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.
Highlights
The domestic pig is an important livestock species and an important protein source worldwide
We have applied these tools to identify genomic regions associated with breed development in a set of commercial and traditional pig breeds
We found strong evidence of genetic differentiation between breeds near genes associated with traits that are used to define breed standards, such as ear morphology and coat colour, as well as in regions of the genome that are associated with pork production traits
Summary
The domestic pig is an important livestock species and an important protein source worldwide. Local pig types were developed in Europe and Asia after domestication, but the development of phenotypically distinct breeds occurred with the commencement of organised breeding in the 18th century [4]. Substantial morphological changes occurred in breeds over a short period of time, resulting in the development of numerous distinct pig breed phenotypes in Britain. Breeds tended to be formed by complex crossing with numerous other breeds, including a number from Asia, to introduce desirable traits [4,5,6], after improvement the breeds were kept distinct, resulting in highly specialised phenotypically distinct and genetically differentiated pig breeds [7]. From the 20th century, with the recognition of the benefits of genetic improvement and changing consumer preferences, certain pig breeds experienced further strong selection for lean meat content, muscularity and enhanced reproduction [5,6]
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