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

Yanliang Jiang,Peng Xu,Songhao Zhang,Xiaowen Sun,Jianxin Feng,Khalid A Al-Ghanim,Jian Xu,Shahid Mahboob,Andrzej T Slominski

doi:10.1371/journal.pone.0108200

Yanliang Jiang, Peng Xu + Show 7 more

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https://doi.org/10.1371/journal.pone.0108200

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Abstract

BackgroundThe 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 FindingsIn 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.ConclusionsIn 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.

Highlights

Coloration is one of the most diverse phenotypic traits in vertebrates, and it exerts multiple adaptive functions, such as species identification, camouflage, warning or threatening of predators, photoprotection, thermoregulation and photoreception [1]
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

Summary

Introduction

Coloration is one of the most diverse phenotypic traits in vertebrates, and it exerts multiple adaptive functions, such as species identification, camouflage, warning or threatening of predators, photoprotection, thermoregulation and photoreception [1]. Skin coloration is the result of diverse pigments synthesized by pigment cells or chromatophores, and it is affected by multiple factors, including environmental, nutritional, physiological, or genetic conditions. Among these factors, the most fundamental and important is the genetic basis of skin pigmentation: which genes are likely to be involved and how. A diversity of pigment cells, associated with a series of cellular, physiological, genetic and environmental factors, makes fish skin pigmentation a complicated biological process. The genetic basis of common carp skin color has not been extensively studied

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