A genome scan for selection signatures in Taihu pig breeds using next-generation sequencing

Abstract

Taihu pig breeds are the most prolific breeds of swine in the world, and they also have superior economic traits, including high resistance to disease, superior meat quality, high resistance to crude feed and a docile temperament. The formation of these phenotypic characteristics is largely a result of long-term artificial or natural selection. Therefore, exploring selection signatures in the genomes of the Taihu pigs will help us to identify porcine genes related to productivity traits, disease and behaviour. In this study, we used both intra-population (Relative Extend Haplotype Homozygosity Test (REHH)) and inter-population (the Cross-Population Extend Haplotype Homozygosity Test (XPEHH); F-STATISTICS, F ST ) methods to detect genomic regions that might be under selection process in Taihu pig breeds. As a result, we found 282 (REHH) and 112 (XPEHH) selection signature candidate regions corresponding to 159.78 Mb (6.15%) and 62.29 Mb (2.40%) genomic regions, respectively. Further investigations of the selection candidate regions revealed that many genes under these genomic regions were related to reproductive traits (such as the TLR9 gene), coat colour (such as the KIT gene) and fat metabolism (such as the CPT1A and MAML3 genes). Furthermore, gene enrichment analyses showed that genes under the selection candidate regions were significantly over-represented in pathways related to diseases, such as autoimmune thyroid and asthma diseases. In conclusion, several candidate genes potentially under positive selection were involved in characteristics of Taihu pig. These results will further allow us to better understand the mechanisms of selection in pig breeding.

Whole-genome sequencing of European autochthonous and commercial pig breeds allows the detection of signatures of selection for adaptation of genetic resources to different breeding and production systems

“…Other studies that involved a few Asian and European pig breeds investigated signatures of selection in the porcine genome using SNP chip or partial/reduced or wholegenome re-sequencing datasets and highlighted loci of economic importance [7,[31][32][33][34][35][36][37][38][39][40][41][42].…”

Genome‐wide detection of copy number variants in European autochthonous and commercial pig breeds by whole‐genome sequencing of DNA pools identified breed‐characterising copy number states

“…These breeds represent genetic resources adapted to local agro-climatic and environmental conditions. To date, the genome architecture of CNVs has been studied mainly in Asian autochthonous populations/ breeds (Li et al 2012;Wang et al 2014Wang et al , 2015bWang et al , 2019bJiang et al 2014;Dong et al 2015;Xie et al 2016). European autochthonous pig breeds have been mainly investigated by exploring their genetic variability using SNP data (e.g.…”

Using High-Density SNP Array to Reveal Selection Signatures Related to Prolificacy in Chinese and Kazakhstan Sheep Breeds

“…We also found that the genes under selection to be overrepresented in pathways related to lipids (e.g., alpha-Linolenic acid metabolism, Corrected p = 0.005; Linoleic acid metabolism, Corrected p = 0.02; Arachidonic acid metabolism, Corrected p = 0.05; ether lipid metabolism, p < 0.05), which were reported to be relevant to lipogenesis in Taihu pigs [32]. This finding indicated that the genes related to lipids traits have experienced intensive selection, and might be correlated with the fat tail trait of Aldabas and Kurdyuchnyj sheep in this study.…”