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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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Related in: MedlinePlus

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).
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pone.0121732.g002: 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).

Mentions: To assess the phylogenetic relationship among the pig breeds, we constructed an unrooted phylogenetic tree of 70 pigs based on pairwise identity-by-state (IBS) distance from the information of all autosomal SNPs. All individuals were grouped into five separate pig breeds as expected (Fig 2). Wild boars had the greatest genetic distance from the other breeds, followed by YMP with the next largest distance from Yorkshires, Landraces, and Durocs. Yorkshires and Landraces were genetically closer to each other than any other two breeds.


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)

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).
© Copyright Policy
Related In: Results  -  Collection

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

pone.0121732.g002: 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).
Mentions: To assess the phylogenetic relationship among the pig breeds, we constructed an unrooted phylogenetic tree of 70 pigs based on pairwise identity-by-state (IBS) distance from the information of all autosomal SNPs. All individuals were grouped into five separate pig breeds as expected (Fig 2). Wild boars had the greatest genetic distance from the other breeds, followed by YMP with the next largest distance from Yorkshires, Landraces, and Durocs. Yorkshires and Landraces were genetically closer to each other than any other two breeds.

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