PMID- 29543898 OWN - NLM STAT- MEDLINE DCOM- 20180702 LR - 20240314 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 13 IP - 3 DP - 2018 TI - Polymorphisms in the Egl nine homolog 3 (EGLN3) and Peroxisome proliferator activated receptor-alpha (PPARalpha) genes and their correlation with hypoxia adaptation in Tibetan chickens. PG - e0194156 LID - 10.1371/journal.pone.0194156 [doi] LID - e0194156 AB - Peroxisome proliferator activated receptor-alpha (PPARalpha) and Egl nine homolog 3 (EGLN3) play critical roles in facilitating the adaptation to a hypoxic environment. However, the relationship between EGLN3 and PPARalpha variants and hypoxic adaptation remains poorly understood in Tibetan chickens. To better understand the effects of genetic variation, we sequenced exons of PPARalpha and EGLN3 in 138 Lowland chickens (LC) from 7 breeds that were located in Emei, Miyi, Shimian, Wanyuan, Pengxian, and Muchuan in the Sichuan province, and Wenchang in the Hainan province (altitudes for these locations are below 1800 meters). Total 166 Tibetan chickens (TC) from 7 subpopulations that were located in Shigatse, Lhoka, Lhasa, Garze, Aba, Diqing and Yushu in the Tibetan area were also sequenced (altitudes greater than 2700 meters). One single-nucleotide polymorphism (rs316017491, C > T) was identified in EGLN3 and was shared by TC and LC with no significant difference for allele frequencies between them (P > 0.05). Six single-nucleotide polymorphisms (SNP1, A29410G; SNP2, rs13886097; SNP3, T29467C; SNP4, rs735915170; SNP5, rs736599044; and SNP6, rs740077421) including one non-synonymous mutation (SNP2, T > C) were identified in PPARalpha. This is the first report of SNP1 and SNP3. There was a difference between TC and LC for allele frequencies (P <0.01), except for SNP1, SNP4, and SNP5) The fix index statistic test indicated that there was population differentiation between TC and LC for SNP2, SNP3, and SNP6 in PPARalpha (P < 0.05). Phylogenetic analysis showed that the genetic distance among chickens, finch and great tit were close for both EGLN3 and PPARalpha. Bioinformatics analysis of PPARalpha showed that SNP2 leads to an amino acid substitution of Ile for Met, which results in the protein being more likely to be hydrolyzed. Thus, genetic variation in PPARalpha may play a role in the ability of TC to adapt to a high altitude environment; however we were unable to identify a relationship between polymorphisms in EGLN3 and environmental adaptability. FAU - Zhong, ChengLin AU - Zhong C AD - Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan Province, P. R. China. FAU - Li, SiChen AU - Li S AD - Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan Province, P. R. China. FAU - Li, JingJing AU - Li J AD - Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan Province, P. R. China. FAU - Li, FengPeng AU - Li F AD - Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan Province, P. R. China. FAU - Ran, MingXia AU - Ran M AD - Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan Province, P. R. China. FAU - Qiu, LingYun AU - Qiu L AD - Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan Province, P. R. China. FAU - Li, DiYan AU - Li D AD - Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan Province, P. R. China. FAU - Zhu, Qing AU - Zhu Q AD - Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan Province, P. R. China. FAU - Wang, Yan AU - Wang Y AD - Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan Province, P. R. China. FAU - Yin, HuaDong AU - Yin H AD - Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan Province, P. R. China. FAU - Shu, Gang AU - Shu G AD - Department of Pharmacy, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan Province, P. R. China. FAU - Yang, Chaowu AU - Yang C AD - Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan Province, P. R. China. FAU - Zhao, XiaoLing AU - Zhao X AUID- ORCID: 0000-0002-0633-4701 AD - Department of Animal Science, College of Animal Science and Technology, Sichuan Agricultural University, P. R. China. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20180315 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (Avian Proteins) RN - 0 (PPAR alpha) RN - EC 1.14.11.29 (Hypoxia-Inducible Factor-Proline Dioxygenases) SB - IM MH - *Acclimatization MH - Altitude MH - Altitude Sickness/genetics/*veterinary MH - Animals MH - Avian Proteins/*genetics MH - Chickens/*genetics/physiology MH - Gene Frequency MH - Hypoxia-Inducible Factor-Proline Dioxygenases/*genetics MH - Models, Molecular MH - PPAR alpha/*genetics MH - Phylogeny MH - *Polymorphism, Single Nucleotide MH - Tibet PMC - PMC5854350 COIS- Competing Interests: The authors have declared that no competing interests exist. EDAT- 2018/03/16 06:00 MHDA- 2018/07/03 06:00 PMCR- 2018/03/15 CRDT- 2018/03/16 06:00 PHST- 2017/09/03 00:00 [received] PHST- 2018/02/26 00:00 [accepted] PHST- 2018/03/16 06:00 [entrez] PHST- 2018/03/16 06:00 [pubmed] PHST- 2018/07/03 06:00 [medline] PHST- 2018/03/15 00:00 [pmc-release] AID - PONE-D-17-32292 [pii] AID - 10.1371/journal.pone.0194156 [doi] PST - epublish SO - PLoS One. 2018 Mar 15;13(3):e0194156. doi: 10.1371/journal.pone.0194156. eCollection 2018.