New microsatellite loci for the green sea urchin Strongylocentrotus droebachiensis using universal M13 labelled markers
© Anglès d’Auriac et al.; licensee BioMed Central Ltd. 2014
Received: 21 March 2014
Accepted: 2 October 2014
Published: 7 October 2014
The green sea urchin Strongylocentrotus droebachiensis has a wide circumpolar distribution and plays a key role in coastal ecosystems worldwide by destructively grazing macroalgae beds and turn them into marine deserts, so-called barren grounds. In the past decades, large established kelp forests have been overgrazed and transformed to such barren grounds on the Norwegian coast. This has important repercussions for the coastal diversity and production, including reproduction of several fish species relying on the kelp forests as nurseries. Genetic diversity is an important parameter for the study and further anticipation of this large scale phenomenon.
Microsatellites were developed using a Norwegian S. droebachiensis individual primarily for the study of Northeast Atlantic populations. The 10 new microsatellite loci were amplified using M13 forward tails, enabling the use of M13 fluorescent tagged primers for multiplex reading. Among these loci, 2 acted polysomic and should therefore not be considered useful for population genetic analysis. We screened 96 individuals sampled from 4 different sites along the Norwegian coast which have shown unexpected diversity.
The new microsatellite loci should be a useful resource for further research into connectivity among S. droebachiensis populations, and assessing the risks for spreading and new overgrazing events.
KeywordsClimate change Heterozygote deficiency Kelp forests Marine invertebrates Microsatellites NE Atlantic Simple DNA preparation Strongylocentrotus droebachiensis
The green sea urchin Strongylocentrotus droebachiensis is one of the dominant grazing species in temperate marine ecosystems. Catastrophic overgrazing events have been recorded in the Pacific  and the Atlantic  including the northern Norwegian and Russian coast, where approximately 2000 km2 of kelp forest were grazed to barren grounds in the 1970s [3, 4]. Because of the persistence of the sea urchin dominance and the large loss of biodiversity and production, it is important to develop new genetic tools for studying and improving our understanding of this species. Microsatellite loci have been previously developed using North American individuals . Further analysis have shown that the Northeast Atlantic population, based on one sampling location in Iceland and one in Norway, is differentiated compared from Northwest Atlantic and Pacific populations . Moreover, when tested on the two Northeast Atlantic locations, locus Sd76 was reported failing to amplify any of the individuals and the remaining 3 loci showed fewer alleles compared with North American locations. These results have motivated our goal to develop the present microsatellite loci using a S. droebachiensis individual from a Norwegian population (Drøbak) in an effort to increase genetic information produced for the study, primarily, of the Northeast Atlantic populations.
Characterization of 10 microsatellite loci for S. droebachiensis using 96 individuals
F & R primer sequences 5’-3’*
Size range (bp)**
A simple optimised DNA extraction was performed using QuickExtract (Epicentre Technologies Corporation, Madison, USA). Briefly, 10 to 20 mg gonad material from one individual preserved in Ethanol 96% was washed in distilled water prior to adding 100 μL QuickExtract buffer. Samples were incubated at 65°C for 10 min followed by 98°C inactivation for 5 min. The lysates were further diluted 10-2 in Tris EDTA buffer (Fluka Chemie GmbH, Buchs, Switzerland) prior to performing PCR. A 3-primer PCR approach using a M13 tail (5’-TGTAAAACGACGGCCAGT) for the forward primer was used for microsatellite loci amplification at concentrations as described previously . Four different dyes were used for the universal M13 forward primer to enable fragment analysis multiplexing . Simplex PCR amplifications, targeting one locus at a time, were performed using a CFX96 thermocycler (Bio-Rad, Hercules, CA, USA) in 10 μL reaction volume containing 5 μL iProof Master Mix (Bio-Rad), 0.04 μM of the forward primer with M13 5’-tail and 0.16 μM of each reverse and forward tagged M13 primers (Eurofins MWG, Ebersberg, Germany) and 2.5 μL sample. Reaction volume was completed with sterile deionised water. PCR amplifications were optimized and carried out under the following conditions: a denaturing step for 1 min at 98°C, followed by 30 cycles of 98°C for 5 s, 62°C for 10 s and 72°C for 15 s followed by 8 cycles of 98°C for 5 s, 57°C for 10 s and 72°C for 15 s. Up to 4 different simplex PCR plates, each with a different dye (Table 2), were mixed and diluted by transferring 5 μL each to a plate prefilled with 100 μL deionized water per well. From this dilution plate 1.2 μL per sample was transferred to the run plate prefilled with 10 μL Hi-Di Formamide (Applied Biosystems, Foster City, CA, USA) and 40% strength orange standard (MCLAB, San Francisco, CA, USA). PCR product sizes were determined using a 3730XL DNA analyser (Applied Biosystems) and scored using GeneMapper software version 4.0 (Applied Biosystems). GenAlEx software version 6.5 was used to report overall observed (Ho) and expected (He) heterozygosity . Linkage disequilibrium and Hardy-Weinberg equilibria (HWE) were tested in Arlequin software version 126.96.36.199 .
We observed linkage (Likelihood ratio test, p < 0.05) among loci in all four populations, but no pair of loci was linked in all of them. Five loci (Strdro-1051, Strdro-1356, Strdro-4147, Strdro-5563, and Strdro-5590) showed heterozygote deficiencies and HWE deviations (Exact test, p < 0.05) in all populations, possibly suggesting inbreeding and substructuring or the presence of null-alleles. The fact that simplex PCR was performed for all loci strongly reduces the risk for weak amplification that may be observed in a multiplex assay and hence reduces possible false negative loci amplification results.
The loci presented in this study show higher allelic diversity than that reported previously for Northeast Atlantic populations using loci developed on Northwest Atlantic individuals . Interestingly, heterozygote deficiencies and significant HWE deviation were also found with 3 of the 4 microsatellites used in this prior study , hence suggesting that S. droebachiensis may naturally deviate from HWE as it has been reported to be the case for many other marine invertebrates . We believe that these new loci will be useful for the study of S. droebachiensis, in particular for the Northeast populations, for better monitoring the observed ongoing population distribution and densities fluctuations along the Norwegian coastline.
Availability of supporting data
The microsatellite sequences are available through the European Molecular Biology Laboratory European Nucleotide Archive (http://www.ebi.ac.uk/ena/) Accession Numbers HG417080 to HG417089.
This work was financed by NIVA Biodiversity Strategic Institute Initiative project. We thank Erling Svensen for the Strongylocentrotus droebachiensis photography used for the cover image.
- Estes JA, Tinker MT, Williams TM, Doak DF: Killer whale predation on Sea otters linking oceanic and nearshore ecosystems. Science. 1998, 282: 473-476.PubMedView ArticleGoogle Scholar
- Steneck RS, Vavrinec J, Leland AV: Accelerating trophic-level dysfunction in kelp forest ecosystems of the western North Atlantic. Ecosystems. 2004, 7: 323-332. 10.1007/s11252-005-6833-9.View ArticleGoogle Scholar
- Norderhaug KM, Christie HC: Sea urchin grazing and kelp re-vegetation in the NE Atlantic. Mar Biol Res. 2009, 5: 515-528. 10.1080/17451000902932985.View ArticleGoogle Scholar
- Sivertsen K: Geographic and environmental factors affecting the distribution of kelp beds and barren grounds and changes in biota associated with kelp reduction at sites along the Norwegian coast. Can J Fish Aquat Sci. 1997, 54: 2872-2887. 10.1139/f97-186.View ArticleGoogle Scholar
- Addison JA, Hart MW: Characterization of microsatellite loci in sea urchins (Strongylocentrotus spp.). Mol Ecol Notes. 2002, 2: 493-494. 10.1046/j.1471-8286.2002.00295.x.View ArticleGoogle Scholar
- Addison JA, Hart MW: Analysis of population genetic structure of the green sea urchin (Strongylocentrotus droebachiensis) using microsatellites. Mar Biol. 2004, 144: 243-251. 10.1007/s00227-003-1193-6.View ArticleGoogle Scholar
- Müller OF: Zoologiae Danicae Prodromus, Seu Animalium Daniae Et Norvegiae Indigenarum. 2009, Whitefish, Montana, USA: Kessinger Publishing, LLC, 1776-Google Scholar
- Schuelke M: An economic method for the fluorescent labeling of PCR fragments. Nat Biotechnol. 2000, 18: 233-234. 10.1038/72708.PubMedView ArticleGoogle Scholar
- Blacket MJ, Robin C, Good RT, Lee SF, Miller AD: Universal primers for fluorescent labelling of PCR fragments—an efficient and cost-effective approach to genotyping by fluorescence. Mol Ecol Resour. 2012, 12: 456-463. 10.1111/j.1755-0998.2011.03104.x.PubMedView ArticleGoogle Scholar
- Peakall R, Smouse PE: GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research-an update. Bioinformatics. 2012, 28: 2537-2539. 10.1093/bioinformatics/bts460.PubMedPubMed CentralView ArticleGoogle Scholar
- Excoffier L, Lischer HEL: Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Mol Ecol Resour. 2010, 10: 564-567. 10.1111/j.1755-0998.2010.02847.x.PubMedView ArticleGoogle Scholar
- Brownlow R, Dawson D, Horsburgh G, Bell J, Fish J: A method for genotype validation and primer assessment in heterozygote-deficient species, as demonstrated in the prosobranch mollusc Hydrobia ulvae. BMC Genet. 2008, 9: 55-PubMedPubMed CentralView ArticleGoogle Scholar
This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.