Journal
PLOS GENETICS
Volume 9, Issue 4, Pages -Publisher
PUBLIC LIBRARY SCIENCE
DOI: 10.1371/journal.pgen.1003453
Keywords
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Categories
Funding
- UK Food Standards Agency
- UK Department of Environment, Food and Rural Affairs
- Genesis Faraday (Biosciences KTN) SPARK award
- Institute Strategic Grant from the UK Biotechnology and Biological Sciences Research Council (BBSRC)
- European Research Council under the European Community's Seventh Framework Programme (FP7)/ERC [ERC-2009-AdG: 249894]
- BBSRC
- Rare Breeds Survival Trust
- Biotechnology and Biological Sciences Research Council [BBS/E/D/20211550, BBS/E/D/05191133, BBS/E/R/00001613, BBS/E/D/05191132, BBS/E/D/20211554] Funding Source: researchfish
- Medical Research Council [MC_PC_U127592696, MC_U127592696, MC_PC_U127527200] Funding Source: researchfish
- BBSRC [BBS/E/D/05191132, BBS/E/R/00001613, BBS/E/D/05191133, BBS/E/D/20211554, BBS/E/D/20211550] Funding Source: UKRI
- MRC [MC_U127592696, MC_PC_U127527200, MC_PC_U127592696] Funding Source: UKRI
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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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