Comparative Transcriptome and DNA methylation analyses of the molecular mechanisms underlying skin color variations in Crucian carp (Carassius carassius L.)

BMC Genetics

Research Article

Wenting Xu¹  Wenbin Liu¹  Shujuan Chen¹  Yamei Xiao¹  Wen Fu¹  Huiqin Zhang¹  Liangyue Peng¹  Yongqin Zhang¹  Jinhui Liu¹ 

[1] State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, 410081, Changsha, Hunan, China;School of Life Sciences, Hunan Normal University, 410081, Changsha, Hunan, China;

关键词: Body color;    Pigment cell;    Transcriptome;    DNA methylation;    Crucian carp;   

DOI  :  10.1186/s12863-017-0564-9

 received in 2017-07-16, accepted in 2017-10-31,  发布年份 2017

来源: Springer

【 摘 要 】

BackgroundCrucian carp is a popular ornamental strain in Asia with variants in body color. To further explore the genetic mechanisms underlying gray and red body color formation in crucian carp, the skin transcriptomes and partial DNA methylation sites were obtained from red crucian carp (RCC) and white crucian carp (WCC). Here, we show significant differences in mRNA expression and DNA methylation sites between skin tissues of RCC and WCC.ResultsTotals of 3434 and 3683 unigenes had significantly lower and higher expression in WCC, respectively, compared with unigenes expressed in RCC. Some potential genes for body color development were further identified by quantitative polymerase chain reaction, such as mitfa, tyr, tyrp1, and dct, which were down-regulated, and foxd3, hpda, ptps, and gch1, which were up-regulated. A KEGG pathway analysis indicated that the differentially expressed genes were mainly related to mitogen activated protein kinase (MAPK), Wnt, cell cycle, and endocytosis signaling pathways, as well as variations in melanogenesis in crucian carp. In addition, some differentially expressed DNA methylation site genes were related to pigmentation, including mitfa, tyr, dct, foxd3, and hpda. The differentially expressed DNA methylation sites were mainly involved in signaling pathways, including MAPK, cAMP, endocytosis, melanogenesis, and Hippo.ConclusionsOur study provides the results of comparative transcriptome and DNA methylation analyses between RCC and WCC skin tissues and reveals that the molecular mechanism of body color variation in crucian carp is strongly related to disruptions in gene expression and DNA methylation during pigmentation.

【 授权许可】

CC BY   
© The Author(s). 2017