Analysis of genetic characteristics of pig breeds using information on single nucleotide polymorphisms

  • Lee, Sang-Min (Department of Animal Biotechnology, Chonbuk National University) ;
  • Oh, Jae-Don (Department of Animal Biotechnology, Chonbuk National University) ;
  • Park, Kyung-Do (Department of Animal Biotechnology, Chonbuk National University) ;
  • Do, Kyoung-Tag (Department of Animal Biotechnology, Jeju National University)
  • Received : 2018.04.19
  • Accepted : 2018.08.06
  • Published : 2019.04.01


Objective: This study was undertaken to investigate the genetic characteristics of Berkshire (BS), Landrace (LR), and Yorkshire (YS) pig breeds raised in the Great Grandparents pig farms using the single nucleotide polymorphisms (SNP) information. Methods: A total of 25,921 common SNP genotype markers in three pig breeds were used to estimate the expected heterozygosity ($H_E$), polymorphism information content, F-statistics ($F_{ST}$), linkage disequilibrium (LD) and effective population size ($N_e$). Results: The chromosome-wise distribution of $F_{ST}$ in BS, LR, and YS populations were within the range of 0-0.36, and the average $F_{ST}$ value was estimated to be $0.07{\pm}0.06$. This result indicated some level of genetic segregation. An average LD ($r^2$) for the BS, LR, and YS breeds was estimated to be approximately 0.41. This study also found an average $N_e$ of 19.9 (BS), 31.4 (LR), and 34.1 (YS) over the last 5th generations. The effective population size for the BS, LR, and YS breeds decreased at a consistent rate from 50th to 10th generations ago. With a relatively faster $N_e$ decline rate in the past 10th generations, there exists possible evidence for intensive selection practices in pigs in the recent past. Conclusion: To develop customized chips for the genomic selection of various breeds, it is important to select and utilize SNP based on the genetic characteristics of each breed. Since the improvement efficiency of breed pigs increases sharply by the population size, it is important to increase test units for the improvement and it is desirable to establish the pig improvement network system to expand the unit of breed pig improvement through the genetic connection among breed pig farms.


Supported by : Rural Development Administration


  1. Hayes BJ, Bowman PJ, Chamberlain A, Goddard M. Invited review: Genomic selection in dairy cattle: Progress and challenges. J Dairy Sci 2009;92:433-43.
  2. Kim K. Genetic structure of Korean native pig using microsatellite markers. Korean J Genet 2002;24:1-7.
  3. Kim T, Kim K, Choi B, et al. Genetic structure of pig breeds from Korea and China using microsatellite loci analysis. J Anim Sci 2005;83:2255-63.
  4. Kim KI, Lee JH, Li K, et al. Phylogenetic relationships of Asian and European pig breeds determined by mitochondrial DNA D‐loop sequence polymorphism. Anim Genet 2002;33:19-25.
  5. Suh Y, Vijg J. SNP discovery in associating genetic variation with human disease phenotypes. Mutat Res Fundamental and Molecular Mechanisms of Mutagenesis 2005;573:41-53.
  6. Ramos AM, Crooijmans RP, Affara NA, et al. Design of a high density SNP genotyping assay in the pig using SNPs identified and characterized by next generation sequencing technology. PloS one 2009;4:e6524.
  7. Duran C, Appleby N, Edwards D, Batley J. Molecular genetic markers: discovery, applications, data storage and visualisation. Curr Bioinform 2009;4:16-27.
  8. Meng Q, Wang K, Liu X, et al. Identification of growth trait related genes in a Yorkshire purebred pig population by genome wide association studies. Asian-Australas J Anim Sci 2017;30:462-9.
  9. Suwannasing R, Duangjinda M, Boonkum W, Taharnklaew R, Tuangsithtanon K. The identification of novel regions for reproduction trait in Landrace and Large White pigs using a single step genome-wide association study. Asian-Australas J Anim Sci 2018;31:1852-62.
  10. 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.
  11. Knol EF, Nielsen B, Knap PW. Genomic selection in commercial pig breeding. Anim Front 2016;6:15-22.
  12. Puig-Oliveras A. Genetic dissection of growth and meat quality traits in pigs [PhD Thesis]. Barcelona, Spain: Autonomous University of Barcelona; 2015.
  13. Qiao R, Gao J, Zhang Z, et al. Genome-wide association analyses reveal significant loci and strong candidate genes for growth and fatness traits in two pig populations. Genet Sel Evol 2015;47:17.
  14. Weir BS. Methods for discrete population genetic data. Genetic data analysis II. Sunderland, UK: Sinauer Associates Incorporated; 1996.
  15. Nagy S, Poczai P, Cernak I, et al. PICcalc: an online program to calculate polymorphic information content for molecular genetic studies. Biochem Genet 2012;50:670-2.
  16. Botstein D, White RL, Skolnick M, Davis RW. Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am J Hum Genet 1980;32:314.
  17. Guo X, Elston R. Linkage information content of polymorphic genetic markers. Hum Hered 1999;49:112-8.
  18. Wright S. The interpretation of population structure by F‐statistics with special regard to systems of mating. Evolution 1965;19:395-420.
  19. Lewontin R. The interaction of selection and linkage. I. General considerations; heterotic models. Genetics 1964;49:49.
  20. Hill W, Robertson A. Linkage disequilibrium in finite populations. Theor Appl Genet 1968; 38:226-31.
  21. Hayes BJ, Visscher PM, McPartlan HC, Goddard ME. A novel multi-locus measure of linkage disequilibrium and its use to estimate past effective population size. Genome Res 2003;13:635-43.
  22. Dempster AP, Laird NM, Rubin DB. Maximum likelihood from incomplete data via the EM algorithm. J R Stat Soc Series B Methodol 1977;39:1-38.
  23. Excoffier L, Slatkin M. Maximum-likelihood estimation of molecular haplotype frequencies in a diploid population. Mol Biol Evol 1995;12:921-7.
  24. Sved J. Linkage disequilibrium and homozygosity of chromosome segments in finite populations. Theor Popul Biol 1971;2:125-41.
  25. 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.
  26. Edea Z, Kim S-W, Lee K-T, Kim TH, Kim K-S. Genetic Structure of and evidence for admixture between Western and Korean native pig breeds revealed by single nucleotide polymorphisms. Asian-Australas J Anim Sci 2014;27:1263-9.
  27. Badke YM, Bates RO, Ernst CW, Schwab C, Steibel JP. Estimation of linkage disequilibrium in four US pig breeds. BMC Genomics 2012;13:24.
  28. Uimari P, Tapio M. Extent of linkage disequilibrium and effective population size in Finnish Landrace and Finnish Yorkshire pig breeds. J Anim Sci 2011;89:609-14.
  29. Sargolzaei M, Schenkel F, Jansen G, Schaeffer L. Extent of linkage disequilibrium in Holstein cattle in North America. J Dairy Sci 2008;91:2106-17.