The seagrass Zostera japonica Asch. & Graebn. is among the few seagrass species that thrive both in temperate and tropical intertidal zones. The degradation of Z. japonica in its native range and continued expansion in some localities have raised concerns with regard to its conservation and management. Population genetic studies of Z. japonica across its biogeographic range and within meadows are scarce. Previously developed microsatellites via traditional methods are not sufficient in quantity and perform inconsistently between the temperate and tropical populations. Thus, this study aimed to develop more reliable polymorphic markers for Z. japonica using next generation sequencing. In total, 6479 sequences containing loci were identified and 1619 pairs of primers were successfully designed. Of these, 63 loci were selected for primary validation in 16 individuals from four populations, with 48 (76.2%) polymorphic loci detected. Seventeen polymorphic loci were selected for further evaluation in 62 individuals from one temperate and one tropical population. The overall probability of identity (PID) for both populations was 2.375e−22 (PIDsib = 3.557e−08). The number of alleles, and expected and observed heterozygosity in the two populations were both relatively high and not significantly different from each other. The pairwise FST = 0.232 (p < 0.0001) and Principal Coordinates Analysis both suggested a large and significant genetic divergence between the two populations. This study makes abundant molecular markers available for genetic studies in Z. japonica, and facilitates its conservation and management strategies.
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Costanza R, dArge R, deGroot R, Farber S, Grasso M, Hannon B, Limburg K, Naeem S, Oneill RV, Paruelo J, Raskin RG, Sutton P, vandenBelt M (1997) The value of the world’s ecosystem services and natural capital. Nature 387(6630):253–260
Orth RJ, Carruthers TJB, Dennison WC, Duarte CM, Fourqurean JW, Heck KL, Hughes AR, Kendrick GA, Kenworthy WJ, Olyarnik S, Short FT, Waycott M, Williams SL (2006) A global crisis for seagrass ecosystems. Bioscience 56(12):987–996
Short F, Carruthers T, Dennison W, Waycott M (2007) Global seagrass distribution and diversity: a bioregional model. J Exp Mar Bio Ecol 350(1–2):3–20
Harrison PG, Bigley RE (1982) The recent introduction of the seagrass Zostera japonica Aschers and Graben to the pacific coast of North-America. Can J Fish Aquat Sci 39(12):1642–1648
Young DR, Clinton PJ, Specht DT, DeWitt TH, Lee H (2008) Monitoring the expanding distribution of nonindigenous dwarf eelgrass Zostera japonica in a pacific northwest USA estuary using high resolution digital aerial orthophotography. J Spat Sci 53(1):87–97
Baldwin JR, Lovvorn JR (1994) Expansion of seagrass habitat by the exotic Zostera japonica, and its use by dabbling ducks and brant in Boundary Bay, British-Columbia. Mar Ecol Prog Ser 103(1–2):119–127
Abe M, Yokota K, Kurashima A, Maegawa M (2009) Temperature characteristics in seed germination and growth of Zostera japonica Ascherson & Graebner from Ago Bay, Mie Prefecture, central Japan. Fish Sci 75(4):921–927
Hodoki Y, Ohbayashi K, Tanaka N, Kunii H (2013) Evaluation of genetic diversity in Zostera japonica (Aschers. et Graebn.) for seagrass conservation in brackish lower reaches of the Hii River System, Japan. Estuar coast 36(1):127–134
Lee S, Ma S, Lim Y, Choi H-K, Shin H (2004) Genetic diversity and its implications in the conservation of endangered Zostera japonica in Korea. J Plant Biol 47(3):275–281
Huang X, Huang L, Li Y, Xu Z, Fang J, Huang D, Han Q, Huang H, Tan Y, Liu S (2006) Main seagrass beds and threats to their habitats in the coastal sea of South China. Chin Sci Bull (S3), 114–119 (in Chinese)
Shafer DJ, Kaldy JE, Gaeckle JL (2014) Science and management of the introduced seagrass Zostera japonica in North America. Environ Manag 53(1):147–162
Procaccini G, Olsen JL, Reusch TB (2007) Contribution of genetics and genomics to seagrass biology and conservation. J Exp Mar Biol Ecol 350(1):234–259
Olsen JL, Stam WT, Coyer JA, Reusch TB, Billingham M, Boström C, Calvert E, Christie H, Granger S, Lumiere RL (2004) North Atlantic phylogeography and large-scale population differentiation of the seagrass Zostera marina L. Mol Ecol 13(7):1923–1941
Coyer JA, Diekmann OE, Serrao EA, Procaccini G, Milchakova N, Pearson GA, Stam WT, Olsen JL (2004) Population genetics of dwarf eelgrass Zostera noltii throughout its biogeographic range. Mar Ecol Prog Ser 281:51–62
Arnaudhaond S, Migliaccio M, Diazalmela E, Teixeira S, De Vliet MSV, Alberto F, Procaccini G, Duarte CM, Serrao EA (2007) Vicariance patterns in the Mediterranean Sea: east–west cleavage and low dispersal in the endemic seagrass Posidonia oceanica. J Biogeogr 34(6):963–976
Hernawan UE, van Dijk K-J, Kendrick GA, Feng M, Biffin E, Lavery PS, McMahon K (2017) Historical processes and contemporary ocean currents drive genetic structure in the seagrass Thalassia hemprichii in the Indo-Australian Archipelago. Mol Ecol 26(4):1008–1021
Araki S, Kunii H (2006) Allozymic implications of the propagation of eelgrass Zostera japonica within a river system. Limnology 7(1):15–21
Jiang K, Tsang P-KE, Xu N-N, Chen X-Y (2018) High genetic diversity and strong differentiation in dramatically fluctuating populations of Zostera japonica (Zosteraceae): implication for conservation. J Plant Ecol 11(5):789–797
Jiang K, Gao H, Xu N-N, Tsang EPK, Chen X-Y (2011) A set of microsatellite primers for Zostera japonica (Zosteraceae). Am J Bot 98(9):e236–e238
Zhang X, Zhou Y, Xue D, Liu J-X (2015) Development of microsatellite loci for the endangered seagrass Zostera japonica (Zosteraceae). Appl Plant Sci. https://doi.org/10.3732/apps.1500064
Zhang X, Zhou Y, Xue D-X, Liu J-X (2016) Genetic divergence of the endangered seagrass Zostera japonica Ascherson & Graebner between temperate and subtropical coasts of China based on partial sequences of matK and ITS. Biochem Syst Ecol 68:51–57
Zalapa JE, Cuevas H, Zhu H, Steffan S, Senalik D, Zeldin E, McCown B, Harbut R, Simon P (2012) Using next-generation sequencing approaches to isolate simple sequence repeat (SSR) loci in the plant sciences. Am J Bot 99(2):193–208
Davey JW, Hohenlohe PA, Etter PD, Boone JQ, Catchen JM, Blaxter ML (2011) Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nat Rev Genet 12(7):499–510
Olsen JL, Rouze P, Verhelst B et al (2016) The genome of the seagrass Zostera marina reveals angiosperm adaptation to the sea. Nature 530(7590):331–335
Schuelke M (2000) An economic method for the fluorescent labeling of PCR fragments. Nat Biotechnol 18(2):233–234
The authors thank all the individuals who assisted in the collection of samples. This research was supported by the National Science & Technology Basic Work Program (2015FY110600), the NSFC-Shandong Joint Fund for Marine Science Research Centers (U1606404), the CPSF-CAS Joint Foundation for Excellent Postdoctoral Fellows (2016LH0032), the China Postdoctoral Science Foundation (2016M600562), the key Research and Development Project of Shandong Province (2017GHY15111), the Key Research Project of Frontier Sciences of CAS (QYZDB-SSW-DQC041-1), the Science and Technology Service Network Initiative of CAS (KFJ-STS-ZDTP-023), the Creative Team Project of the Laboratory for Marine Ecology and Environmental Science from the Qingdao National Laboratory for Marine Science and Technology (LMEES-CTSP-2018-1), and the Taishan Scholars Program (Distinguished Taishan Scholars).
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The authors declare that there is no conflict of interests.
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Zhang, X., Zhou, Y., Li, YL. et al. Development of microsatellite markers for the seagrass Zostera japonica using next-generation sequencing. Mol Biol Rep 46, 1335–1341 (2019). https://doi.org/10.1007/s11033-018-4491-2
- Zostera japonica
- Population genetics