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Updated: Oct 28, 2026

Manipulation of Gene Function in Mexican Cavefish
Published on: April 22, 2019
Transcriptomic and long non-coding RNA profiling suggests molecular mechanisms underlying skin color variation in
Jianjun Fu1, Wenbin Zhu1, Mingkun Luo1
1Key Laboratory of Freshwater Fisheries and Germplasm Resource Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China.
Abstract:
Skin color is an economically important trait in cultured fish, but the transcriptional basis of orange pigmentation in the FFRC No. 2 strain of common carp (Cyprinus carpio) remains unclear. This study compared messenger RNA and long non-coding RNA (lncRNA) expression in dorsal skin from five orange and five gray six-month-old full siblings. Transcriptome sequencing, differential-expression and functional-enrichment analyses, target-gene prediction, and quantitative polymerase chain reaction validation were performed. In orange relative to gray skin, 1014 genes and 519 lncRNAs were differentially expressed. Differentially expressed genes were enriched in melanin biosynthesis, melanocyte differentiation, melanosome organization, tyrosine metabolism, and melanogenesis. Most melanogenesis-associated genes, including tyr, tyrp1a, tyrp1b, mc1r, mreg, pmel, and kita, were down-regulated in orange fish, whereas asip and slc7a11 were up-regulated. Up-regulated genes were also enriched in lipid-metabolism-related processes and pathways. Target prediction identified 2346 potential relationships between differentially expressed lncRNAs and genes, comprising 48 cis and 2298 trans relationships; 48 lncRNAs were linked to 20 pigmentation-associated genes. Quantitative polymerase chain reaction results were consistent with the sequencing data. These results suggest that a possible switch from eumelanin to pheomelanin production may be the cause of orange coloration. The predicted lncRNA-gene regulatory networks provide valuable candidate targets for future functional studies and molecular breeding in common carp.
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