Cite this paper:
SHANGGUAN Jingbo, LI Zhongbao. Development of novel microsatellite markers for Holothurian scabra (Holothuriidae), Apostichopus japonicas (Stichopodidae) and cross-species testing in other sea cucumbers[J]. HaiyangYuHuZhao, 2018, 36(2): 519-527

Development of novel microsatellite markers for Holothurian scabra (Holothuriidae), Apostichopus japonicas (Stichopodidae) and cross-species testing in other sea cucumbers

SHANGGUAN Jingbo1,2, LI Zhongbao1,2
1 Fujian Provincial Key Laboratory of Marine Fishery Resources and Eco-Environment, Xiamen 361021, China;
2 Fisheries College, Jimei University, Xiamen 361021, China
Abstract:
Thirty-five new microsatellite loci from the sea cucumbers Holothurian scabra (Jaeger, 1833) and Apostichopus japonicas (Selenka, 1867) were screened and characterized using the method of magnetic bead enrichment. Of the twenty-four polymorphic loci tested, eighteen were consistent with Hardy-Weinberg equilibrium after a modified false discovery rate (B-Y FDR) correction, whereas six showed statistically significant deviations (CHS2 and CHS11:P<0.014 790; FCS1, FCS6, FCS8 and FCS14:P<0.015 377). Furthermore, four species of plesiomorphous and related sea cucumbers (Holothurian scabra, Holothuria leucospilota, Stichopus horrens and Apostichopus japonicas) were tested for mutual cross-amplification using a total of ninety microsatellite loci. Although transferability and universality of all loci were generally low, the results of the cross-species study showed that the markers can be applied to identify individuals to species according to the presence or absence of specific microsatellite alleles. The microsatellite markers reported here will contribute to the study of genetic diversity, assisted breeding, and population conservation in sea cucumbers, as well as allow for the identification of individuals to closely related species.
Key words:    sea cucumber|microsatellite loci (SSR)|genetic diversity|cross-amplification|species identification   
Received: 2016-12-03   Revised:
Tools
PDF (227 KB) Free
Print this page
Add to favorites
Email this article to others
Authors
Articles by SHANGGUAN Jingbo
Articles by LI Zhongbao
References:
Balloux F, Ecoffey E, Fumagalli L, Goudet J, Wyttenbach A, Hausser J. 1998. Microsatellite conservation, polymorphism, and GC content in shrews of the genus Sorex (Insectivora, Mammalia). Mol. Biol. Evol., 15(4):473-475.
Barbará T, Palma-Silva C, Paggi G M, Bered F, Fay M F, Lexer C. 2007. Cross-species transfer of nuclear microsatellite markers:potential and limitations. Mol. Ecol., 16(18):3 759-3 767.
Battaglene S C, Seymour J E. 1998. Detachment and grading of the tropical sea cucumber sandfish, Holothuria scabra, juveniles from settlement substrates. Aquaculture, 159(3-4):263-274.
Bordbar S, Anwar F, Saari N. 2011. High-value components and bioactives from sea cucumbers for functional foods-A review. Mar. Drugs, 9(10):1 761-1 805.
Botstein D, White R L, Skolnick M, Davis R W. 1980.Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am. J. Hum.Genet, 32(3):314-331.
Chan Y M, Twyford A D, Tnah L H, Lee C T. 2015.Characterisation of EST-SSR markers for Begonia maxwelliana (Begoniaceae) and cross-amplification in 23species from 7 Asian sections. Sci. Hortic., 190:70-74.
Chen M, Gao L L, Zhang W J, You H Z, Sun Q, Chang Y Q. 2013. Identification of forty-five gene-derived polymorphic microsatellite loci for the sea cucumber, Apostichopus japonicus. J. Genet. 92(2):e31-e35.
Conand C, Bryne M. 1993. A review of recent developments in the world sea cucumber fisheries. Mar. Fish. Rev., 55(4):1-13.
Conand C. 1990. The fishery Resources of Pacific Island Countries. Part 2:Holothurians. FAO Fisheries Technical Paper, No. 272.2. Food and Agriculture Organization of the United Nations, Rome, Italy. p.143.
Conand C. 2006. Sea Cucumber Biology, Taxonomy, Distribution:Conversation Status. In:Proceedings of the Convention on International Trade in Endangered Species of Wild Fauna and Flora Tech Workshop on the Conversation of Sea Cucumbers in the Families Holothuridae and Stichopodidae. Kuala Lumpur, Malaysia. p.1-3.
Dai G, Li Z B, Shangguan J B, Ning Y F, Deng H W, Yuan Y, Huang Y S, Yang H, Lu J. 2015. Development and characterization of polymorphic microsatellite loci in the sea cucumber Holothuria leucospilota. Genet. Mol. Res., 14(1):538-541.
Fitch A J, Leeworthy G, Li X X, Bowman W, Turner L, Gardner M G. 2013. Isolation and characterisation of eighteen microsatellite markers from the sea cucumber Holothuria scabra (Echinodermata:Holothuriidae). Aust.J. Zool., 60(6):368-371.
Kalinowski S T, Taper M L, Marshall T C. 2007. Revising how the computer program CERVUS accommodates genotyping error increases success in paternity assignment. Mol. Ecol., 16(5):1 099-1 106.
Kanno M, Li Q, Kijima A. 2005. Isolation and characterization of twenty microsatellite loci in Japanese sea cucumber(Stichopus japonicus). Mar. Biotechnol., 7(3):179-183.
Lalitha S. 2000. Primer Premier 5. Biotech Softw. Int. Rep., 1(6):270-272.
Lee G A, Kwon S J, Park Y J, Lee M C, Kim H H, Lee J S, Lee S Y, Gwag J G, Kim C K, Ma K H. 2011. Crossamplification of SSR markers developed from Allium sativum to other Allium species. Sci. Hortic., 128(4):401-407.
Li Q and Wan JM. 2005. SSRHunter:Development of a local searching software for SSR sites. Hereditas, 27:808-810.
Li Q, Chen L, Kong L. 2009. A genetic linkage map of the sea cucumber, Apostichopus japonicus (Selenka), based on AFLP and microsatellite markers. Anim. Genet., 40(5):678-685.
Li Z B, Dai G, Shangguan J B, Ning Y F, Li Y Y, Chen R B, Huang Y S, Yuan Y. 2015a. Isolation and characterization of polymorphic microsatellite loci in the sea cucumber Holothuria scabra. Genet. Mol. Res., 14(2):6 529-6 532.
Li Z B, Dai G, Shangguan J B, Ning Y F, Li Y Y, Chen R B, Yuan Y, Huang Y S. 2015b. Isolation and characterization of microsatellite markers of sea cucumber Stichopus horrens. Genet. Mol. Res., 14(3):8 496-8 499.
Liu Z J, Cordes J F. 2004. DNA marker technologies and their applications in aquaculture genetics. Aquaculture, 238:1-37.
Luo W, Qu H Y, Li J Y, Wang X, Lin Q. 2015. A novel method for the identification of seahorses (genus Hippocampus) using cross-species amplifiable microsatellites. Fish. Res., 172:318-324.
Nair A, Gopalan S V, George S, Kumar K S, Teacher A G F, Merilä J. 2012. High cryptic diversity of endemic Indirana frogs in the Western Ghats biodiversity hotspot. Anim.Conserv., 15(5):489-498.
Narum S R. 2006. Beyond bonferroni:less conservative analyses for conservation genetics. Conserv. Genet., 7(5):783-787.
Peng W, Bao Z M, Du H X, Yan J J, Zhang L L, Hu J J. 2012.Development and characterization of 70 novel microsatellite markers for the sea cucumber (Apostichopus japonicus). Genet. Mol. Res., 11(1):434-439.
Primmer C R, Painter J N, Koskinen M T, Palo J U, Merilä J. 2005. Factors affecting avian cross-species microsatellite amplification. J. Avian Biol., 36(4):348-360.
Serapion J, Kucuktas H, Feng J N, Liu Z J. 2004. Bioinformatic mining of type I microsatellites from expressed sequence tags of channel catfish (Ictalurus punctatus). Mar.Biotechnol., 6(4):364-377.
Shangguan J B, Li Z B, Ning Y F, Huang Y S, Yuan Y, Lu J, Li B B, Mao X Q. 2014a. Screening and characterization of novel polymorphic microsatellite markers from sea cucumber Holothuria leucospilota. Genet. Mol. Res., 14(2):6 555-6 560.
Shangguan J B, Li Z B, Yuan Y, Huang Y S. 2014b. Identification and characterization of microsatellite markers from the tropical sea cucumber, Stichopus horrens (Selenka). Genet. Mol. Res., 14(4):13 582-13 587.
Shikano T, Ramadevi J, Shimada Y, Merilä J. 2010. Utility of sequenced genomes for microsatellite marker development in non-model organisms:a case study of functionally important genes in nine-spined sticklebacks (Pungitius pungitius). BMC Genomics, 11(1):334.
Soldati M C, Inza M V, Fornes L, Zelener N. 2014. Cross transferability of SSR markers to endangered Cedrela species that grow in Argentinean subtropical forests, as a valuable tool for population genetic studies. Biochem.Syst. Ecol., 53(8):8-16.
Taiyeb-Ali T B, Zainuddin S L, Swaminathan D, Yaacob H. 2003. Efficacy of ‘Gamadent’ toothpaste on the healing of gingival tissues:a preliminary report. J. Oral Sci., 45(3):153-159.
Tautz D. 1989. Hypervariabflity of simple sequences as a general source for polymorphic DNA markers. Nucleic Acids Res., 17(16):6 463-6 471.
Tian C Y, Li Q, Liang Y. 2008. Healthy Aquaculture Techniques of the Sea Cucumber Apostichopus japonicus. Ocean University of China Press, Qingdao, China. (in Chinese)
van Oosterhout C, Hutchinson W F, Wills D P M, Shipley P. 2004. MICRO-CHECKER:software for identifying and correcting genotyping errors in microsatellite data. Mol.Ecol. Notes, 4(3):535-538.
Varshney R K, Graner A, Sorrells M E. 2005. Genic microsatellite markers in plants:features and applications.Trends Biotechnol., 23(1):48-55.
Vogiatzi E, Hanel R, Dailianis T, Lagnel J, Hassan M, Magoulas A, Tsigenopoulos C S. 2012. Description of microsatellite markers in four mullids based on the development and cross-species amplification of 18 new markers in red mullet (Mullus barbatus). Biochem. Syst.Ecol., 44:279-285.
Xia J J, Ren C H, Yu Z H, Wu X Y, Qian J, Hu C Q. 2016.Complete mitochondrial genome of the sandfish Holothuria scabra (Holothuroidea, Holothuriidae).Mitochondr. DNA Part A, 27(6):4 174-4 175.
Yeh F C, Yang R, Boyle T J, Ye Z, Xiyan J M. 2000. PopGene32, Microsoft Windows-Based freeware for Population. Genetic Analysis. Version 1.32. Molecular Biology and Biotechnology Centre, University of Alberta, Edmonton.
Zane L, Bargelloni L and Patarnello T. 2002. Strategies for microsatellite isolation:a review. Mol. Ecol., 11:1-16.
Zhan A B, Bao Z M, Lu W, Hu X L, Peng W, Wang M L, Hu J J. 2007. Development and characterization of 45 novel microsatellite markers for sea cucumber (Apostichopus japonicus). Mol. Ecol. Notes, 7(6):1 345-1 348.