Abstract
BackgroundBody color and coloration patterns are important phenotypic traits to maintain survival and reproduction activities. The Oujiang color varieties of common carp (Cyprinus carpio var. color), with a narrow distribution in Zhejiang Province of China and a history of aquaculture for over 1,200 years, consistently exhibit a variety of body color patterns. The molecular mechanism underlying diverse color patterns in these variants is unknown. To the practical end, it is essential to develop molecular markers that can distinguish different phenotypes and assist selective breeding.Methodology/Principal FindingsIn this exploratory study, we conducted Roche 454 transcriptome sequencing of two pooled skin tissue samples of Oujiang common carp, which correspond to distinct color patterns, red with big black spots (RB) and whole white (WW), and a total of 737,525 sequence reads were generated. The reads obtained in this study were co-assembled jointly with common carp Roche 454 sequencing reads downloaded from NCBI SRA database, resulting in 43,923 isotigs and 546,676 singletons. Over 31 thousand (31,445; 71.6%) isotigs were found with significant BLAST matches (E<1e-10) to the nr protein database, which corresponds to 12,597 annotated zebrafish genes. A total of 70,947 isotigs and singletons (transcripts) were annotated with Gene Ontology, and 60,221 transcripts were found with corresponding EC numbers. Out of 145 zebrafish pigmentation genes, orthologs for 117 were recovered in Oujiang color carp transcriptome, including 18 found only among singletons. Our transcriptome analysis revealed over 52,902 SNPs in Oujiang common carp, and identified 63 SNP markers that are putatively unique either for RB or WW.ConclusionsThe transcriptome of Oujiang color varieties of common carp obtained through this study, along with the pigmentation genes recovered and the color pattern-specific molecular markers developed, will facilitate future research on the molecular mechanism of color patterns and promote aquaculture of Oujiang color varieties of common carp through molecular marker assisted-selective breeding.
Highlights
Body color and coloration patterns are important phenotypic traits associated with the survival and reproduction activities in many organisms, including their camouflage, mimicry, social communication and selective mating [1,2,3]
The transcriptome of Oujiang color varieties of common carp obtained through this study, along with the pigmentation genes recovered and the color pattern-specific molecular markers developed, will facilitate future research on the molecular mechanism of color patterns and promote aquaculture of Oujiang color varieties of common carp through molecular marker assisted-selective breeding
We investigated the pigmentation genes expressed in the skin of Oujiang color varieties of common carp and found a set of candidate single nucleotide polymorphism (SNP) markers that can be used for selective molecular breeding in the future
Summary
Body color and coloration patterns are important phenotypic traits associated with the survival and reproduction activities in many organisms, including their camouflage, mimicry, social communication and selective mating [1,2,3]. Six types of pigment cells, including melanocytes (black, dark brown), xanthophores (yellow), erythrophores (red/orange), iridophores (reflecting), leucophores (white), and cyanophores (blue), have been reported in vertebrates [4]. The molecular mechanism of melanin biosynthesis has been xextensively studied due to its biomedical significance; the melanogenesis pathways have been found conserved in vertebrates [8,9,10]. The biosynthesis of other types of pigments may involve different pathways and regulatory networks, but are in general less studied [6]. Body color and coloration patterns are important phenotypic traits to maintain survival and reproduction activities. It is essential to develop molecular markers that can distinguish different phenotypes and assist selective breeding
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