Exploring the genetic signature of body size in Yucatan miniature pig

Abstract

Since being domesticated about 10,000-12,000 years ago, domestic pigs (Sus scrofa domesticus) have been selected for traits of economic importance, in particular large body size. However, Yucatan miniature pigs have been selected for small body size to withstand high temperature environment and for laboratory use. This renders the Yucatan miniature pig a valuable model for understanding the evolution of body size. We investigate the genetic signature for selection of body size in the Yucatan miniature pig. Phylogenetic distance of Yucatan miniature pig was compared to other large swine breeds (Yorkshire, Landrace, Duroc and wild boar). By estimating the XP-EHH statistic using re-sequencing data derived from 70 pigs, we were able to unravel the signatures of selection of body size. We found that both selections at the level of organism, and at the cellular level have occurred. Selection at the higher levels include feed intake, regulation of body weight and increase in mass while selection at the molecular level includes cell cycle and cell proliferation. Positively selected genes probed by XP-EHH may provide insight into the docile character and innate immunity as well as body size of Yucatan miniature pig.

Fig 1. Nucleotide diversity (A and C) and cumulative average of nucleotide diversity (B) for each swine breed.

Nucleotide diversity of 10⁷-bp non-overlapping window is shown. Each pig breed is marked by a colored line; orange for wild boar, blue for Landrace, green for Yorkshire, purple for Yucatan miniature pig and yellow for Duroc.

Fig 2. Unrooted phylogenetic tree of 70 pigs based on pairwise identity-by-state (IBS) distance from the entire autosomal SNPs.

Each pig breed is marked by a colored circle; orange for wild boar, blue for Landrace, green for Yorkshire, purple for Yucatan miniature pig and yellow for Duroc. Scale bar indicate distance measure between each individual (1-IBS).

Fig 3. Hierarchical clustering of biological process GO terms associated with genes located in outlier loci (regions) detected by XP-EHH method in comparisons between Yucatan miniature pig and Duroc (A), Landrace (B) and Yorkshire (C).

The gene list of each GO term clustered using DAVID was compared to calculate the distance between the GO terms. For a distance value of > 0.4~0.5, GO terms were re-clustered, and GO term groups are shown in boxes. The representative GO terms manually selected are shown in red. The numbers of genes in the GO terms are in brackets with the corresponding p-values.