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Genome‐wide scans to detect positive selection in Large White and Tongcheng pigs
Author(s) -
Li Xiuling,
Yang Songbai,
Tang Zhonglin,
Li Kui,
Rothschild Max F.,
Liu Bang,
Fan Bin
Publication year - 2014
Publication title -
animal genetics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.756
H-Index - 81
eISSN - 1365-2052
pISSN - 0268-9146
DOI - 10.1111/age.12128
Subject(s) - biology , domestication , selection (genetic algorithm) , candidate gene , quantitative trait locus , haplotype , genetics , evolutionary biology , genotyping , white (mutation) , trait , adaptation (eye) , genome , gene , allele , genotype , artificial intelligence , neuroscience , computer science , programming language
Summary Due to the direction, intensity, duration and consistency of genetic selection, especially recent artificial selection, the production performance of domestic pigs has been greatly changed. Therefore, we reasoned that there must be footprints or selection signatures that had been left during domestication. In this study, with porcine 60K BeadChip genotyping data from both commercial Large White and local Chinese Tongcheng pigs, we calculated the extended haplotype homozygosity values of the two breeds using the long‐range haplotype method to detect selection signatures. We found 34 candidate regions, including 61 known genes, from Large White pigs and 25 regions comprising 57 known genes from Tongcheng pigs. Many selection signatures were found on SSC 1, SSC 4, SSC 7 and SSC 14 regions in both populations. According to quantitative trait loci and network pathway analyses, most of the regions and genes were linked to growth, reproduction and immune responses. In addition, the average genetic differentiation coefficient F ST was 0.254, which means that there had already been a significant differentiation between the breeds. The findings from this study can contribute to further research on molecular mechanisms of pig evolution and domestication and also provide valuable references for improvement of their breeding and cultivation.