Comparative transcriptome analysis reveals the genetic basis of skin color variation in common carp

PLoS One. 2014 Sep 25;9(9):e108200. doi: 10.1371/journal.pone.0108200. eCollection 2014.


Background: The common carp is an important aquaculture species that is widely distributed across the world. During the long history of carp domestication, numerous carp strains with diverse skin colors have been established. Skin color is used as a visual criterion to determine the market value of carp. However, the genetic basis of common carp skin color has not been extensively studied.

Methodology/principal findings: In this study, we performed Illumina sequencing on two common carp strains: the reddish Xingguo red carp and the brownish-black Yellow River carp. A total of 435,348,868 reads were generated, resulting in 198,781 assembled contigs that were used as reference sequences. Comparisons of skin transcriptome files revealed 2,012 unigenes with significantly different expression in the two common carp strains, including 874 genes that were up-regulated in Xingguo red carp and 1,138 genes that were up-regulated in Yellow River carp. The expression patterns of 20 randomly selected differentially expressed genes were validated using quantitative RT-PCR. Gene pathway analysis of the differentially expressed genes indicated that melanin biosynthesis, along with the Wnt and MAPK signaling pathways, is highly likely to affect the skin pigmentation process. Several key genes involved in the skin pigmentation process, including TYRP1, SILV, ASIP and xCT, showed significant differences in their expression patterns between the two strains.

Conclusions: In this study, we conducted a comparative transcriptome analysis of Xingguo red carp and Yellow River carp skins, and we detected key genes involved in the common carp skin pigmentation process. We propose that common carp skin pigmentation depends upon at least three pathways. Understanding fish skin color genetics will facilitate future molecular selection of the fish skin colors with high market values.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Carps / genetics*
  • Computational Biology
  • Gene Expression Profiling
  • Gene Expression Regulation
  • Gene Ontology
  • Gene Regulatory Networks
  • High-Throughput Nucleotide Sequencing
  • Molecular Sequence Annotation
  • Skin Pigmentation / genetics*
  • Transcriptome*

Associated data

  • BioProject/PRJNA254191

Grant support

This work was supported by the Special Scientific Research Funds for Central Non-profit Institutes, Chinese Academy of Fishery Sciences (2014C011, 2013C010 and 2013C011), the National High-Technology Research and Development Program of China (863 program; 2011AA100401), and PX was supported by the Visiting Professorship Program, Deanship of Scientific Research, College of Sciences at King Saud University, Riyadh. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.