Genome‐wide scans to detect positive selection in Large White and Tongcheng pigs |
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Authors: | Xiuling Li Songbai Yang Zhonglin Tang Kui Li Max F. Rothschild Bang Liu Bin Fan |
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Affiliation: | 1. Key Laboratory of Agricultural Animal Genetics, Breeding & Reproduction of Ministry of Education, College of Animal Science & Technology, Huazhong Agricultural University, , Wuhan, 430070 China;2. The Key Laboratory for Domestic Animal Genetic Resources and Breeding of Ministry of Agriculture of China, Institute of Animal Science, Chinese Academy of Agricultural Sciences, , Beijing, 100193 China;3. Department of Animal Science and Center for Integrated Animal Genomics, Iowa State University, , Ames, IA, 50011 USA |
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Abstract: | 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 SSC1, SSC4, SSC7 and SSC14 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 FST 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. |
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Keywords: | extended haplotype homozygosity genetic differentiation long‐range haplotype pig selective sweep |
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