Screening and preliminary analysis of differentially expressed genes in quail embryos for feather colour based on RNA-Sequencing

Abstract

The purpose of this study was to use RNA-Sequencing (RNA-Seq) to screen differentially expressed genes (DEGs) and analyse transcriptomic data from embryonic skin tissues of maroon-feather and white-feather quails. The transcriptome of embryonic skin tissues from quails was sequenced using the Illumina HiSeqTM 2000 sequencing platform. A total of 2 512 DEGs were found. Of these, 550 DEGs were up-regulated and 1 562 DEGs were down-regulated in the skin tissues of white-feather quail embryos. Five hundred and ninety-seven DEGs were enriched and annotated into 50 entries in Gene Ontology (GO) database. The total number of DEGs annotated in each entry in the Kyoto Encyclopedia of Genes and Genomes (KEGG) database was 341, enriched in 230 pathways, of which the tight junction pathway and neuroactive ligand-receptor interaction were the most significantly enriched. Candidate genes were analysed using real-time quantitative reverse transcription polymerase chain reaction (to verify the accuracy and reliability of the RNA-Seq results. The relative expression of agouti signalling protein (ASIP) and DOPA decarboxylase (DDC) in white-feather quails were increased. Relative expression of homeobox D1 (HOXD1), cathepsin D (CTSD), keratin 2 (KRT2), methyl-CpG binding domain protein 2 (MBD2), and melatonin receptor 1 (MT1) were decreased. The results of this study provide useful data on the analysis of the feather colour regulatory mechanism in white- and maroon-feather quails.