ (2013)[DOI]
- Muñoz M, "Genomic diversity, linkage disequilibrium and selection signatures in European local pig breeds assessed with a high density SNP chip", Sci Rep, 9, pp.13546~ (2019)[DOI]
- Qin M, "Genetic diversities and differentially selected regions between Shandong indigenous pig breeds and Western pig breeds", Front Genet, 10, pp.1351~ (2020)[DOI]
- Sambrook J, "Molecular cloning: a laboratory manual" (2001), Cold Spring Harbor Laboratory Press
- Purcell S, "PLINK : a tool set for whole-genome association and population-based linkage analyses", Am J Hum Genet, 81, pp.559~575 (2007)[DOI]
- McQuillan R, "Runs of homozygosity in European populations", Am J Hum Genet, 83, pp.359~372 (2008)[DOI]
- Sved JA, "Linkage disequilibrium and homozygosity of chromosome segments in finite populations", Theor Popul Biol, 2, pp.125~141 (1971)[DOI]
- Tortereau F, "A high density recombination map of the pig reveals a correlation between sex-specific recombination and GC content", BMC Genomics, 13, pp.586~ (2012)[DOI]
- Hayes BJ, "Novel multilocus measure of linkage disequilibrium to estimate past effective population size", Genome Res, 13, pp.635~643 (2003)[DOI]
- Alexander DH, "Fast model-based estimation of ancestry in unrelated individuals", Genome Res, 19, pp.1655~1664 (2009)[DOI]
- Weir BS, "Estimating F-statistics for the analysis of population structure", Evolution, 38, pp.1358~1370 (1984)[DOI]
- Tajima F, "Estimation of evolutionary distance between nucleotide sequences", Mol Biol Evol, 1, pp.269~285 (1984)[DOI]
- Saitou N, "The neighbor-joining method : a new method for reconstructing phylogenetic trees", Mol Biol Evol, 4, pp.406~425 (1987)[DOI]
- Kumar S, "MEGA7 : molecular evolutionary genetics analysis version 7. 0 for bigger datasets", Mol Biol Evol, 33, pp.1870~1874 (2016)[DOI]
- Ramos AM, "Design of a high density SNP genotyping assay in the pig using SNPs identified and characterized by next generation sequencing technology", PLoS One, 4, pp.e6524~ (2009)[DOI]
- Quan J, "Population genetics assessment model reveals priority protection of genetic resources in native pig breeds in China", Glob Ecol Conserv, 21, pp.e00829~ (2020)[DOI]
- Sato K, "Multiple ways to prevent transmission of paternal mitochondrial DNA for maternal inheritance in animals", J Biochem, 162, pp.247~253 (2017)[DOI]
- Zuidema D, "The domestic pig as a model for the study of mitochondrial inheritance", Cell Tissue Res, 380, pp.263~271 (2020)[DOI]
- Badke YM, "Estimation of linkage disequilibrium in four US pig breeds", BMC Genomics, 13, pp.24~ (2012)[DOI]
- Uimari P, "Extent of linkage disequilibrium and effective population size in Finnish Landrace and Finnish Yorkshire pig breeds", J Anim Sci, 89, pp.609~614 (2011)[DOI]
- Purfield DC, "Runs of homozygosity and population history in cattle", BMC Genet, 13, pp.70~ (2012)[DOI]
- Meuwissen TH, "Accuracy of breeding values of 'unrelated'individuals predicted by dense SNP genotyping", Genet Sel Evol, 41, pp.35~ (2009)[DOI]
- Wright S, "Isolation by distance", Genetics, 28, pp.114~138 (1943)
- Hartl DL, "Principles of population genetics" (1997), Sinauer Associates Inc