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A Candidate Gene Association Study for Growth Performance in an Improved Giant Freshwater Prawn (Macrobrachium rosenbergii) Culture Line

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Abstract

A candidate gene approach using type I single nucleotide polymorphism (SNP) markers can provide an effective method for detecting genes and gene regions that underlie phenotypic variation in adaptively significant traits. In the absence of available genomic data resources, transcriptomes were recently generated in Macrobrachium rosenbergii to identify candidate genes and markers potentially associated with growth. The characterisation of 47 candidate loci by ABI re-sequencing of four cultured and eight wild samples revealed 342 putative SNPs. Among these, 28 SNPs were selected in 23 growth-related candidate genes to genotype in 200 animals selected for improved growth performance in an experimental GFP culture line in Vietnam. The associations between SNP markers and individual growth performance were then examined. For additive and dominant effects, a total of three exonic SNPs in glycogen phosphorylase (additive), heat shock protein 90 (additive and dominant) and peroxidasin (additive), and a total of six intronic SNPs in ankyrin repeats-like protein (additive and dominant), rolling pebbles (dominant), transforming growth factor-β induced precursor (dominant), and UTP-glucose-1-phosphate uridylyltransferase 2 (dominant) genes showed significant associations with the estimated breeding values in the experimental animals (P = 0.001 − 0.031). Individually, they explained 2.6 − 4.8 % of the genetic variance (R 2 = 0.026 − 0.048). This is the first large set of SNP markers reported for M. rosenbergii and will be useful for confirmation of associations in other samples or culture lines as well as having applications in marker-assisted selection in future breeding programs.

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Acknowledgements

Authors wish to thank to Dr. Woo-Jin Kim, Dr. Peter Prentis and two anonymous reviewers for useful comments. This research forms a part of Hyungtaek Jung’s PhD project, and is supported by an International Postgraduate Research Scholarship (Australia) and a Queensland University of Technology Postgraduate Award (N7333978). Additional funding for this work was provided by Queensland University of Technology awarded to Peter B. Mather (VC NPSG award).

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Authors and Affiliations

  1. Earth, Environmental and Biological Sciences, Science and Engineering Faculty, Queensland University of Technology, Brisbane, Queensland, 4000, Australia

    Hyungtaek Jung, Hung Dinh, David A. Hurwood & Peter B. Mather

  2. CSIRO Animal, Food and Health Sciences, St Lucia, Queensland, 4067, Australia

    Russell E. Lyons & Yutao Li

  3. School of Biotechnology, International University in Vietnam, Ho Chi Minh City, Vietnam

    Nguyen Minh Thanh

  4. School of Aquaculture and Biotechnology, Kerala University of Fisheries and Ocean Studies, Kochi, 682 506, India

    Krishna R. Salin

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  1. Hyungtaek Jung
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Correspondence to Hyungtaek Jung.

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Jung, H., Lyons, R.E., Li, Y. et al. A Candidate Gene Association Study for Growth Performance in an Improved Giant Freshwater Prawn (Macrobrachium rosenbergii) Culture Line. Mar Biotechnol 16, 161–180 (2014). https://doi.org/10.1007/s10126-013-9555-7

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  • DOI: https://doi.org/10.1007/s10126-013-9555-7

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