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. 2019 Jul 15;11(13):4672-4687.
doi: 10.18632/aging.102078.

Genome-wide association and evolutionary analyses reveal the formation of swine facial wrinkles in Chinese Erhualian pigs

Tao Huang  1 , Mingpeng Zhang  1 , Guorong Yan  1 , Xiaochang Huang  1 , Hao Chen  1 , Liyu Zhou  1 , Wenjiang Deng  1 , Zhen Zhang  1 , Hengqing Qiu  1 , Huashui Ai  1 , Lusheng Huang  1
Affiliations

Genome-wide association and evolutionary analyses reveal the formation of swine facial wrinkles in Chinese Erhualian pigs

Tao Huang et al. Aging (Albany NY). .

Abstract

Wrinkles are uneven concave-convex folds, ridges or creases in skin. Facial wrinkles appear in head, typically increasing along with aging. However in several Chinese indigenous pigs, such as Erhualian pigs, rich facial wrinkles have been generated during the growth stages as one of their breed characteristics. To investigate the genetic basis underlying the development of swine facial wrinkles, we estimated the folding extent of facial wrinkles in a herd of Erhualian pigs (n=332), and then conducted genome-wide association studies and multi-trait meta-analysis for facial wrinkles using 60K porcine chips. We found that facial wrinkles had high heritability estimates of ~0.7 in Erhualian pigs. Notably, only one genome-wide significant QTL was detected at 34.8 Mb on porcine chromosome 7. The most significant SNP rs80983858 located at the 3255-bp downstream of candidate gene GRM4, and the G allele was of benefit to increase facial wrinkles. Evolutionary and selection analyses suggested that the haplotypes containing G allele were under artificial selection, which was consistent with local animal sacrificial custom praying for longevity. Our findings made important clues for further deciphering the molecular mechanism of swine facial wrinkles formation, and shed light on the research of skin wrinkle development in human or other mammals.

Keywords: GWAS; artificial selection; evolutionary analyses; facial wrinkles; pig.

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Conflict of interest statement

CONFLICTS OF INTEREST: The authors have no conflicts of interest to declare.

Figures

Figure 1
Figure 1
Manhattan plots for QTL affecting facial wrinkles in Erhualian pigs. (A) Genome-wide association study (GWAS) plot for wrinkle pixel ratio. (B) GWAS plot for wrinkle score. (C) Meta-trait GWAS plot for facial wrinkles. (D) Boxplot for the significant SNPs grouped by different genotypes. The dashed line delineates the suggestive significance threshold (P = 2.78 × 10-5); the solid line delineates the genome-wide significant threshold (P = 1.39 × 10-6).
Figure 2
Figure 2
Evolutionary and selection analyses on the candidate region affecting swine facial wrinkles using the 60K SNP dataset. (A) Tajima’s D tests. (B) Population differentiation analysis between Erhualian pigs and Chinese wild boars. (C) XPEHH score estimation. (D) Maximum likelihood tree of the haplotypes on the candidate region.
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