Signatures of Diversifying Selection in European Pig Breeds

Overview

Journal PLoS Genet

Specialty Genetics

Date 2013 May 3

PMID 23637623

Citations 108

Authors

Samantha Wilkinson

Zen H Lu

Hendrik-Jan Megens

Alan L Archibald

Chris Haley

Ian J Jackson

Martien A M Groenen

Richard P M A Crooijmans

Rob Ogden

Pamela Wiener

Affiliations

Soon will be listed here.

Abstract

Following domestication, livestock breeds have experienced intense selection pressures for the development of desirable traits. This has resulted in a large diversity of breeds that display variation in many phenotypic traits, such as coat colour, muscle composition, early maturity, growth rate, body size, reproduction, and behaviour. To better understand the relationship between genomic composition and phenotypic diversity arising from breed development, the genomes of 13 traditional and commercial European pig breeds were scanned for signatures of diversifying selection using the Porcine60K SNP chip, applying a between-population (differentiation) approach. Signatures of diversifying selection between breeds were found in genomic regions associated with traits related to breed standard criteria, such as coat colour and ear morphology. Amino acid differences in the EDNRB gene appear to be associated with one of these signatures, and variation in the KITLG gene may be associated with another. Other selection signals were found in genomic regions including QTLs and genes associated with production traits such as reproduction, growth, and fat deposition. Some selection signatures were associated with regions showing evidence of introgression from Asian breeds. When the European breeds were compared with wild boar, genomic regions with high levels of differentiation harboured genes related to bone formation, growth, and fat deposition.

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References

Wiener P, Wilkinson S . Deciphering the genetic basis of animal domestication. Proc Biol Sci. 2011; 278(1722):3161-70. PMC: 3169034. DOI: 10.1098/rspb.2011.1376. View

Fuchs S, Amiel J, Claudel S, Lyonnet S, Corvol P, Pinet F . Functional characterization of three mutations of the endothelin B receptor gene in patients with Hirschsprung's disease: evidence for selective loss of Gi coupling. Mol Med. 2001; 7(2):115-24. PMC: 1950018. View

Hellemans J, Preobrazhenska O, Willaert A, Debeer P, Verdonk P, Costa T . Loss-of-function mutations in LEMD3 result in osteopoikilosis, Buschke-Ollendorff syndrome and melorheostosis. Nat Genet. 2004; 36(11):1213-8. DOI: 10.1038/ng1453. View

Uemoto Y, Soma Y, Sato S, Ishida M, Shibata T, Kadowaki H . Genome-wide mapping for fatty acid composition and melting point of fat in a purebred Duroc pig population. Anim Genet. 2012; 43(1):27-34. DOI: 10.1111/j.1365-2052.2011.02218.x. View

Wigginton J, Cutler D, Abecasis G . A note on exact tests of Hardy-Weinberg equilibrium. Am J Hum Genet. 2005; 76(5):887-93. PMC: 1199378. DOI: 10.1086/429864. View

Bannasch D, Young A, Myers J, Truve K, Dickinson P, Gregg J . Localization of canine brachycephaly using an across breed mapping approach. PLoS One. 2010; 5(3):e9632. PMC: 2835769. DOI: 10.1371/journal.pone.0009632. View

Boyko A, Quignon P, Li L, Schoenebeck J, Degenhardt J, Lohmueller K . A simple genetic architecture underlies morphological variation in dogs. PLoS Biol. 2010; 8(8):e1000451. PMC: 2919785. DOI: 10.1371/journal.pbio.1000451. View

JACKSON I . Homologous pigmentation mutations in human, mouse and other model organisms. Hum Mol Genet. 1997; 6(10):1613-24. DOI: 10.1093/hmg/6.10.1613. View

Rodriguez C, Tomas A, Alves E, Ramirez O, Arque M, Munoz G . QTL mapping for teat number in an Iberian-by-Meishan pig intercross. Anim Genet. 2005; 36(6):490-6. DOI: 10.1111/j.1365-2052.2005.01358.x. View

10.

Ramos A, Crooijmans R, Affara N, Amaral A, Archibald A, Beever J . 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. PMC: 2716536. DOI: 10.1371/journal.pone.0006524. View

11.

Vaysse A, Ratnakumar A, Derrien T, Axelsson E, Pielberg G, Sigurdsson S . Identification of genomic regions associated with phenotypic variation between dog breeds using selection mapping. PLoS Genet. 2011; 7(10):e1002316. PMC: 3192833. DOI: 10.1371/journal.pgen.1002316. View

12.

Arnaud-Dabernat S, Bourbon P, Dierich A, Le Meur M, Daniel J . Knockout mice as model systems for studying nm23/NDP kinase gene functions. Application to the nm23-M1 gene. J Bioenerg Biomembr. 2003; 35(1):19-30. DOI: 10.1023/a:1023561821551. View

13.

Baxter L, Hou L, Loftus S, Pavan W . Spotlight on spotted mice: a review of white spotting mouse mutants and associated human pigmentation disorders. Pigment Cell Res. 2004; 17(3):215-24. DOI: 10.1111/j.1600-0749.2004.00147.x. View

14.

Flori L, Fritz S, Jaffrezic F, Boussaha M, Gut I, Heath S . The genome response to artificial selection: a case study in dairy cattle. PLoS One. 2009; 4(8):e6595. PMC: 2722727. DOI: 10.1371/journal.pone.0006595. View

15.

Megens H, Crooijmans R, San Cristobal M, Hui X, Li N, Groenen M . Biodiversity of pig breeds from China and Europe estimated from pooled DNA samples: differences in microsatellite variation between two areas of domestication. Genet Sel Evol. 2007; 40(1):103-28. PMC: 2674914. DOI: 10.1186/1297-9686-40-1-103. View

16.

Zhang Z, Anthony R . Porcine stem cell factor/c-kit ligand: its molecular cloning and localization within the uterus. Biol Reprod. 1994; 50(1):95-102. DOI: 10.1095/biolreprod50.1.95. View

17.

Gibbs R, Taylor J, Van Tassell C, Barendse W, Eversole K, Gill C . Genome-wide survey of SNP variation uncovers the genetic structure of cattle breeds. Science. 2009; 324(5926):528-32. PMC: 2735092. DOI: 10.1126/science.1167936. View

18.

Kijas J, Wales R, Tornsten A, Chardon P, Moller M, Andersson L . Melanocortin receptor 1 (MC1R) mutations and coat color in pigs. Genetics. 1998; 150(3):1177-85. PMC: 1460407. DOI: 10.1093/genetics/150.3.1177. View

19.

Harlizius B, Rattink A, de Koning D, Faivre M, Joosten R, van Arendonk J . The X chromosome harbors quantitative trait loci for backfat thickness and intramuscular fat content in pigs. Mamm Genome. 2000; 11(9):800-2. DOI: 10.1007/s003350010147. View

20.

Akey J, Zhang G, Zhang K, Jin L, Shriver M . Interrogating a high-density SNP map for signatures of natural selection. Genome Res. 2002; 12(12):1805-14. PMC: 187574. DOI: 10.1101/gr.631202. View