Acknowledgement
This research was supported by the Natural Science Foundation of Heilongjiang Province (LH2019C017).
References
- Huang M, Yang B, Chen H, et al. The fine-scale genetic structure and selection signals of Chinese indigenous pigs. Evol Appl 2020;13:458-75. https://doi.org/10.1111/eva.12887
- Frantz L, Meijaard E, Gongora J, Haile J, Groenen MA, Larson G. The evolution of Suidae. Annu Rev Anim Biosic 2016;4:61-85. https://doi.org/10.1146/annurev-animal-021815-111155
- Larson G, Dobney K, Albarella U, et al. Worldwide phylogeography of wild boar reveals multiple centers of pig domestication. Science 2005;307:1618-21. https://doi.org/10.1126/science.1106927
- Giuffra E, Kijas JM, Amarger V, Carlborg O, Jeon JT, Andersson L. The origin of the domestic pig: Independent domestication and subsequent introgression. Genetics 2000;154:1785-91. https://doi.org/10.1093/genetics/154.4.1785
- Wang LY, Wang AG, Wang LX, et al. In: China National Commission of Animal Genetic Resources. Animal genetic resources in China: Pigs. Beijing, China: China Agriculture Press; 2011.
- Yang H. Livestock development in China: animal production, consumption and genetic resources. J Anim Breed Genet 2013;130:249-51. https://doi.org/10.1111/jbg.12045
- Xu P, Wang X, Ni L, et al. Genome-wide genotyping uncovers genetic diversity, phylogeny, signatures of selection, and population structure of chinese jiangquhai pigs in a global perspective. J Anim Sci 2019;97:1491-500. https://doi.org/10.1093/jas/skz028
- Caballero A, Toro MA. Interrelations between effective population size and other pedigree tools for the management of conserved populations. Genet Res 2000;75:331-43. https://doi.org/10.1017/S0016672399004449
- 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
- Wang X, Wang C, Huang M, et al. Genetic diversity, population structure and phylogenetic relationships of three indigenous pig breeds from Jiangxi province, China, in a worldwide panel of pigs. Anim Genet 2018;49:275-83. https://doi.org/10.1111/age.12687
- 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
- Sved JA. Linkage disequilibrium and homozygosity of chromosome segments in finite populations. Theor Popul Biol 1971;2:125-41. https://doi.org/10.1016/0040-5809(71)90011-6
- Hayes BJ, Visscher PM, McPartlan HC, Goddard ME. Novel multilocus measure of linkage disequilibrium to estimate past effective population size. Genome Res 2003;13:635-43. https://doi.org/10.1101/gr.387103
- Tortereau F, Servin B, Frantz L, et al. A high density recombination map of the pig reveals a correlation between sex-specific recombination and GC content. BMC Genomics 2012;13:586. https://doi.org/10.1186/1471-2164-13-586
- McQuillan R, Leutenegger AL, Abdel-Rahman R, et al. Runs of homozygosity in European populations. Am J Hum Genet 2008;83:359-72. https://doi.org/10.1016/j.ajhg.2008.08.007
- Yang J, Lee SH, Goddard ME, Visscher PM. GCTA: a tool for genome-wide complex trait analysis. Am J Hum Genet 2011;88:76-82. https://doi.org/10.1016/j.ajhg.2010.11.011
- Alexander DH, Novembre J, Lange K. Fast model-based estimation of ancestry in unrelated individuals. Genome Res 2009;19:1655-64. https://doi.org/10.1101/gr.094052.109
- Xu Z, Sun H, Zhang Z, et al. Assessment of autozygosity derived from runs of homozygosity in jinhua pigs disclosed by sequencing data. Front Genet 2019;10:274. https://doi. org/10.3389/fgene.2019.00274
- Fang YF, Hao XY, Xu Z, et al. Genome-wide detection of runs of homozygosity in laiwu pigs revealed by sequencing data. Front Genet 2021;12:629966. https://doi.org/10.3389/fgene.2021.629966
- Liu C, Li P, Zhou W, et al. Genome data uncover conservation status, historical relatedness and candidate genes under selection in chinese indigenous pigs in the taihu lake region. Front Genet 2020;11:591. https://doi.org/10.3389/fgene.2020.00591
- Corbin LJ, Liu AY, Bishop SC, Woolliams JA. Estimation of historical effective population size using linkage disequilibria with marker data. J Anim Breed Genet 2012;129:257-70. https://doi.org/10.1111/j.1439-0388.2012.01003.x
- Simon DL. European approaches to conservation of farm animal genetic resources. Anim Genet Res Info 1999;25:77-97. https://doi.org/10.1017/S1014233900005794
- 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
- Marras G, Gaspa G, Sorbolini S, et al. Analysis of runs of homozygosity and their relationship with inbreeding in five cattle breeds farmed in Italy. Anim Genet 2015;46:110-21. https://doi.org/10.1111/age.12259
- Zhan H, Zhang S, Zhang K, et al. Genome-wide patterns of homozygosity and relevant characterizations on the population structure in pietrain pigs. Genes 2020;11:577. https://doi.org/10.3390/genes11050577
- Ai H, Fang X, Yang B, et al. Adaptation and possible ancient interspecies introgression in pigs identified by whole-genome sequencing. Nat Genet 2015;47:217-25. https://doi.org/10.1038/ng.3199
- Traspov A, Deng W, Kostyunina O, et al. Population structure and genome characterization of local pig breeds in Russia, Belorussia, Kazakhstan and Ukraine. Genet Sel Evol 2016; 48:16. https://doi.org/10.1186/s12711-016-0196-y
- Qin M, Li C, Li Z, Chen W, Zeng Y. Genetic diversities and differentially selected regions between shandong indigenous pig breeds and western pig breeds. Front Genet 2020;10: 1351. https://doi.org/10.3389/fgene.2019.01351
- Sanders K, Bennewitz J, Kalm E. Wrong and missing sire information affects genetic gain in the Angeln dairy cattle population. J Dairy Sci 2006;89:315-21. https://doi.org/10.3168/jds.S0022-0302(06)72096-3
- VanRaden PM. Efficient methods to compute genomic predictions. J Dairy Sci 2008;91:4414-23. https://doi.org/10.3168/jds.2007-0980