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) |
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 |