Polymorphisms in the Egl nine homolog 3 (<i>EGLN3</i>) and Peroxisome proliferator activated receptor-alpha (<i>PPARα</i>) genes and their correlation with hypoxia adaptation in Tibetan chickens

<div><p><i>Peroxisome proliferator activated receptor-alpha (PPARα)</i> and <i>Egl nine homolog 3</i> (<i>EGLN3)</i> play critical roles in facilitating the adaptation to a hypoxic environment. However, the relationship between <i>EGLN3</i> and <i>PPARα</i> variants and hypoxic adaptation remains poorly understood in Tibetan chickens. To better understand the effects of genetic variation, we sequenced exons of <i>PPARα</i> and <i>EGLN3</i> 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 <i>EGLN3</i> 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 <i>PPARα</i>. 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 <i>PPARα</i> (P < 0.05). Phylogenetic analysis showed that the genetic distance among chickens, finch and great tit were close for both <i>EGLN3</i> and <i>PPARα</i>. Bioinformatics analysis of <i>PPARα</i> 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 <i>PPARα</i> 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 <i>EGLN3</i> and environmental adaptability.</p>