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Journal of Integrative Agriculture  2020, Vol. 19 Issue (5): 1314-1322    DOI: 10.1016/S2095-3119(19)62833-9
Special Issue: 动物科学合辑Animal Science
Animal Science · Veterinary Medicine Advanced Online Publication | Current Issue | Archive | Adv Search |
Genome-wide detection of selective signatures in a Jinhua pig population
XU Zhong1, SUN Hao1, ZHANG Zhe1, Zhao Qing-bo1, Babatunde Shittu Olasege1, Li Qiu-meng1, Yue Yang1, Ma Pei-pei1, Zhang Xiang-zhe1, Wang Qi-shan1, Pan Yu-chun1, 2 
1 Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, P.R.China
2 Shanghai Key Laboratory of Veterinary Bio-technology, Shanghai 200240, P.R.China
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The aim of this study was to detect evidence for signatures of recent selection in the Jinhua pig genome.  These results can be useful to better understand the regions under selection in Jinhua pigs and might shed some lights on groups of genes that control production traits.  In the present study, we performed extended haplotype homozygosity (EHH) tests to identify significant core regions in 202 Jinhua pigs.  A total of 26 161 core regions spanning 636.42 Mb were identified, which occupied approximately 28% of the genome across all autosomes, and 1 158 significant (P<0.01) core haplotypes were selected.  Genes in these regions were related to several economically important traits, including meat quality, reproduction, immune responses and exterior traits.  A panel of genes including ssc-mir-365-2, KDM8, RABEP2, GSG1L, RHEB, RPH3AL and a signal pathway of PI3K-Akt were detected with the most extreme P-values.  The findings in our study could draw a comparatively genome-wide map of selection signature in the pig genome, and also help to detect functional candidate genes under positive selection for further genetic and breeding research in Jinhua and other pigs.
Keywords:  pig genome        selection signatures        extended haplotype homozygosity (EHH)        candidate genes  
Received: 12 April 2019   Accepted:
Fund: This work was supported by the Key Technology R&D Program of China (2016C02054-2) and the National Natural Science Foundation of China (31872976).
Corresponding Authors:  Correspondence PAN Yu-chun, Tel: +86-21-34205836, Fax: +86-21-34206394, E-mail:; WANG Qi-shan, E-mail:   
About author:  XU Zhong, E-mail:; 9

Cite this article: 

XU Zhong, SUN Hao, ZHANG Zhe, Zhao Qing-bo, Babatunde Shittu Olasege, Li Qiu-meng, Yue Yang, Ma Pei-pei, Zhang Xiang-zhe, Wang Qi-shan, Pan Yu-chun . 2020.

Genome-wide detection of selective signatures in a Jinhua pig population
. Journal of Integrative Agriculture, 19(5): 1314-1322.

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