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The Genetic Basis of Skin Color and Body Shape of Domesticated Purse Red Carp Revealed by Comparative Transcriptome Analysis

The Genetic Basis of Skin Color and Body Shape of Domesticated Purse Red Carp Revealed by Comparative Transcriptome Analysis

Songhao Zhang1, Yiwen Gong1, Jian Xu1, Mou Hu2, Peng Xu3 and Yanliang Jiang1,2,4,*

1Key Laboratory of Aquatic Genomics, Ministry of Agriculture; CAFS Key Laboratory of Aquatic Genomics and Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing 100141, China
2Hangzhou Qiandaohu Xunlong Sci-Tech Development Company Limited, Quzhou 324000, China, China
3Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Xiamen University, Xiamen 361102, China
4Key Laboratory of Applied Marine Biotechnology, Ningbo University, Ministry of Education, Ningbo 315211, China

*      Corresponding author:



Purse red carp is an economic important and well-known domesticated variety of common carp in China. During a long history of domestication, purse red carp displays consumer-favored morphological traits such as red skin color and purse-shaped body form. However, the underlying genetic basis is less studied. In the present study, we utilized the powerful approach of comparative transcriptome analysis via high throughput sequencing, and examined transcriptome profiles of purse red carp by comparing with Yellow River carp, of which the skin color and body shape are quite similar to wild carp. A total of 434 million reads was generated, resulted in 203,590 assembled contigs, which was used as the reference sequences. Comparing the skin and blood transcriptome files showed that 2,767 unigenes were significantly differentially expressed, including 1,663 genes up-regulated and 1,806 down-regulated in purse red carp. Moreover, gene pathway analysis of the differentially expressed genes was conducted. We proposed the skin color and body shape depended upon at least four pathways including melanin biosynthesis, TGF-beta signaling, Wnt signaling and MAPK signaling pathways. We obtained candidate genes that may affect the morphological characteristics of purse red carp resulted from the long history of domestication, including TYRP1b, PMELa, KITa, BMP8a, ACVR2aa, TGFB1a, TGFB3, TGFBR2. Understanding the molecular mechanisms underlying the biological characteristics of purse red carp will advance our knowledge of the genetic differentiation between different common carp varieties caused by domestication, and accelerate the molecular selection of fish species with consumer-favored skin color and body shape.

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Pakistan Journal of Zoology


Vol. 53, Iss. 5, Pages 1603-2000


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