Detection of genomic signatures for pig hairlessness using high-density SNP data

Abstract

Hair provides thermal regulation for mammals and protects the skin from wounds, bites and ultraviolet (UV) radiation, and is important in adaptation to volatile environments. Pigs in nature are divided into hairy and hairless, which provide a good model for deciphering the molecular mechanisms of hairlessness. We conducted a genomic scan for genetically differentiated regions between hairy and hairless pigs using 60K SNP data, with the aim to better understand the genetic basis for the hairless phenotype in pigs. A total of 38405 SNPs in 498 animals from 36 diverse breeds were used to detect genomic signatures for pig hairlessness by estimating between-population (F_ST) values. Seven diversifying signatures between Yucatan hairless pig and hairy pigs were identified on pig chromosomes (SSC) 1, 3, 7, 8, 10, 11 and 16, and the biological functions of two notable genes, RGS17 and RB1, were revealed. When Mexican hairless pigs were contrasted with hairypigs, strong signatures were detected on SSC1 and SSC10, which harbor two functionally plausible genes, REV3L and BAMBI. KEGG pathway analysis showed a subset of overrepresented genes involved in the T cell receptor signaling pathway, MAPK signaling pathway and the tight junction pathways. All of these pathways may be important in local adaptability of hairless pigs. The potential mechanisms underlying the hairless phenotype in pigs are reported for the first time. RB1 and BAMBI are interesting candidate genes for the hairless phenotype in Yucatan hairless and Mexico hairless pigs, respectively. RGS17, REV3L, ICOS and RASGRP1 as well as other genes involved in the MAPK and T cell receptor signaling pathways may be important in environmental adaption by improved tolerance to UV damage in hairless pigs. These findings improve our understanding of the genetic basis for inherited hairlessness in pigs.

Graphical abstract

Keywords

hairlessness / pig / selective sweeping

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Acknowledgements

This research was supported by National Natural Science Foundation of China (31071089), Program for New Century Excellent Talents in Universities, the National Key Technology R&D Program (2011BAD28B01), Program for Youth Scientist of Jiangxi Province and the earmarked fund for Jiangxi Agriculture Research System and The graduate innovation fund of Jiangxi Province (YC2012-S057).

Supplementary materialsƒThe online version of this article at http://dx.doi.org/10.15302/J-FASE-2014039 contains supplementary material (Appendix A).

Compliance with ethics guidelinesƒYing Su, Yi Long, Xinjun Liao, Huashui Ai, Zhiyan Zhang, Bin Yang, Shijun Xiao, Jianhong Tang, Wenshui Xin, Lusheng Huang, Jun Ren and Nengshui Ding declare that they have no conflict of interest or financial conflicts to disclose.ƒAll applicable institutional and national guidelines for the care and use of animals were followed.

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Higher Education Press and Springer-Verlag Berlin Heidelberg