Comparative Transcriptome Analysis Reveals the Genetic Basis of Skin Color Variation in Common Carp
Xu1,3, Yanliang Jiang1, Songhao Zhang1, Jian Xu1, Jianxin Feng2, Shahid Mahboob3, Khalid A. Al-Ghanim3, Xiaowen Sun1, Peng . 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 upregulated
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.
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