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

doi:10.15302/J-FASE-2014039

Front. Agr. Sci. Eng.

2014, Vol. 1

Issue (4) : 307-313 https://doi.org/10.15302/J-FASE-2014039

RESEARCH ARTICLE

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

Ying SU¹, Yi LONG¹, Xinjun LIAO^1,², Huashui AI¹, Zhiyan ZHANG¹, Bin YANG¹, Shijun XIAO¹, Jianhong TANG¹, Wenshui XIN¹, Lusheng HUANG¹, Jun REN¹, Nengshui DING¹(

)

¹. State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang 330045, China
². College of Life Science of Jinggangshan University, Ji’an 343009, China

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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.

Keywords hairlessness pig selective sweeping

Corresponding Author(s): Nengshui DING

Online First Date: 28 January 2015 Issue Date: 10 March 2015

Cite this article:

Ying SU,Yi LONG,Xinjun LIAO, et al. Detection of genomic signatures for pig hairlessness using high-density SNP data[J]. Front. Agr. Sci. Eng. , 2014, 1(4): 307-313.

URL:

https://academic.hep.com.cn/fase/EN/10.15302/J-FASE-2014039
https://academic.hep.com.cn/fase/EN/Y2014/V1/I4/307

Tab.1 Pig breeds, their origin and sample size in this study

Fig.1 The distribution of the F_ST density for selection signatures in Mexico hairless pig (a) and Yucatan pigs (b). The dotted line is the outlier analogous to the top 0.5% of the empirical distribution. The data to the right of the vertical dotted line ran to an extreme.

Fig.2 Neighbor-joining phylogenetic tree of the tested breeds. MXHL and USYU are underlined. Duroc (D), Brazil Moura (BRMO), Mexico cuino (MXCU) and Mexico hairless (MXHL) pig define a separate grouping, while Iberian (IB), wild boar (WB), Black sicily (ITSI), Argentina creole pig (ARFP), Argentina semi pig (ARFO), Peru creole pig (PECR), Bolivia creole pig (BOCR), Ecuador Creole pig (ECCR), Guatemala creole pig (GUCR), Cuba creole pig (CUWE) and USA yucatan (USYU) appear as a closely related population cluster.

Fig.3 Genome-wide distribution of F_ST values between hairless pigs and norml pigs. (a) Genomic signatures for hairlessness in Yucatan pigs; (b) genomic signatures of selection in Mexico hairless pigs. The chromosomes are plotted along the x-axis, and the F_ST values are plotted along the y-axis, and the 99.5% percentile is denoted with a dashed line. The top candidate gene SNPs for hairlessness are circled in red, while candidate gene SNPs for UV radiation are circled in blue, with the gene names labeled above.

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