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

• Published in: Journal of genetics 2018-12, Vol.97 (5), p.1363-1369
• Main Authors: Pereira, Vanessa Alves, Forte, Jamille Martins, Arruda-Júnior, José Pedro Vieira, Diniz, Fábio Mendonça, Maggioni, Rodrigo, Salmito-Vanderley, Carminda Sandra Brito
• Format: Article
• Language: English
• Subjects: Alleles; Animal Genetics and Genomics; Animals; Aquaculture; Biomedical and Life Sciences; Brazil; Evolutionary Biology; Female; Gene Frequency; Genetic Loci - genetics; Genetic markers; Genomes; Genotype; Heterozygotes; Holothuria - genetics; Holothuria grisea; Life Sciences; Linkage disequilibrium; Male; Microbial Genetics and Genomics; Microsatellite Repeats - genetics; Microsatellites; Plant Genetics and Genomics; Polymorphism, Genetic; Research Article; Whole Genome Sequencing - methods
• ISSN: 0022-1333; 0973-7731
• DOI: 10.1007/s12041-018-1022-9

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 ( Hgr 15607) 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 Hgr 15607. 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.