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http://dx.doi.org/10.5713/ajas.19.0884

Single nucleotide polymorphism-based analysis of the genetic structure of Liangshan pig population  

Liu, Bin (College of Animal Science and Technology, Sichuan Agricultural University)
Shen, Linyuan (College of Animal Science and Technology, Sichuan Agricultural University)
Guo, Zhixian (College of Animal Science and Technology, Sichuan Agricultural University)
Gan, Mailing (College of Animal Science and Technology, Sichuan Agricultural University)
Chen, Ying (Sichuan Province General Station of Animal Husbandry)
Yang, Runling (Agriculture and Rural Bureau of Mabian Yi Autonomous County)
Niu, Lili (College of Animal Science and Technology, Sichuan Agricultural University)
Jiang, Dongmei (College of Animal Science and Technology, Sichuan Agricultural University)
Zhong, Zhijun (Sichuan Academy of Animal Sciences)
Li, Xuewei (College of Animal Science and Technology, Sichuan Agricultural University)
Zhang, Shunhua (College of Animal Science and Technology, Sichuan Agricultural University)
Zhu, Li (College of Animal Science and Technology, Sichuan Agricultural University)
Publication Information
Animal Bioscience / v.34, no.7, 2021 , pp. 1105-1115 More about this Journal
Abstract
Objective: To conserve and utilize the genetic resources of a traditional Chinese indigenous pig breed, Liangshan pig, we assessed the genetic diversity, genetic structure, and genetic distance in this study. Methods: We used 50K single nucleotide polymorphism (SNP) chip for SNP detection of 139 individuals in the Liangshan Pig Conservation Farm. Results: The genetically closed conserved population consisted of five overlapping generations, and the total effective content of the population (Ne) was 15. The whole population was divided into five boar families and one non-boar family. Among them, the effective size of each generation subpopulation continuously decreased. However, the proportion of polymorphic markers (PN) first decreased and then increased. The average genetic distance of these 139 Liangshan pigs was 0.2823±0.0259, and the average genetic distance of the 14 boars was 0.2723±0.0384. Thus, it can be deduced that the genetic distance changed from generation to generation. In the conserved population, 983 runs of homozygosity (ROH) were detected, and the majority of ROH (80%) were within 100 Mb. The inbreeding coefficient calculated based on ROH showed an average value of 0.026 for the whole population. In addition, the inbreeding coefficient of each generation subpopulation initially increased and then decreased. In the pedigree of the whole conserved population, the error rate of paternal information was more than 11.35% while the maternal information was more than 2.13%. Conclusion: This molecular study of the population genetic structure of Liangshan pig showed loss of genetic diversity during the closed cross-generation reproduction process. It is necessary to improve the mating plan or introduce new outside blood to ensure long-term preservation of Liangshan pig.
Keywords
Single Nucleotide Polymorphism (SNP) Chip; Liangshan Pig; Inbreeding Coefficient; Genetic Distance; Genetic Diversity;
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1 Wang X, Cao HH, Geng SM, Li HB. Genetic diversity of 10 indigenous pig breeds in China by using microsatellite markers. Asian-Australas J Anim Sci 2004;17:1219-22. https://doi.org/10.5713/ajas.2004.1219   DOI
2 Chen J, Peng J, Xiao Q, et al. The genetic diversity and population structures of indigenous pig breeds in Zhejiang Province revealed by GGRS sequencing. Anim Genet 2018;49:36-42. https://doi.org/10.1111/age.12625   DOI
3 Kirin M, McQuillan R, Franklin CS, Campbell H, McKeigue PM, Wilson JF. Genomic runs of homozygosity record population history and consanguinity. PLoS One 2010;5:e13996. https://doi.org/10.1371/journal.pone.0013996   DOI
4 Wang L, Sorensen P, Janss L, Ostersen T, Edwards D. Genome-wide and local pattern of linkage disequilibrium and persistence of phase for 3 Danish pig breeds. BMC Genet 2013;14:115. https://doi.org/10.1186/1471-2156-14-115   DOI
5 Ai H, Huang L, Ren J. Genetic diversity, linkage disequilibrium and selection signatures in Chinese and Western pigs revealed by genome-wide SNP markers. PLoS One 2013;8:e56001. https://doi.org/10.1371/journal.pone.0056001   DOI
6 Bjelland DW, Weigel KA, Vukasinovic N, Nkrumah JD. Evaluation of inbreeding depression in Holstein cattle using wholegenome SNP markers and alternative measures of genomic inbreeding. J Dairy Sci 2013;96:4697-706. https://doi.org/10.3168/jds.2012-6435   DOI
7 Zanella R, Peixoto JO, Cardoso FF, et al. Genetic diversity analysis of two commercial breeds of pigs using genomic and pedigree data. Genet Sel Evol 2016;48:24. https://doi.org/10.1186/s12711-016-0203-3   DOI
8 Bosse M, Megens HJ, Madsen O, et al. Regions of homozygosity in the porcine genome: consequence of demography and the recombination landscape. PLoS Genet 2012;8:e1003100. https://doi.org/10.1371/journal.pgen.1003100   DOI
9 Powell JE, Visscher PM, Goddard ME. Reconciling the analysis of IBD and IBS in complex trait studies. Nat Rev Genet 2010;11:800-5. https://doi.org/10.1038/nrg2865   DOI
10 Luo J, Lei H, Shen L, et al. Estimation of growth curves and suitable slaughter weight of the Liangshan pig. Asian-Australas J Anim Sci 2015;28:1252-8. https://doi.org/10.5713/ajas.15.0010   DOI
11 Barbato M, Orozco-terWengel P, Tapio M, Bruford MW. SNeP: a tool to estimate trends in recent effective population size trajectories using genome-wide SNP data. Front Genet 2015;6:109. https://doi.org/10.3389/fgene.2015.00109   DOI
12 Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 2018;35:1547-9. https://doi.org/10.1093/molbev/msy096   DOI
13 Chomczynski P, Sacchi N. The single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction: twenty-something years on. Nat Protoc 2006;1:581-5. https://doi.org/10.1038/nprot.2006.83   DOI
14 Fang M, Hu X, Jiang T, et al. The phylogeny of Chinese indigenous pig breeds inferred from microsatellite markers. Anim Genet 2005;36:7-13. https://doi.org/10.1111/j.1365-2052.2004.01234.x   DOI
15 Jones GF. Genetic aspects of domestication, common breeds and their origin. In: Rothschild MF, Ruvinsky A, editors. The genetics of the pig. Wallingford, UK: CAB International; 1998. pp. 17-50.
16 Ai H, Yang B, Li J, Xie X, Chen H, Ren J. Population history and genomic signatures for high-altitude adaptation in Tibetan pigs. BMC Genomics 2014;15:834. https://doi.org/10.1186/1471-2164-15-834   DOI
17 Silio L, Rodriguez MC, Fernandez A, et al. Measuring inbreeding and inbreeding depression on pig growth from pedigree or SNP-derived metrics. J Anim Breed Genet 2013;130:34960. https://doi.org/10.1111/jbg.12031   DOI
18 Purcell S, Neale B, Todd-Brown K, et al. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet 2007;81:559-75. https://doi.org/10.1086/519795   DOI
19 Chan BKC. Data analysis using R programming. In: Bio-statistics for epidemiology and public health using RAdv. New York, USA: Springer Publishing Company; 2015. pp. 81-154. https://doi.org/10.1891/9780826110268.0003
20 VanRaden PM. Efficient methods to compute genomic predictions. J Dairy Sci 2008;91:4414-23. https://doi.org/10.3168/jds.2007-0980   DOI
21 Wiggans GR, VanRaden PM, Bacheller LR, et al. Selection and management of DNA markers for use in genomic evaluation. J Dairy Sci 2010;93:2287-92. https://doi.org/10.3168/jds.2009-2773   DOI
22 Munoz PR, Resende MFR, Huber DA, et al. Genomic relationship matrix for correcting pedigree errors in breeding populations: impact on genetic parameters and genomic selection accuracy. Crop Sci 2014;54:1115-23. https://doi.org/10.2135/cropsci2012.12.0673   DOI
23 Waples RS. Making sense of genetic estimates of effective population size. Mol Ecol 2016;25:4689-91. https://doi.org/10.1111/mec.13814   DOI
24 Shin D, Kim SH, Park J, Lee HK, Song KD. Extent of linkage disequilibrium and effective population size of the Landrace population in Korea. Asian-Australas J Anim Sci 2018;31:1078-87. https://doi.org/10.5713/ajas.17.0237   DOI
25 Waples RK, Larson WA, Waples RS. Estimating contemporary effective population size in non-model species using linkage disequilibrium across thousands of loci. Heredity 2016;117:233-40. https://doi.org/10.1038/hdy.2016.60   DOI
26 Visscher PM, Woolliams JA, Smith D, Williams JL. Estimation of pedigree errors in the UK dairy population using microsatellite markers and the impact on selection. J Dairy Sci 2002;85:2368-75. https://doi.org/10.3168/jds.S0022-0302(02)74317-8   DOI
27 SanCristobal M, Chevalet C, Haley CS, et al. Genetic diversity within and between European pig breeds using micro-satellite markers. Anim Genet 2006;37:189-98. https://doi.org/10.1111/j.1365-2052.2005.01385.x   DOI