Gurgul Artur, Jasielczuk Igor, Ropka-Molik Katarzyna, Semik-Gurgul Ewelina, Pawlina-Tyszko Klaudia, Szmatoła Tomasz, Szyndler-Nędza Magdalena, Bugno-Poniewierska Monika, Blicharski Tadeusz, Szulc Karolina, Skrzypczak Ewa, Krupiński Jędrzej
National Research Institute of Animal Production, Department of Animal Molecular Biology, Krakowska 1, 32-083, Balice, Poland.
National Research Institute of Animal Production, Department of Pig Breeding, Krakowska 1, 32-083, Balice, Poland.
BMC Genet. 2018 Oct 22;19(1):95. doi: 10.1186/s12863-018-0681-0.
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. 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.
A two largely complementary statistical methods were used for signatures detection, including: pairwise F 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.
The 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.
选择特征的识别能够直接洞察人工选择的机制，并有助于进一步揭示与动物表型变异相关的候选基因。驯化及随后的长期选择导致家猪出现了广泛的表型变化，涉及行为、身体组成、抗病性、繁殖和毛色等多个性状。在本研究中，基于从猪60K单核苷酸多态性（SNP）Illumina检测中获得的基因型，我们试图在属于四个品种的530头猪中检测多样化选择和品种内选择特征，这四个品种分别为波兰大白猪、普瓦夫斯卡猪、兹沃尼克白猪和兹沃尼克斑点猪，其中后三个品种是保守育种的对象，并且在很大程度上代表了本地种群。
我们使用了两种在很大程度上相互补充的统计方法来检测选择特征，包括：成对F检验和相对扩展单倍型纯合性（REHH）检验。品种特异性多样化选择信号包括几个参与生育、生长和代谢过程的基因，这些基因可能是所研究品种不同表型的原因。多样化选择信号还包括PPARD基因，该基因先前被发现对猪的外耳形状有很大影响，或者包括两个编码神经肽Y受体（Y2和Y5）的基因，它们参与脂肪沉积和应激反应，这些是区分所研究品种的重要特征。REHH统计允许检测到几个与一系列功能相关的基因重叠的品种内选择特征，这些功能包括：代谢途径、免疫系统反应或胚胎着床与发育。
本研究提供了许多与各个品种所选性状相关的潜在候选基因，并为进一步研究旨在确定所研究猪品种间变异来源提供了有力依据。
