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Genomic Scan Reveals Loci under Altitude Adaptation in Tibetan and Dahe Pigs

By Kunzhe Dong (646303), Na Yao (182961), Yabin Pu (646304), Xiaohong He (646305), Qianjun Zhao (646306), Yizhao Luan (646307), Weijun Guan (646308), Shaoqi Rao (14985) and Yuehui Ma (646309)

Abstract

<div><p>High altitude environments are of particular interest in the studies of local adaptation as well as their implications in physiology and clinical medicine in human. Some Chinese pig breeds, such as Tibetan pig (TBP) that is well adapted to the high altitude and Dahe pig (DHP) that dwells at the moderate altitude, provide ideal materials to study local adaptation to altitudes. Yet, it is still short of in-depth analysis and understanding of the genetic adaptation to high altitude in the two pig populations. In this study we conducted a genomic scan for selective sweeps using <i>F<sub>ST</sub></i> to identify genes showing evidence of local adaptations in TBP and DHP, with Wuzhishan pig (WZSP) as the low-altitude reference. Totally, we identified 12 specific selective genes (<i>CCBE1, F2RL1, AGGF1, ZFPM2, IL2, FGF5, PLA2G4A, ADAMTS9, NRBF2, JMJD1C</i>, <i>VEGFC</i> and <i>ADAM19</i>) for TBP and six (<i>OGG1</i>, <i>FOXM</i>, <i>FLT3</i>, <i>RTEL1</i>, <i>CRELD1</i> and <i>RHOG</i>) for DHP. In addition, six selective genes (<i>VPS13A</i>, <i>GNA14, GDAP1, PARP8, FGF10 and ADAMTS16</i>) were shared by the two pig breeds. Among these selective genes, three (<i>VEGFC</i>, <i>FGF10</i> and <i>ADAMTS9</i>) were previously reported to be linked to the local adaptation to high altitudes in pigs, while many others were newly identified by this study. Further bioinformatics analysis demonstrated that majority of these selective signatures have some biological functions relevant to the altitude adaptation, for examples, response to hypoxia, development of blood vessels, DNA repair and several hematological involvements. These results suggest that the local adaptation to high altitude environments is sophisticated, involving numerous genes and multiple biological processes, and the shared selective signatures by the two pig breeds may provide an effective avenue to identify the common adaptive mechanisms to different altitudes.</p></div

Topics: Biological Sciences, parp, pig breeds, fgf, WZSP, ZFPM, 2G, 13a, FOXM, NRBF, adaptation, GDAP, Dahe Pigs High altitude environments, flt, CRELD, AGGF, Chinese pig breeds, adam, vegfc, rhog, RTEL, tbp, gene, 1c, fst, CCBE, dna, pla, adamts, 2RL, gna, JMJD, vps, il, dhp, OGG
Year: 2014
DOI identifier: 10.1371/journal.pone.0110520
OAI identifier: oai:figshare.com:article/1208111
Provided by: FigShare
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