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Identification of differentially expressed genes associated with differential body size in mandarin fish (Siniperca chuatsi)

Genetica volume 144, pages 445–455 (2016)Cite this article

Abstract

Body size is an obvious and important characteristic of fish. Mandarin fish Siniperca chuatsi (Basilewsky) is one of the most valuable perciform species widely cultured in China. Individual differences in body size are common in mandarin fish and significantly influence the aquaculture production. However, little is currently known about its genetic control. In this study, digital gene expression profiling and transcriptome sequencing were performed in mandarin fish with differential body size at 30 and 180 days post-hatch (dph), respectively. Body weight, total length and body length of fish with big-size were significantly higher than those with small-size at both 30 and 180 dph (P < 0.05). 2171 and 2014 differentially expressed genes were identified between small-size and big-size fish at 30 and 180 dph, respectively. RT quantitative PCR (qPCR) analysis showed that the differential expression of 10 selected genes in mandarin fish that went through the same training procedure. The genes were involved in the growth hormone–insulin-like growth factor axis, cell proliferation and differentiation, appetite control, glucose metabolism, reproduction and sexual size dimorphism pathways. This study will help toward a comprehensive understanding of the complexity of regulation of body size in mandarin fish individuals and provide valuable information for future research.

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Acknowledgments

This work was financially supported by the National Natural Science Foundation of China (31272641), the Key Projects in the National Science & Technology Pillar Program during the Twelfth 5-year Plan Period (2012BAD25B04) and the Fundamental Research Funds for the Central Universities (2662015PY041, 2015BQ040 and 2013PY072).

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    Affiliations

    1. College of Fisheries, Chinese Perch Research Center, Huazhong Agricultural University, Wuhan, 430070, China

      Changxu Tian, Ling Li, Xu-Fang Liang, Shan He, Wenjie Guo, Liyuan Lv, Qingchao Wang & Yi Song

    2. Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Wuhan, 430070, China

      Changxu Tian, Ling Li, Xu-Fang Liang, Shan He, Wenjie Guo, Liyuan Lv, Qingchao Wang & Yi Song

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    1. Changxu Tian
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    2. Ling Li
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    3. Xu-Fang Liang
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    Correspondence to Xu-Fang Liang.

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    Changxu Tian and Ling Li have contributed equally to this work.

    Electronic supplementary material

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    10709_2016_9913_MOESM1_ESM.pptx

    Supplementary Fig. S1. Distribution of Total Tags and Distinct Tags. S30B indicate brain of small-size fish at 30 dph; B30B indicate brain of big-size fish at 30 dph. Tags Containing N: the number of tags containing N; Only adaptors: the reads contain only the adaptors sequence; Copy Number < 2: the copy number of tag is less than 2; Clean tags: the tags used to analysis after filtering the dirty tags (PPTX 83 kb)

    10709_2016_9913_MOESM2_ESM.pptx

    Supplementary Fig. S2. Distribution of Clean Tag Copy Number. S30B indicate brain of small-size group at 30 dph; B30B indicate brain of big-size group at 30 dph (PPTX 100 kb)

    10709_2016_9913_MOESM3_ESM.pptx

    Supplementary Fig. S3. Alignment statistics of the Clean tags. S30B indicate brain of small-size group at 30 dph; B30B indicate brain of big-size group at 30 dph. PM (Sense): perfect match to gene (Sense); 1 MM (Sense): match to gene (Sense) with 1 bp mismatch; 1 tag->1 gene: match to one gene; 1 tag->n gene: match to more than one gene; PM (AntiSense): perfect match to gene (Anti-Sense); 1 MM (AntiSense): match to gene (Anti-Sense) with 1 bp mismatch; Unkown Tag: not match to gene (Sense and Anti-Sense) (PPTX 108 kb)

    Supplementary material 4 (DOC 63 kb)

    Supplementary material 5 (DOCX 21 kb)

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    Tian, C., Li, L., Liang, XF. et al. Identification of differentially expressed genes associated with differential body size in mandarin fish (Siniperca chuatsi). Genetica 144, 445–455 (2016). https://doi.org/10.1007/s10709-016-9913-2

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    • DOI: https://doi.org/10.1007/s10709-016-9913-2

    Keywords

    • Body size
    • Individual difference
    • Mandarin fish
    • Digital gene expression profiling
    • Transcriptome sequencing