Identifying Candidate Genes for Hypoxia Adaptation of Tibet Chicken Embryos by Selection Signature Analyses and RNA Sequencing.

Genes
Xiayi LiuHaiGang Bao

Abstract

The Tibet chicken (Gallus gallus) lives on the Qinghai-Tibet Plateau and adapts to the hypoxic environment very well. The objectives of this study was to obtain candidate genes associated with hypoxia adaptation in the Tibet chicken embryos. In the present study, we used the fixation index (Fst) and cross population extended haplotype homozygosity (XPEHH) statistical methods to detect signatures of positive selection of the Tibet chicken, and analyzed the RNA sequencing data from the embryonic liver and heart with HISAT, StringTie and Ballgown for differentially expressed genes between the Tibet chicken and White leghorn (Gallus gallus, a kind of lowland chicken) embryos hatched under hypoxia condition. Genes which were screened out by both selection signature analysis and RNA sequencing analysis could be regarded as candidate genes for hypoxia adaptation of chicken embryos. We screened out 1772 genes by XPEHH and 601 genes by Fst, and obtained 384 and 353 differentially expressed genes in embryonic liver and heart, respectively. Among these genes, 89 genes were considered as candidate genes for hypoxia adaptation in chicken embryos. ARNT, AHR, GSTK1 and FGFR1 could be considered the most important candidate genes. Our findings...Continue Reading

References

Nov 1, 1992·Respiration Physiology·H J MeuerS Jopp
Feb 1, 1985·Journal of Applied Physiology·A H Visschedijk
Jun 6, 1995·Proceedings of the National Academy of Sciences of the United States of America·G L WangG L Semenza
Nov 4, 2000·American Journal of Respiratory Cell and Molecular Biology·N JinR A Rhoades
Nov 16, 2005·Annual Review of Genetics·Rasmus Nielsen
Jul 18, 2006·Biochemical and Biophysical Research Communications·Young Min ChungYoung Do Yoo
Apr 4, 2007·The Journal of Clinical Investigation·Erinn B RankinVolker H Haase
Sep 11, 2007·American Journal of Obstetrics and Gynecology·Tal Biron-ShentalYoel Sadovsky
Jun 11, 2008·Critical Reviews in Eukaryotic Gene Expression·Timothy V BeischlagGary H Perdew
Jul 16, 2008·Brain Research·Gauri H Malthankar-PhatakJames C K Lai
Nov 4, 2008·Genetical Research·John Maynard Smith, John Haigh
Feb 10, 2009·American Journal of Human Genetics·Brian L Browning, Sharon R Browning
Mar 17, 2009·Comparative Biochemistry and Physiology. Part A, Molecular & Integrative Physiology·Jacopo P Mortola
Jun 23, 2009·Comparative Biochemistry and Physiology. Toxicology & Pharmacology : CBP·Carrie R FlemingRichard T Di Giulio
Aug 19, 2009·Nature Reviews. Genetics·Kent E Holsinger, Bruce S Weir
Feb 25, 2010·Current Biology : CB·Jonathan K PritchardGraham Coop
May 15, 2010·Science·Tatum S SimonsonRiLi Ge
Mar 15, 2011·American Journal of Physiology. Heart and Circulatory Physiology·Milena Segato KomniskiAnna Bogdanova
Jun 10, 2011·Bioinformatics·Petr DanecekUNKNOWN 1000 Genomes Project Analysis Group
Jan 10, 2012·Arteriosclerosis, Thrombosis, and Vascular Biology·Eric W HolroydRobert D Simari
Jun 22, 2012·Journal of Cellular Physiology·Yali XiongOssie Geifman-Holtzman
Sep 25, 2012·Comparative Biochemistry and Physiology. Part A, Molecular & Integrative Physiology·C LiuN Li
Nov 16, 2012·Proceedings of the National Academy of Sciences of the United States of America·Carl-Johan RubinLeif Andersson
Jan 30, 2013·BMC Genomics·Andreas KranisDavid W Burt
May 16, 2013·Nature Communications·Ri-Li GeJian Wang
Jun 21, 2013·American Journal of Physiology. Regulatory, Integrative and Comparative Physiology·Andrea J MorashAndrew J Murray
Mar 7, 2014·Genetics, Selection, Evolution : GSE·Ana M Pérez O'BrienJohann Sölkner
Jul 13, 2014·Molecular Biology and Evolution·Zachary A Szpiech, Ryan D Hernandez
Jul 30, 2014·Genetics and Molecular Biology·João José de Simoni GouveiaSônia Maria Pinheiro de Oliveira
Feb 19, 2015·Nature Biotechnology·Mihaela PerteaSteven L Salzberg
Mar 10, 2015·Nature Methods·Daehwan KimSteven L Salzberg

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Datasets Mentioned

BETA
GSE77166

Methods Mentioned

BETA
Genotyping
PCR
GTPase

Software Mentioned

VCFtools
DAVID
HISAT2
SELSCAN
PLINK
StringTie
SAM
XPEHH
BEAGLE
SAMtools

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