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Journal of Genetics

, Volume 97, Issue 5, pp 1363–1369 | Cite as

Identification and characterization of microsatellite loci in West Atlantic sea cucumber Holothuria grisea (Selenka 1867)

  • Vanessa Alves PereiraEmail author
  • Jamille Martins Forte
  • José Pedro Vieira Arruda-Júnior
  • Fábio Mendonça Diniz
  • Rodrigo Maggioni
  • Carminda Sandra Brito Salmito-Vanderley
Research Article
  • 141 Downloads

Abstract

The sea cucumber Holothuria grisea has become the subject of intense and unregulated fishing in northeastern Brazil due to their growing demand in Asian market. However, there is little knowledge about the dynamics and genetics of H. grisea wild populations on the South American coast. In this study, we present the first set of H. grisea microsatellite markers, identified and characterized using Illumina paired-end reads of whole genome shotgun sequencing. From 50 strictly selected candidates, eight novel microsatellite markers were successfully developed. We then genotyped 30 individuals to evaluate the degree of polymorphism and validate the markers. The number of alleles ranged from three to 14, while observed and expected heterozygotes ranged from 0.156 to 0.906 and from 0.283 to 0.774, respectively. After correcting for multiple tests, we found no evidence of linkage disequilibrium in all pairwise combinations between the loci. One locus (Hgr15607) revealed deviation from the Hardy–Weinberg equilibrium, as well as the presence of null alleles. However, we observed significant differences in frequency distribution between males and females at locus Hgr15607. We believe that the markers described here will be useful for conservation efforts and management of H. grisea fisheries and for prospective aquaculture of these organisms.

Keywords

microsatellite next-generation sequencing genetic diversity sea cucumber Holothuria grisea 

Notes

Acknowledgements

We thank Cristália Produtos Químicos e Farmacêutios for their assistance in collecting H. grisea samples and partial funding. We kindly thank Ms Kellie Johns, from James Cook University, for English editing. All NGS were conducted at NPDM-UFC. All genotyping was conducted at CEDECAM-LABOMAR. R. Maggioni is a visiting scholar at James Cook University, Australia on a grant from CAPES (Proc. 88881.119752/2016-01).

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Copyright information

© Indian Academy of Sciences 2018

Authors and Affiliations

  • Vanessa Alves Pereira
    • 1
    Email author
  • Jamille Martins Forte
    • 2
  • José Pedro Vieira Arruda-Júnior
    • 3
  • Fábio Mendonça Diniz
    • 4
  • Rodrigo Maggioni
    • 2
  • Carminda Sandra Brito Salmito-Vanderley
    • 1
  1. 1.Faculdade de VeterináriaUniversidade Estadual do CearáFortalezaBrazil
  2. 2.Instituto de Ciências do Mar (LABOMAR)Universidade Federal do CearáFortalezaBrazil
  3. 3.Centro de CiênciasUniversidade Federal do CearáFortalezaBrazil
  4. 4.EMBRAPA Caprinos e OvinosSobralBrazil

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