Abstract
Blood clam, Tegillarca granosa, is an important shellfish in Chinese mariculture industry. Investigative research in this species, such as genetic linkage mapping, requires a large panel of molecular markers. In present study, a total of 89 polymorphic microsatellite markers were developed in T. granosa using the sequence database of Life Sciences Technology 454 next generation sequencing technology. All 89 loci were characterized in 20 individual clams from a natural population inhabiting Yueqing Gulf, Zhejiang Province, China. The number of alleles per polymorphic locus varied between 2 and 15, while the observed heterozygosity, expected heterozygosity and polymorphic information content varied between 0.000 and 1.000, 0.102 and 0.921, and 0.048 and 0.886, respectively. Of the 89 loci identified, 32 loci deviated significantly from Hardy-Weinberg equilibrium following Bonferroni correction. Thirty nine markers, which were shown to be polymorphic in a full-sibling family, were tested in Mendelian segregations. As expected, 32 loci were co-dominantly segregated in a Mendelian fashion. These novel developed microsatellite markers represent useful research tools for investigation of population genetic structure and genetic diversity in this species.
Article PDF
Similar content being viewed by others
Avoid common mistakes on your manuscript.
References
Abdelkrim, J., Robertson, B. C., Stanton, J. L., and Gemmell, N. J., 2009. Fast, cost-effective development of species-specific microsatellite markers by genomic sequencing. Biotechniques, 46 (3): 185–192.
Bowman, J. S., Rasmussen, S., Blom, N., Deming, J. W., and Rysgaard, S., 2012. Microbial community structure of Arctic multiyear sea ice and surface seawater by 454 sequencing of the 16S RNA gene. The ISME Journal, 6: 11–20.
Broom, M. J., 1983. Gonad development and spawning in Anadara granosa (L.) (Bivalvia: Arcidae). Aquaculture, 30: 211–219.
Castoe, T. A., Polle, A. W., Gu, W., de Koning, A. P. J., Daza, J. M., Smith, E. N., and Pollock, D. D., 2010. Rapid identification of thousands of copperhead snake (Agkistrodon contortrix) microsatellite loci from modest amounts of 454 shotgun genome sequence. Molecular Ecology Resources, 10: 341–347.
Dong, Y. H., Wu, G. X., Yao, H. H., Bian, P. J., Zhao, D. M., and Lin, Z. H., 2013. Characterization of 34 polymorphic EST-SSR markers in Tegillarca granosa and their transferability in Anadara craticulata. Journal of Fisheries of China, 37: 70–77.
Dong, Y. H., Yao, H. H., Lin, Z. H., Zhang, L. L., and Bao, Z. M., 2012. Characterization of 62 polymorphic EST-SSR markers in the blood clam (Tegillarca granosa) and their cross-amplification in Scapharca subcrenata. Conservation Genetic Resources, 4: 991–997.
Gu, X. Y., Zeng, Q. G., You, Z. J., and Lin, Z. H., 2008. Isolation and characteristics of six microsatellite primers of Tegillarca granosa. Oceanologia et Limnologia Sinica, 39: 661–664.
Hubert, S., and Hedgecock, D., 2004. Linkage maps of microsatellite DNA marker for the Pacific oyster, Crassostrea gigas. Journal of Shellfish Research, 23: 379–385.
Jones, A. G., Stockwell, C. A., Walker, D., and Avise, J. C., 1998. The molecular basis of a microsatellite null allele from the white sands pupfish. Journal of Heredity, 89: 339–342.
Kim, W. J., Jung, H., and Gaffney, P. M., 2011. Development of type I genetic markers from expressed sequence tags in highly polymorphic species. Marine Biotechnology, 13: 127–132.
Li, Q., Park, C., and Kijima, A., 2002. Isolation and characterization of microsatellite loci in the Pacific abalone, Haliotis discus hannai. Journal of Shellfish Research, 21: 811–815.
Li, Q., Wang, Q. Z., Qi, M. J., Ge, J. L., and Cong, R. H., 2011. Development, characterization, and inheritance of 113 novel EST-SSR in the Pacific oyster (Crassostrea gigas). Genes & Genomics, 33: 313–316.
Li, R. H., and Li, Q., 2011. Mating systems and reproductive success in hermaphroditic bay scallop, Argopecten irradians irradians (Lamarck 1819), inferred by microsatellite-based parentage analysis. Journal of the World Aquaculture Society, 42: 888–898.
Liu, B., Teng, S. S., Shao, Y. Q., Chai, X. L., and Xiao, G. Q., 2012. Isolation and characterization of 39 novel polymorphic EST-SSR loci for the blood clam, Tegillarca granosa. Conservation Genetic Resources, 4: 375–378.
Liu, Y. G., Chen, S. L., and Li, B. F., 2004. Assessing the genetic structure of three Japanese flounder (Paralichthys olivaceus) stocks by microsatellite markers. Aquaculture, 243: 103–111.
Macas, J., Neumann, P., and Navratilova, A., 2007. Repetitive DNA in the pea (Pisum sativum L.) genome: Comprehensive characterization using 454 sequencing and comparison to soybean and Medicago truncatula. BMC Genomics, 8: 427.
Muchero, W., Ehlers, J. D., Close, T. J., and Roberts, P. A., 2011. Genic SNP markers and legume synteny reveal candidate genes underlying QTL for Macrophomina phaseolina resistance and maturity in cowpea (Vigna unguivulata (L) Walp). BMC Genomics, 12: 8.
Rahmann, S., Beygo, J., Kanber, D., Martin, M., Horsthemke, B., and Buiting, K., 2013. Amplikyzer: Automated methylation analysis of amplicons from bisulfite flowgram sequencing. Peer J Preprints, http://peedj.com/preprints/122v2.
Reece, K. S., Ribeiro, W. L., Gaffney, P. M., Carnegie, R. B., and Allen, S. K., 2004. Microsatellite marker development and analysis in the eastern oyster (Crassostrea virginica): Confirmation of null alleles and non-Mendenlian segregation ratios. Journal of Heredity, 95: 346–352.
Rice, W. R., 1989. Analyzing tables of statistical tests. Evolution, 43 (1): 223–225.
Shi, S. F., Yao, H. H., Lin, Z. H., Zhou, X. L., Qi, X. Y., and Dong, Y. H., 2013. Characterization and analysis of 24 polymorphic EST-SSR loci in Tegillarca granosa. Marine Sciences, 37 (8): 42–46.
Sithichoke, T., Prakit, S., pichahpuk, U., Juntima, C., Duangjai, S., Worapa, S., Warunee, S., Somvong, T., and Peerasak, S., 2009. Characterization of microsatellites and gene contents from genome shotgun sequences of mungbean (Vigna radiate (L.) Wilczek). BMC Plant Biology, 9: 137.
Wang, H. X., Huan, P., Lu, X., and Liu, B. Z., 2011. Mining of EST-SSR markers in clam Meretrix meretrix larvae from 454 shotgun transcriptome. Genes & Genetic Systems, 86: 197–205.
Wang, R. C., Wang, Z. P., and Zhang, J., 2008. Science of Marine Shellfish Culture. Ocean University of China Press, Qingdao, 337–339 (in Chinese).
Wicker, T., Schlagenhauf, E., Graner, A., Close, T. J., Keller, B., and Stein, N., 2006. 454 sequencing put to the test using the complex genome of barley. BMC Genomics, 7: 275.
Xiong, G., Ma, X., Wang, X. Q., Zeng, Z. N., Zhu, D. L., Kang, L., and Wu, Q. S., 2015. Development and characterization of 18 microsatellite markers for the Babylonia lutosa. Conservation Genetic Resources, 7: 471–472.
Zhou, X. L., Zhu, J. H., Dong, Y. H., Lin, Z. H., Fu, K. L., Yao, H. H., and Qi, X. Y., 2013. Development and comparative study of genomic-SSR and EST-SSR in Tegillarca granosa. Oceanologia et Limnologia Sinica, 44 (2): 467–475.
Acknowledgements
The study was supported by the National High Technology Research and Development Program of China (863 Program) (No. 2012AA10A410), the National Project for Agricultural Technology System (No. CARS-48), National Infrastructure of Fishery Germplasm Resources of China (No. 2015DKA30470), and Zhejiang Major Program of Science and Technology (No. 2012C12907-4).
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Teng, S., Fang, J., Cai, Y. et al. Development and validation of 89 novel expressed sequence tag-derived microsatellite markers in blood clam, Tegillarca granosa . J. Ocean Univ. China 16, 509–516 (2017). https://doi.org/10.1007/s11802-017-3260-5
Received:
Revised:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s11802-017-3260-5