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1 September 2015 Development of Microsatellite Loci for the Endangered Seagrass Zostera japonica (Zosteraceae)
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Seagrass beds are recognized as critical to threatened coastal habitats around the world (Duffy, 2006). The seagrass Zostera japonica Asch. & Graebn. (Zosteraceae), an annual/perennial marine flowering angiosperm, is mainly distributed in the intertidal and shallow subtidal zones from temperate to subtropical regions along the North Pacific coast, especially in East Asia (Short et al., 2007). Meanwhile, Z. japonica is an introduced species on the west coast of North America (Harrison and Bigey, 1982) and has been reported from British Columbia (Canada) and Washington, Oregon, and California (USA) (Short et al., 2007). Zostera japonica can rapidly thrive and form extensive meadows through vegetative reproduction in the intertidal zone (Zhang et al., 2015). However, anthropogenic activities have led to a strong decline of natural populations in Asia.

To conserve and restore Z. japonica, much attention should be paid to genetic diversity and population genetic structure, yet few studies have been reported. Microsatellite markers prevail in genetic studies of seagrasses. In the genus Zostera L., microsatellites have been developed for quite a few species, such as Z. marina Gaertn. (Peng et al., 2012), Z. muelleri Irmisch ex Asch. (Sherman et al., 2012), and Z. nigricaulis (J. Kuo) S. W. L. Jacobs & Les (Smith et al., 2013), but specialized primers for Z. japonica were limited until now. Jiang et al. (2011) have developed a set of dinucleotide microsatellite loci for this species, and the analysis of short tandem repeat (STR) loci by PCR methods has proven to be informative. However, the PCR products of dinucleotide loci often produce multiple visible stutter bands that sometimes complicate the interpretation of alleles. The amplification of tetranucleotides is easier to interpret because only a single stutter band is typically observed (Walsh et al., 1996). Here we report isolation and characterization of the first set of polymorphic tetranucleotide microsatellite loci for Z. japonica, which will be used to investigate genetic diversity and population structure of this species.


Genomic DNA was isolated from fresh leaf tissue of a single individual of Z. japonica collected from Qingdao, China (36°05′N, 120°34′E) (Appendix 1). Genomic DNA extraction was undertaken using the E.Z.N.A. HP Plant DNA Mini Kit (OMEGA Bio-tek, Norcross, Georgia, USA) according to manufacturer's protocols. A DNA extract of 50 µL with a concentration of 118 µg/µL was obtained. Microsatellites were isolated following the enrichment protocols of Glenn and Schable (2005). Total genomic DNA was digested with RsaI (New England Biolabs, Ipswich, Massachusetts, USA). The digested fragments were ligated to double-stranded SuperSNX-24 linkers and then hybridized with a 5′-biotinylated oligonucleotide probe (AGAT)8 (Life Technologies, Shanghai, China). The DNA fragments containing microsatellite sequences were captured on streptavidin-coated Dynabeads (Invitrogen, Carlsbad, California, USA), and the captured DNA was recovered by PCR using the SuperSNX-24 forward primer (Life Technologies). The PCR products were purified using TaKaRa MiniBEST DNA Fragment Purification Kit ver.3.0 (TaKaRa Biotechnology Co., Dalian, Liaoning, China), ligated into pEASY-T1 cloning vector (TransGen, Beijing, China), and transformed into Trans1-T1 competent cells (TransGen). A total of 201 positive clones were sent to Life Technologies for sequencing. Fragments containing microsatellite repeats were screened using MISA software (Thiel et al., 2003;

Twenty-five primer pairs were designed by Primer Premier ver.5.00 (PREMIER Biosoft International, Palo Alto, California, USA). The primers were optimized and polymorphisms were tested by genotyping eight individuals collected from Qingdao, China (36°05′N, 120°34′E). The 5′ end of each forward primer was fluorescently labeled (FAM, HEX, or TAMRA; Life Technologies). All loci were amplified separately on a Mastercycler (Eppendorf, Hamburg, Germany) in a 10-µL reaction containing 10–50 ng of genomic DNA, 5 µL of PCR mix (Dongsheng Bio Co., Guangzhou, Guangdong, China), 0.25 µM reverse and labeled forward primer, and 3.5 µL of ultrapure water. PCR cycling conditions were 94°C for 3 min; 35 cycles of 30 s at 94°C, 30 s at an annealing temperature gradient of 50–60°C, and 1 min at 72°C; with a final extension at 72°C held for 10 min. PCR products were visualized on a 1.5% agarose gel to judge if the loci were successfully amplified. Pooled products were sent to Life Technologies for genotyping. A final set of 12 microsatellite loci were found to be polymorphic in Z. japonica (Table 1).

Table 1.

Characterization of 15 microsatellite loci for Zostera japonica.


To assess the genetic diversity of the selected loci, we used 32 individuals of two Z. japonica populations from China, i.e., Qingdao (36°05′N, 120°34′E) and Fangchenggang (21°36′N, 108°13′E) (Appendix 1). Samples were collected at least 2 m apart in the field. Allele scoring was performed using GeneMarker 2.2.0 (SoftGenetics, State College, Pennsylvania, USA). The number of alleles per locus ranged from one to 11, and the expected and observed heterozygosity ranged from 0 to 0.772 and from 0 to 1.000, respectively (Table 2). Significant deviation from Hardy–Weinberg equilibrium was observed at three loci (P < 0.0042) in the Fangchenggang population after Bonferroni correction using the software program GENEPOP 4.0 (Rousset, 2008). Linkage disequilibrium among loci was also detected using GENEPOP 4.0, with Fisher's method (Raymond and Rousset, 1995; Rousset, 2008), and was detected between locus pairs Zj025 and Zj042, Zj011 and Zj018/Zj037, and Zj001 and Zj028/Zj029/Zj036 (P < 0.0042) after Bonferroni correction (Rousset, 2008), but was most likely due to low polymorphism levels at those loci.

Table 2.

Summary genetic statistics for two populations of Zostera japonica screened with 12 newly developed polymorphic microsatellites.a



The new polymorphic microsatellite loci developed in this study have proved to be useful to evaluate genetic diversity of Z. japonica. The two studied populations showed different frequencies of alleles at these loci and both displayed fixed alleles. Therefore, it is expected that more alleles will be detected if sampling is conducted more broadly across the species' range. These available microsatellite loci will facilitate future studies of population genetic and clonal structure, connectivity, and gene flow in Z. japonica, which will contribute to the conservation and management of this species.



J. E. Duffy 2006. Biodiversity and the functioning of seagrass ecosystems. Marine Ecology Progress Series 311: 233–250. Google Scholar


T. C. Glenn , and N. A. Schable . 2005. Isolating microsatellite DNA loci. Methods in Enzymology 395: 202–222. Google Scholar


P. G. Harrison , and R. E. Bigey . 1982. The recent introduction of the seagrass Zostera japonica Ascherson and Graebner to the Pacific coast of North America. Canadian Journal of Fisheries and Aquatic-Sciences 39: 1642–1648. Google Scholar


K. Jiang , H. Gao , N. N. Xu , E. P. K. Tsang , and X. Y. Chen . 2011. A set of microsatellite primers for Zostera japonica (Zosteraceae). American Journal of Botany 98: e236–e238. Google Scholar


J. Peng , L. A. Zhang , X. Jiang , C. J. Cui , R. N. Wu , and J. P. Zhao . 2012. Isolation and characterization of microsatellite markers for Zostera marina and their cross-species amplification in Zostera caespitosa. Conservation Genetics Resources 4: 455–458. Google Scholar


M. Raymond , and F. Rousset . 1995. GENEPOP (version 1.2): Population genetics software for exact tests and ecumenicism. Journal of Heredity 86: 248–249. Google Scholar


F. Rousset 2008. GENEPOP'007: A complete re-implementation of the GENEPOP software for Windows and Linux. Molecular Ecology Resources 8: 103–106. Google Scholar


C. D. H. Sherman , A. M. Stanley , M. J. Keough , M. G. Gardner , and P. I. Macreadie . 2012. Development of twenty-three novel microsatellite markers for the seagrass, Zostera muelleri from Australia. Conservation Genetics Resources 4: 689–693. Google Scholar


F. Short , T. Carruthers , W. Dennison , and M. Waycott . 2007. Global seagrass distribution and diversity: A bioregional model. Journal of Experimental Marine Biology and Ecology 350: 3–20. Google Scholar


T. M. Smith , P. H. York , A. M. Stanley , P. I. Macreadie , M. J. Keough , D. J. Rose , and C. D. H. Sherman . 2013. Microsatellite primer development for the seagrass Zostera nigricaulis (Zosteraceae). Conservation Genetics Resources 5: 607–610. Google Scholar


T. Thiel , W. Michalek , R. K. Varshney , and A. Graner . 2003. Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.). Theoretical and Applied Genetics 10: 411–422. Google Scholar


P. S. Walsh , N. J. Fildes , and R. Reynolds . 1996. Sequence analysis and characterization of stutter products at the tetranucleotide repeat locus vWA. Nucleic Acids Research 24: 2807–2812. Google Scholar


X. Zhang , Y. Zhou , P. Liu , F. Wang , B. Liu , X. Liu , and H. Yang . 2015. Temporal pattern in biometrics and nutrient stoichiometry of the intertidal seagrass Zostera japonica and its adaptation to air exposure in a temperate marine lagoon (China): Implications for restoration and management. Marine Pollution Bulletin 94: 103–113. Google Scholar


Appendix 1.

Voucher and location information for Zostera japonica populations used in this study. One voucher was collected for each population used; all vouchers were deposited in the Marine Biological Museum, Chinese Academy of Sciences, Qingdao, China.



[1] The authors acknowledge funding from the National Science and Technology Basic Work Program (2015FY110600), the 100 Talents Program of the Chinese Academy of Sciences to J.X.L., and the National Marine Public Welfare Research Project (201305043).

Xiaomei Zhang, Yi Zhou, Dongxiu Xue, and Jin-Xian Liu "Development of Microsatellite Loci for the Endangered Seagrass Zostera japonica (Zosteraceae)," Applications in Plant Sciences 3(9), (1 September 2015).
Received: 3 June 2015; Accepted: 1 July 2015; Published: 1 September 2015

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