Abstract
BackgroundIdentification of selection signatures can provide a direct insight into the mechanism of artificial selection and allow further disclosure of the candidate genes related to the animals’ phenotypic variation. Domestication and subsequent long-time selection have resulted in extensive phenotypic changes in domestic pigs, involving a number of traits, like behavior, body composition, disease resistance, reproduction and coat color. In this study, based on genotypes obtained from PorcineSNP60 Illumina assay we attempt to detect both diversifying and within-breed selection signatures in 530 pigs belonging to four breeds: Polish Landrace, Puławska, Złotnicka White and Złotnicka Spotted, of which the last three are a subject of conservative breeding and substantially represent the native populations.ResultsA two largely complementary statistical methods were used for signatures detection, including: pairwise FST and relative extended haplotype homozygosity (REHH) test. Breed-specific diversifying selection signals included several genes involved in processes connected with fertility, growth and metabolism which are potentially responsible for different phenotypes of the studied breeds. The diversifying selection signals also comprised PPARD gene that was previously found to have a large effect on the shape of the external ear in pigs or two genes encoding neuropeptide Y receptors (Y2 and Y5) involved in fat deposition and stress response which are important features differentiating the studied breeds. REHH statistics allowed detecting several within-breed selection signatures overlapping with genes connected with a range of functions including, among others: metabolic pathways, immune system response or implantation and development of the embryo.ConclusionsThe study provides many potential candidate genes with implication for traits selected in the individual breeds and gives strong basis for further studies aiming at identification of sources of variation among the studied pig breeds.
Highlights
Identification of selection signatures can provide a direct insight into the mechanism of artificial selection and allow further disclosure of the candidate genes related to the animals’ phenotypic variation
Single nucleotide polymorphism (SNP) polymorphism parameters and breeds genetic differentiation The applied SNPs filtering criteria allowed obtaining a common set of 43,923 SNPs polymorphic across the whole population with mean inter-marker distance of 55.7 kb (±78.0)
FST-derived signatures were useful to detect diversifying selection signals across breeds and allowed us to indicate genes connected e.g. with fertility, growth and metabolism which are potentially responsible for phenotypes of the studied breeds
Summary
Identification of selection signatures can provide a direct insight into the mechanism of artificial selection and allow further disclosure of the candidate genes related to the animals’ phenotypic variation. Numerous studies have shown applicability of genomics in the field of quantitative genetics and identification of sources of variation of important phenotypic features such as production traits [1]. Detection of selection signals in conjunction with subsequent candidate gene identification approach may indicate the location of major genes responsible for selected traits [3]. The advantage of such approach is that it is independent of the availability of detailed information on the phenotype of individual animals and is applicable to relatively small study populations [2]. Selection patterns in pig breeds differ depending on their evolution and breeding histories, so exploration of selection signatures in possibly the largest number of different breeds will help to better understand the genetic variation underlying the traits of interest
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
