Transcript expression profiling of fibromelanosis-related genes in black-bone chickens

ABSTRACT

1. The aim of the present study was to identify differentially expressed genes (DEGs) and metabolic pathways involved in this phenotype. Fibromelanosis is the most striking feature of black-bone chickens, such as the Silkie and Dongxiang indigenous breeds. Due to the accumulation of eumelanin in connective tissues, fibromelanosis manifests as black colouration of the skin, muscles, gut, and periosteum. Studies on fibromelanosis can provide useful information pertaining to human diseases and offer commercial value to the poultry industry. However, the genetic basis of fibromelanosis remains unclear.

2. Digital gene expression analysis was performed on black and white skin samples collected from the HW1 black-bone chicken line to detect differences in genome-wide expression patterns. A total of >30 billion bp were sequenced, and 2,707,926,466 bp and 2,948,782,964 bp of clean data obtained for creation of libraries for black and white skin, respectively. In total, 252 DEGs from 15,508 mapped genes were identified with 83 up-regulated in white skin and 169 up-regulated in black skin.

3. Gene ontology analysis highlighted that genes from the extracellular region and associated components were abundant among the DEGs. Pathway analysis revealed that many DEGs were linked to amino acid metabolism and the immune system. qRT-PCR validation using 14 genes showed good conformity with the sequence analysis of fibromelanosis-related genes.

4. The results showed that L-dopachrometautomerase precursor (DCT), tyrosine aminotransferase (TAT), 4-hydroxyphenylpyruvate dioxygenase (HPD) from the tyrosine metabolism pathway, coagulation factor II (F2), fibrinogen beta chain (FGB), plasminogen (PLG) and complement component 7 (C7) from the complement and coagulation cascades were important genes in the fibromelanosis process in black-bone chickens. These candidate genes require further correlation analysis and functional verification.

KEYWORDS:

• Fibromelanosis
• black-bone chicken
• gene expression
• transcriptome

Disclosure statement

No potential conflict of interest was reported by the author(s).

Data availability statement

The authors confirm that all data underlying the findings of this study are fully available without restriction. All raw DEG data have been uploaded to the Sequence Read Archive (SRA) database (National Center for Biotechnology Information). The accession numbers of the two files are SRR 1923276 and SRR 1923288. Funding: This work was funded by the Active Design Project of Agricultural Scientific Research (20162012A04, The Science and Technology Department of Hangzhou City, Zhejiang Province, China). The funder had no role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Supplementary material

Supplemental data for this article can be accessed here.

Additional information

Funding

This work was supported by the Agricultural and Social Development Research Project of Hangzhou [20162012A04].