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Exploring the genetic signature of body size in Yucatan miniature pig.

Kim H, Song KD, Kim HJ, Park W, Kim J, Lee T, Shin DH, Kwak W, Kwon YJ, Sung S, Moon S, Lee KT, Kim N, Hong JK, Eo KY, Seo KS, Kim G, Park S, Yun CH, Kim H, Choi K, Kim J, Lee WK, Kim DK, Oh JD, Kim ES, Cho S, Lee HK, Kim TH, Kim H - PLoS ONE (2015)

Bottom Line: Phylogenetic distance of Yucatan miniature pig was compared to other large swine breeds (Yorkshire, Landrace, Duroc and wild boar).We found that both selections at the level of organism, and at the cellular level have occurred.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Agricultural Biotechnology, Animal Biotechnology Major, and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea.

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.

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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.
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pone.0121732.g003: 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.

Mentions: For outlier loci (genes) in each comparison, we performed Gene Ontolgy (GO) term enrichment analyses with EASE < 0.05 to investigate their representation of functional groups (Fig 3). There were 45 enriched GO terms in all three comparisons. To reduce GO term list to the most relevant terms, we picked up representative GO terms based on the list of genes involved in. Representative GO terms associated with genes located in outlier loci (regions) detected by XP-EHH are shown in Table 1. The outlier loci (genes) between YMP and Duroc were mainly associated with detection of fungus, sensory perception of smell, ion transport, protein amino acid phosphorylation, cell proliferation, microtubule-based process and cell cycle in GO term. The outlier genes detected between YMP and Landrace were mainly associated with neuron fate commitment, response to organic substance, transcytosis, sensory perception of smell, regulation of cyclase activity and neurological system process. The outlier genes detected between YMP and Yorkshire were mainly associated with glutamate signaling pathway, vesicle-mediated transport, regulation of cell migration and learning. Nucleotide diversity plot of 14 genes in the intersection of all three XP-EHH analyses and 5 genes of interest which are known for their relation to growth is shown in S8 Fig.


Exploring the genetic signature of body size in Yucatan miniature pig.

Kim H, Song KD, Kim HJ, Park W, Kim J, Lee T, Shin DH, Kwak W, Kwon YJ, Sung S, Moon S, Lee KT, Kim N, Hong JK, Eo KY, Seo KS, Kim G, Park S, Yun CH, Kim H, Choi K, Kim J, Lee WK, Kim DK, Oh JD, Kim ES, Cho S, Lee HK, Kim TH, Kim H - PLoS ONE (2015)

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.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4401510&req=5

pone.0121732.g003: 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.
Mentions: For outlier loci (genes) in each comparison, we performed Gene Ontolgy (GO) term enrichment analyses with EASE < 0.05 to investigate their representation of functional groups (Fig 3). There were 45 enriched GO terms in all three comparisons. To reduce GO term list to the most relevant terms, we picked up representative GO terms based on the list of genes involved in. Representative GO terms associated with genes located in outlier loci (regions) detected by XP-EHH are shown in Table 1. The outlier loci (genes) between YMP and Duroc were mainly associated with detection of fungus, sensory perception of smell, ion transport, protein amino acid phosphorylation, cell proliferation, microtubule-based process and cell cycle in GO term. The outlier genes detected between YMP and Landrace were mainly associated with neuron fate commitment, response to organic substance, transcytosis, sensory perception of smell, regulation of cyclase activity and neurological system process. The outlier genes detected between YMP and Yorkshire were mainly associated with glutamate signaling pathway, vesicle-mediated transport, regulation of cell migration and learning. Nucleotide diversity plot of 14 genes in the intersection of all three XP-EHH analyses and 5 genes of interest which are known for their relation to growth is shown in S8 Fig.

Bottom Line: Phylogenetic distance of Yucatan miniature pig was compared to other large swine breeds (Yorkshire, Landrace, Duroc and wild boar).We found that both selections at the level of organism, and at the cellular level have occurred.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Agricultural Biotechnology, Animal Biotechnology Major, and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea.

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.

Show MeSH
Related in: MedlinePlus