Genomic diversity in pig (Sus scrofa) and its comparison with human and other livestock

Current Genomics

Volumn 12, Issue 2, 2011, Pages 138-146

  Zhang, Chunyan ^a   Plastow, Graham ^a  

^a UNIVERSITY OF ALBERTA   (Canada)

Author keywords

Genomic diversity; Human; Linkage disequilibrium; Livestock; Pig

Indexed keywords

ASIAN; CATTLE; COMPARATIVE STUDY; EUROPE; EUROPEAN AMERICAN; GENE LINKAGE DISEQUILIBRIUM; GENETIC DISTANCE; GENETIC DRIFT; GENETIC SELECTION; GENETIC VARIABILITY; GOAT; HETEROZYGOSITY; HUMAN; INBREEDING; INTROGRESSION; LIVESTOCK; NONHUMAN; POPULATION DIFFERENTIATION; POPULATION GENETICS; POPULATION SIZE; REVIEW; SHEEP; SINGLE NUCLEOTIDE POLYMORPHISM; SWINE;

BOS; OVIS ARIES; SUIDAE; SUS; SUS SCROFA;

EID: 79955596565     PISSN: 13892029     EISSN: None     Source Type: Journal    
DOI: 10.2174/138920211795564386     Document Type: Review

References (75)

1. Kim, K. I.; Lee, J. H.; Li, K.; Zhang, Y. P.; Lee, S. S.; Gongora, J.; Moran, C. Phylogenetic relationships of Asian and European pig breeds determined by mitochondrial DNA D-loop sequence polymorphism. Anim. Genet., 2002, 33(1), 19-25.
2. Larson, G.; Dobney, K.; Albarella, U.; Fang, M.; Matisoo-Smith, E.; Robins, J.; Lowden, S.; Finlayson, H.; Brand, T.; Willerslev, E.; Rowley-Conwy, P.; Andersson, L.; Cooper, A. Worldwide phylogeography of wild boar reveals multiple centers of pig domestication. Science, 2005, 307(5715), 1618.
3. Giuffra, E.; Kijas, J. M. H.; Amarger, V.; Carlborg, Ö.; Jeon, J. T.; Andersson, L. The origin of the domestic pig: independent domestication and subsequent introgression. Genetics, 2000, 154(4), 1785-1791.
4. Plastow, G.; Siggens, K.; McLaren, D. A genetic case study. Engineering biotechnologies for practical application to livestock. IEEE Potentials, 1994, 13, 22-25.
5. Evans, G. J.; Giuffra, E.; Sanchez, A.; Kerje, S.; Davalos, G.; Vidal, O.; Illán, S.; Noguera, J. L.; Varona, L.; Velander, I.; Southwood, O. I.; de Koning, D. J.; Haley, C. S.; Plastow, G. S.; Andersson, L. Identification of quantitative trait loci for production traits in commercial pig populations. Genetics, 2003, 164(2), 621-627.
6. Hu, Z. L.; Park, C. A.; Fritz, E. R.; Reecy, J. M. QTLdb: A Comprehensive Database Tool Building Bridges between Genotypes and Phenotypes. Invited Lecture with full paper published electronically on The 9th World Congress on Genetics Applied to Livestock Production. Leipzig, Germany, 2010, 1-6, 2010.
7. Wei, W. H.; Skinner, T. M.; Anderson, J. A.; Southwood, O. I.; Plastow, G.; Archibald, A. L.; Haley, C. S. Mapping QTL in the porcine MHC region affecting fatness and growth traits in a Meishan/ Large White composite population. Anim. Gen., 2010, DOI: 10.1111/j.1365-2052.2010.02062.x
8. Rothschild, M.F.; Newman, S. Eds. Intellectual Property Rights in Animal Breeding and Genetics. CABI Publishing, 2002, 179-196.
9. Rothschild, M.; Jacobson, C.; Vaske, D.; Tuggle, C.; Wang, L.; Short, T.; Eckardt, G.; Sasaki, S.; Vincent, A.; McLaren, D.; Southwood, O.; van der Steen, H.; Mileham, A.; Plastow, G. The estrogen receptor locus is associated with a major gene influencing litter size in pigs. Proc. Natl. Acad. Sci. USA, 1996, 93(1), 201-205.
10. Short, T. H.; Rothschild, M. F.; Southwood, O. I.; McLaren, D. G.; de Vries, A.; van der Steen, H.; Eckardt, G. R.; Tuggle, C. K.; Helm, J.; Vaske, D. A.; Mileham, A. J.; Plastow, G. S. Effect of estrogen receptor locus on reproduction and production traits in four commercial lines of pigs. J. Anim. Sci., 1997, 75(12), 3138-3142.
11. van der Steen, H. A. M.; Prall, G. F. W.; Plastow, G. S. Application of genomics to the pork industry. J. Anim. Sci., 2005, 83(13), E1-E8.
12. de Roos, A. P. W.; Hayes, B. J.; Spelman, R. J.; Godd, M. E. Linkage disequilibrium and persistence of phase in Holstein Friesian, Jersey and Angus cattle. Genetics, 2008, 179(3), 1503-1512.
13. McKay, S. D.; Schnabel, R. D.; Murdoch, B. M.; Matukumalli, L. K.; Aerts, J.; Coppieters, W.; Crews, D.; Neto, E. D.; Gill, C. A.; Gao, C.; Mannen, H.; Stothard, P.; Wang, Z.; van Tassell, C. P.; Williams, J. L.; Taylor, J. F.; Moore, S. S. Whole genome linkage disequilibrium maps in cattle. BMC Genet., 2007, 8, 74.
14. Biswas, S.; Scheinfeldt, L. B.; Akey, J. M. Genome-wide Insights into the Patterns and Determinants of Fine-Scale Population Structure in Humans. Am. J. Hum. Genet., 2009, 84(5), 641-650.
15. Qanbari, S.; Pimentel, E. C. G.; Tetens, J.; Thaller, G.; Lichtner, P.; Sharifi, A. R.; Simianer, H. The pattern of linkage disequilibrium in German Holstein cattle. Anim. Genet., 2009, 41(4), 346-356.
16. Upkin, E.; Straus, K.; Stein, T. R.; Bagnato, A.; Schiavini, F.; Fontanesi, L.; Russo, V.; Medugorac, I.; Foerster, M.; Sölkner, J.; Dolezal, M.; Medrano, J. F.; Friedmann, A.; Soller, M. Extensive long-range and nonsyntenic linkage disequilibrium in livestock populations: deconstruction of a conundrum. Genetics, 2009, 181(2), 691-699.
17. Amaral, A. J.; Megens, H.; Crooijmans, R. P. M. A.; Heuven, H. C. M.; Groenen, M. A. M. Linkage disequilibrium decay and haplotype block structure in the pig. Genetics, 2008, 179(1), 569-579.
18. Du, F. X.; Clutter, A. C.; Lohuis, M. M. Characterizing Linkage Disequilibrium in Pig Populations. Int. J. Biol. Sci., 2007, 3(3), 166.
19. Fan, B.; Wang, Z. G.; Li, Y. J.; Zhao, X. L.; Liu, B.; Zhao, S. H.; Yu, M.; Li, M. H.; Chen, S. L.; Xiong, T. A.; Li, K. Genetic variation analysis within and among Chinese indigenous swine populations using microsatellite markers. Anim. Genet., 2002, 33(6), 422-427.
20. Luetkemeier, E. S.; Sodhi, M.; Schook, L. B.; Malhi, R. S. Multiple Asian pig origins revealed through genomic analyses. Mol. Phylogenet. Evol., 2010, 54(3), 680-686.
21. Nsengimana, J.; Baret, P.; Haley, C. S.; Visscher, P. M. Linkage disequilibrium in the domesticated pig. Genetics, 2004, 166(3), 1395-1404.
22. Ojeda, A.; Ramos-Onsins, S. E.; Marletta, D.; Huang, L. S.; Folch, J. M.; Pérez-Enciso, M. Evolutionary study of a potential selection target region in the pig. Heredity, 2011, 106, 330-338.
23. Ramos, A. M.; Crooijmans, R. P. M. A.; Affara, N. A.; Amaral, A. J.; Archibald, A. L.; Beever, J. E.; Bendixen, C.; Churcher, C.; Clark, R.; Dehais, P.; Hansen, M. S.; Hedegaard, J.; Hu, Z. L.; Kerstens, H. H.; Law, A. S.; Megens, H. J.; Milan, D.; Nonneman, D. J.; Rohrer, G. A.; Rothschild, M. F.; Smith, T. P. L.; Schnabel, R. D.; Van Tassell, C. P.; Taylor, J. F.; Wiedmann, R. T.; Schook, L. B.; Groenen, M. A. M. 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(8), e6524.
24. Hu, X. S.; Yeh, F. C.; Wang, Z. Structural genomics: correlation blocks, population structure, and genome architecture. Curr. Genomics, 2011, 12 (1), 55-70.
25. Laval, G.; Iannuccelli, N.; Legault, C.; Milan, D.; Groenen, M. A. M.; Giuffra, E.; Andersson, L.; Nissen, P. H.; Jargensen, C. B.; Beeckmann, P.; Geldermann, H.; Foulley, J. L.; Chevalet, C.; Ollivier, L. Genetic diversity of eleven European pig breeds. Genet. Sel. Evol., 2000, 32(2), 187-203.
26. Yang, S. L.; Wang, Z. G.; Liu, B.; Zhang, G. X.; Zhao, S. H.; Yu, M.; Fan, B.; Li, M. H.; Xiong, T. A.; Li, K. Genetic variation and relationships of eighteen Chinese indigenous pig breeds. Genet. Sel. Evol., 2003, 35(6), 657-671.
27. The 1000 Genomes Project Consortium. A map of human genome variation from population-scale sequencing. Nature, 2010, 467(7319), 1063-1073.
28. Fahrenkrug, S. C.; Freking, B. A.; Smith, T. P.; Rohrer, G. A.; Keele, J. W. Single nucleotide polymorphism (SNP) discovery in porcine expressed genes. Anim. Genet., 2002, 33(3), 186-195.
29. Jungerius, B. J.; Rattink, A. P.; Crooijmans, R. P.; van der Poel, J. J.; van Oost, B. A.; te Pas, M. F.; Groenen, M. A. Development of a single nucleotide polymorphism map of porcine chromosome 2. Anim. Genet., 2003, 34(6), 429-43.
30. Kerstens, H. H. D.; Kollers, S.; Kommadath, A.; Rosario, M.; Dibbits, B.; Kinders, S. M.; Crooijmans, R. P.; Groene, M. A. M. Mining for Single Nucleotide Polymorphisms in Pig genome sequence data. BMC Genomics, 2009, 10, 4.
31. Wang, D. G.; Fan, J. B.; Siao, C. J.; Berno, A.; Young, P.; Sapolsky, R.; Ghandour, G.; Perkins, N.; Winchester, E.; Spencer, J.; Kruglyak, L.; Stein, L.; Hsie, L.; Topaloglou, T.; Hubbell, E.; Robinson, E.; Mittmann, M.; Morris, M. S.; Shen, N.; Kilburn, D.; Rioux, J.; Nusbaum, C.; Rozen, S.; Hudson, T. J.; Lipshutz, R.; Chee, M.; Lander, E. S. Large-scale identification, mapping and genotyping of single nucleotide polymorphisms in the human genome. Science, 1998, 280(5366), 1077-1082.
32. Archibald, A. L.; Bolund, L.; Churcher, C.; Fredholm, M.; Groenen, M. A. M.; Harlizius, B.; Lee, K. T.; Milan, D.; Rogers, J.; Rothschild, M. F.; Uenishi, H.; Wang, J.; Schook, L. B. Pig genome sequence-analysis and publication strategy. BMC Genomics, 2010, 11, 438.
33. Martinez, A. M.; Delgado, J. V.; Rodero, A.; Vega-Pla, J. L. Genetic structure of the Iberian pig breed using microsatellites. Anim. Genet., 2000, 31(5), 295-301.
34. Huang, Y. F.; Shi, X. W.; Zhang, Y. P. Mitochondrial Genetic Variation in Chinese Pigs and Wild Boars. Biochem. Genet., 1999, 37(11-12), 335-343.
35. Fang, M.; Andersson, L. Mitochondrial diversity in European and Chinese pigs is consistent with population expansions that occurred prior to domestication. Proc. R. Soc. B, 2006, 273(1595), 1803-1810.
36. Carza, J. C.; Slatkin, M.; Freimer, N. B. Microsatellite allele frequencies in Humans and Chimpanzees, with implications for constraints on allele size. Mol. Biol. Evol., 1995, 12(4), 594-603.
37. Thalmann, O.; Fischer, A.; Lankester, F.; Pääbo, S.; Vigilant, L. The complex evolutionary history of gorillas: insights from genomic data. Mol. Biol. Evol., 2007, 24(1), 146-158.
38. The Chimpanzee Sequencing and Analysis Consortium. Initial sequence of the chimpanzee genome and comparison with the human genome. Nature, 2005, 437(7055), 69-87.
39. Auton, A.; Bryc, K.; Boyko, A.; Lohmueller, K.; Novembre, J.; Reynolds, A.; Indap, A.; Wright, M. H.; Degenhardt, J.; Gutenkunst, R.; King, K. S.; Nelson, M. R.; Bustamante, C. D. Global distribution of genomic diversity underscores rich complex history of continental human populations. Genome Res., 2009, 19(5), 795-803.
40. Barreiro, L. B.; Laval, G.; Quach, H.; Patin, E.; Quintana-Murci, L. Natural selection has driven population differentiation in modern humans. Nat. Genet., 2008, 40(3), 340-345.
41. International Hap Map Consortium. A haplotype map of the human genome. Nature, 2005, 437(7063), 1299-1320.
42. Weir, B. S.; Cardon, L. R.; Anderson, A. D.; Nielsen, D. M.; Hill, W. G. Measures of human population structure show heterogeneity among genomic regions. Genome Res., 2005, 15(11), 1468-1476.
43. Xing, J.; Watkins, W. S.; Witherspoon, D. J.; Zhang, Y.; Guthery, S. L.; Thara, R.; Mowry, B. J.; Bulayeva, K.; Weiss, R. B.; Jorde, L. B. Fine-scaled human genetic structure revealed by SNP microarrays. Genome Res., 2009, 19(5), 815-825.
44. Redon, R.; Ishikawa, S.; Fitch, K. R.; Feuk, L.; Perry, G. H.; Andrews, T. D.; Fiegler, H.; Shapero, M. H.; Carson, A. R.; Chen, W.; Cho, E. K.; Dallaire, S.; Freeman, J. L.; González, J. R.; Gratacòs, M.; Huang, J.; Kalaitzopoulos, D.; Komura, D.; MacDonald, J. R.; Marshall, C. R.; Mei, R.; Montgomery, L.; Nishimura, K.; Okamura, K.; Shen, F.; Somerville, M. J.; Tchinda, J.; Valsesia, A.; Woodwark, C.; Yang, F.; Zhang, J.; Zerjal, T.; Zhang, J.; Armengol, L.; Conrad, D. F.; Estivill, X.; Tyler-Smith, C.; Carter, N. P.; Aburatani, H.; Lee, C.; Jones, K. W.; Scherer, S. W.; Hurles, M. E. Global variation in copy number in the human genome. Nature, 2007, 444(7118), 444-454.
45. Bruno-de-Sousa, C.; Martinez, A. M.; Ginja, C.; Santos-Silva, F.; Carolino, M. I.; Delgado, J. V.; Gama, L. T. Genetic diversity and population structure in Portuguese goat breeds. Livest. Sci., 2010, doi:10.1016/j.livsci.2010.06.159.
46. Dixit, S. P.; Verma, N. K.; Aggarwal, R. A. K.; Kumar, S.; Chander, R.; Vyas, M. K.; Singh, K. P. Genetic structure and differentiation of three Indian goat breeds. Asian-Aust. J. Anim. Sci., 2009, 22, 1234-1240.
47. Serrano, M.; Calvo, J. H.; Martinez, M.; Marcos-Carcavilla, A.; Cuevas, J.; Gonzallez, C.; Jurado, J. J.; Tejada, P. D. Microsatellite based genetic diversity and population structure of the endangered Spanish Guadarrama goat breed. BMC Genet., 2009, 10, 61.
48. Agha, SH.; Pilla, F.; Galal, S.; Shaat, I.; Andrea, M. D.; Reale, S.; Abdelsalam, A. Z. A.; Li, M. H. Genetic diversity in Egyptian and Italian goat breeds measured with microsatellite polymorphism. J. Anim. Breed. Genet., 2008, 125(3), 194-200.
49. Chenyambuga, S. W.; Hanotte, O.; Hirbo, J.; Watts, P. C.; Kemp, S. J.; Kifaro, G. C.; Gwakisa, P. S.; Petersen, P. H.; Rege, J. E. O. Genetic characterization of indigenous goats of Sub-Saharan Africa using microsatellite DNA markers. Asian-Aust. J. Anim. Sci., 2004, 17(4), 445-452.
50. Zhou, G. L.; Jin, H. G.; Zhu, Q.; Guo, S. L.; Wu, Y. H. Genetic diversity analysis of five cattle breeds native to China using microsatellites. J. Genet., 2005, 84(1), 77-80.
51. Canon, J.; Alexandrino, P.; Bessa, I.; Carleos, C.; Carretero, Y.; Dunner, S.; Ferran, N.; Garcia, D.; Jordana, J.; Laloe, D.; Pereira, A.; Sanchez, A.; Moazami-Goudarzi, K. Genetic diversity measures of local European beef cattle breeds for conservation purposes. Genet. Sel. Evol., 2001, 33(3), 311-332.
52. Kantanen, J.; Olsaker, I.; Holm, L. E.; Lien, S.; Vilkki, J.; Brusgaard, K.; Eythorsdottir, E.; Danell, B.; Adalsteinsson, S. Genetic diversity and population structure of 20 north European cattle breeds. J. Hered., 2000, 91(6), 446-457.
53. Egito, A. A.; Paiva, S. R.; Albuquerque, M. S. M.; Mariante, A. S.; Almeida, L. D.; Castro, S. R.; Grattapaglia, D. Microsatellite based genetic diversity and relationships among ten Creole and commercial cattle breeds raised in Brazil. BMC Genet., 2007, 8, 83.
54. Rehman, M. S.; Khan, M. S. Genetic diversity of hariana and hissar cattle from Pakistan using microsatellite analysis. Pakistan Vet. J., 2009, 29(2), 67-71.
55. Harmegnies, N.; Farnir, F.; Davin, F.; Buys, N.; Georges, M.; Coppieters, W. Measuring the extent of linkage disequilibrium in commercial pig populations. Anim. Genet., 2006, 37(3), 225-231.
56. Uimari, P.; Tapio, M. Extent of linkage disequilibrium and effective population size in Finnish Landrace and Finnish Yorkshire pig breeds. J. Anim. Sci., 2010, doi:10.2527/jas.2010-3249.
57. Jungerius, B. J.; Gu, J.; Crooijmans, R. P. M. A.; Poel, J. J.; Groenen, M. A. M.; van Oost, B. A.; te Pas, M. F. Estimation of the extent of linkage disequilibrium in seven regions of the porcine genome. Anim. Biotechnol., 2005, 16(1), 41-54.
58. Megens, H. J.; Crooijmans, R. P. M. A.; Heuven, H. C. M.; Groenen, M. A. M. Linkage disequilibrium decay and haplotype block structure in the pig. Genetics, 2008, 179(1), 569-579.
59. Welsh, C. S.; Stewart, T. S.; Schwab, C.; Blackburn, H. D. Pedigree analysis of 5 swine breeds in the United States and the implications for genetic conservation. J. Anim. Sci., 2010, 88(5), 1610-1618.
60. Dunning, A. M.; Durocher, F.; Healey, C. S.; Teare, M. D.; McBride, S. E.; Carlomagno, F.; Xu, C. F.; Dawson, E.; Rhodes, S.; Ueda, S.; Lai, E.; Luben, R. N.; van Rensburg, E. J.; Mannermaa, A.; Kataja, V.; Rennart, G.; Dunham, I.; Purvis, I.; Easton, D.; Ponder, B. A. J. The extent of linkage disequilibrium in four populations with distinct demographic histories. Am. J. Hum. Genet., 2000, 67(6), 1544-1554.
61. Kruglyak, L. Prospects for whole-genome linkage disequilibrium mapping of common disease genes. Nat. Genet., 1999, 22(2), 139-144.
62. Abecasis, G. R.; Noguchi, E.; Heinzmann, A.; Traherne, J. A.; Bhattacharyya, S.; Leaves, N. I.; Anderson, G. G.; Zhang, Y.; Lench, N. J.; Carey, A.; Cardon, L. R.; Moffatt, M. F.; Cookson, W. O. C. Extent and distribution of linkage disequilibrium in three genomic regions. Am. J. Hum. Genet., 2001, 68(1), 191-197.
63. Taillon-Miller, P.; Bauer-Sardiña, I.; Saccone, N. L.; Putzel, J.; Laitinen, T.; Cao, A.; Kere, J.; Pilia, G.; Rice, J. P.; Kwok, P. Y. Juxtaposed regions of extensive and minimal linkage disequilibrium in human Xq25 and Xq28. Nat. Genet., 2000, 25(3), 324-328.
64. Ardlie, K. G.; Kruglyak, L.; Seielstad, M. Patterns of linkage disequilibrium in the human genome. Nat. Rev. Genet., 2002, 3(4), 299-309.
65. Reich, D. E.; Cargill, M.; Bolk, S.; Ireland, J.; Sabeti, P. C.; Richter, D. J.; Lavery, T.; Kouyoumjian, R.; Farhadian, S. F.; Ward, R.; Lander, E. S. Linkage disequilibrium in the human genome. Nature, 2001, 411(6834), 199-204.
66. Tenesa, A.; Navarro, P.; Hayes, B. J.; Duffy, D. L.; Clarke, G. M.; Goddard, M. E.; Visscher, P. M. Recent human effective population size estimated from linkage disequilibrium. Genome Res., 2007, 17(4), 520-526.
67. Flury, C.; Tapio, M.; Sonstegard, T.; Drögemüller, C.; Leeb, T.; Simianer, H.; Hanotte, O.; Rieder, S. Effective population size of an indigenous Swiss cattle breed estimated from linkage disequilibrium. J. Anim. Breed. Genet., 2010, 127(5), 339-347.
68. Khatkar, M. S.; Nicholas, F. W.; Collins, A. Q.; Zenger, K. R.; Cavanagh, J. A. L.; Barris, W.; Schnabel, R. D.; Taylor, J. F.; Raadsma, H. W. Extent of genome-wide linkage disequilibrium in Australian Holstein-Friesian cattle based on a high-density SNP panel. BMC Genomics, 2008, 9, 187.
69. Sargolzaei, M.; Schenkel, F. S.; Jansen, G. B.; Schaeffer, L. R. Extent of linkage disequlibrium in Holstein cattle in North America. J. Dairy Sci., 2008, 91(5), 2106-2117.
70. Kim, E. S.; Kirkpatrick, B. W. Linkage disequilibrium in the North American Holstein population. Anim. Genet., 2009, 40(3), 279-88.
71. McRae, A. F.; McEwan, J. C.; Dodds, K. G.; Wilson, T.; Crawford, A. M.; Slate, J. Linkage disequilibrium in domestic sheep. Genetics, 2002, 160(3), 1113-1122.
72. McRae, A. F.; Pemberton, J. M.; Visscher, P. M. Modeling linkage disequilibrium in natural populations: the example of the soay sheep population of St. Kilda, Scotland. Genetics, 2005, 171(1), 251-258.
73. Meadows, J. R. S.; Chan, E. K.; Kijas, J. W. Linkage disequilibrium compared between five populations of domestic sheep. BMC Genet., 2008, 9, 61.
74. Ramirez, O.; Ojeda, A.; Tomas, A.; Gallardo, D.; Huang, L. S.; Folch, J. M.; Clop, A.; Sánchez, A.; Badaoui, B.; Hanotte, O.; Galman-Omitogun, O.; Makuza, S. M.; Soto, H.; Cadillo, J.; Kelly, L.; Cho, I. C.; Yeghoyan, S.; Pérez-Enciso, M.; Amills, M. Integrating Y-chromosome, mitochondrial and autosomal data to analyse the origin of pig breeds. Mol. Biol. Evol., 2009, 26(9), 2061-2072.
75. Xing, J.; Watkins, W. S.; Shlien, A.; Walker, E.; Huff, C. D.; Witherspoon, D. J.; Zhang, Y.; Simonson, T. S.; Weiss, R. B.; Schiffman, J. D.; Malkin, D.; Woodward, S. R.; Jorde, L. B. Toward a more uniform sampling of human genetic diversity: A survey of worldwide populations by high-density genotyping. Genomics, 2010, 96(4), 199-210.