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Comparative Transcriptome Analysis Reveals Growth-Related Genes in Juvenile Chinese Sea Cucumber, Russian Sea Cucumber, and Their Hybrids

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Abstract

Heterosis is important for sea cucumber breeding, but its molecular mechanism remains largely unexplored. In this study, parental lines of Apostichopus japonicus from Russia (R) and China (C) were used to construct hybrids (CR and RC) by reciprocal crossing. We examined the transcriptional profiles of the hybrids (CR and RC) and the purebreds (CC and RR) at different developmental times. A total of 60.27 Gb of clean data was obtained, and 176,649 unigenes were identified, of which 50,312 unigenes were annotated. A total of 414,536 SNPs were identified. A total of 7011 differentially expressed genes (DEGs) were obtained between the purebreds and hybrids at 45 days after fertilization (DAF), and a total of 8218 DEGs were obtained between the purebreds and hybrids at 75 DAF. In addition, a total of 7652 DEGs were obtained between 45 DAF and 75 DAF. The significant DEGs were mainly involved in the MAPK and FOXO signaling pathways, especially in the Ras-Raf-MEK1/2-ERK module, which may be a key regulator of development and growth in juvenile A. japonicus. In addition, we also identified key growth-related genes, such as fgfs, igfs, megfs and hgfs, which were upregulated in the hybrids (RC and CR); these genes may play important roles in heterosis in A. japonicus. Our study provides fundamental information on the molecular mechanisms underlying heterosis in sea cucumber and might suggest strategies for the selection of rapidly growing strains of sea cucumber in aquaculture.

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Funding

This project was supported by the National Natural Science Foundation of China (No. 31572608).

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Author notes

  1. Zhicheng Wang and Jun Cui contributed equally to this work.

Authors and Affiliations

  1. Key Laboratory of Mariculture & Stock Enhancement in the North China Sea, Ministry of Agriculture, Dalian Ocean University, Dalian, 116023, China

    Zhicheng Wang, Jian Song, Xiuli Wang & Yaqing Chang

  2. College of Fisheries and Life Science, Dalian Ocean University, 52 Heishijiao Street, Shahekou District, Dalian, 116023, China

    Zhicheng Wang, Jun Cui, Haoze Wang, Kailun Gao, Xuemei Qiu, Xin Li, Ziwen Hu, Xiuli Wang & Yaqing Chang

  3. School of Life Science, Liaoning Normal University, Dalian, 116081, China

    Meng Gou

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  1. Zhicheng Wang
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Correspondence to Xiuli Wang or Yaqing Chang.

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Electronic Supplementary Material

Supplementary Figure 1.

Transcript length distribution (GIF 108 kb)

High resolution image (TIFF 11658 kb)

Supplementary Figure 2.

Box plot of FPKM and the correlation coefficients of gene expression levels. T01 to T04 represent RR, CC, CR and RC at 45 DAF, respectively. T05 to T08 represent RR, CC, CR and RC at 75 DAF, respectively. (GIF 44 kb)

High resolution image (TIFF 5579 kb)

Supplementary Figure 3.

GO enrichment analysis. T01 to T04 represent RR, CC, CR and RC at 45 DAF, respectively. T05 to T08 represent RR, CC, CR and RC at 75 DAF, respectively. (GIF 115 kb)

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Supplementary Figure 4.

COG functional classification. T01 to T04 represent RR, CC, CR and RC at 45 DAF, respectively. T05 to T08 represent RR, CC, CR and RC at 75 DAF, respectively. (GIF 78 kb)

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Supplementary Figure 5.

KEGG enrichment analysis. T01 to T04 represent RR, CC, CR and RC at 45 DAF, respectively. T05 to T08 represent RR, CC, CR and RC at 75 DAF, respectively. (JPEG 2828 kb)

High resolution image (TIFF 21292 kb)

Supplementary Table 1

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Supplementary Table 2

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Supplementary Table 3

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Supplementary Table 4

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Supplementary Table 5

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Supplementary Table 6

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Wang, Z., Cui, J., Song, J. et al. Comparative Transcriptome Analysis Reveals Growth-Related Genes in Juvenile Chinese Sea Cucumber, Russian Sea Cucumber, and Their Hybrids. Mar Biotechnol 20, 193–205 (2018). https://doi.org/10.1007/s10126-018-9796-6

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  • DOI: https://doi.org/10.1007/s10126-018-9796-6

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