Abstract
Background
The blood clam Barbatia virescens is an ecologically and economically important species in the southern coast of China. Understanding of the genetic structure of B. virescens populations is vital to breeding strategies and conservation programs.
Objective
To develop and characterize a set of microsatellites loci primers for B. virescens, and provide helpful information for reasonable utilization and protection of B. virescens natural resources.
Methods
The microsatellites of B. virescens were detected using a RAD-seq approach based on an Illumina sequencing platform. For the test of microsatellite development, we calculated the number of alleles (Na), observed heterozygosities (Ho), expected heterozygosities (He) and exact tests for deviations from Hardy–Weinberg equilibrium (HWE). Twelve polymorphic loci were used to access the genetic diversity and population structure of four B. virescens populations.
Results
In this study, 50,729 microsatellites of B. virescens were detected. Twenty-two polymorphic microsatellite loci were developed for B. virescens. The number of alleles per locus ranged from 6 to 15, and expected heterozygosities varied from 0. 567 to 0.911. All the PIC values of the 22 loci were greater than 0.5, indicating that these markers were highly informative for further genetic analysis. Twelve loci were selected to analyze genetic diversity and population structure of four B. virescens populations collected from different geographical regions along the southern coast of China. The results showed moderate to high levels of genetic diversity in the four populations (mean Ar = 7.756–8.133; mean Ho = 0.575–0.639; mean He = 0.754–0.775). Pairwise FST estimates indicated that there was significant divergence among the four populations.
Conclusion
This study not only provides a large scale of sequence information of microsatellites which are valuable for future genetic mapping, trait association and kinship among B. virescens, but also offers useful information for the sustainable management of natural stocks and the development of breeding industry of B. virescens.
Similar content being viewed by others
References
Astanei I, Gosling E, Wilson JIM, Powell E (2005) Genetic variability and phylogeography of the invasive zebra mussel, Dreissena polymorpha (Pallas). Mol Ecol 14:1655–1666
Baus E, Darrock DJ, Bruford MW (2005) Gene-flow patterns in Atlantic and Mediterranean populations of the Lusitanian sea star Asterina gibbosa. Mol Ecol 14:3373–3382
Berman M, Austin CM, Miller AD (2014) Characterisation of the complete mitochondrial genome and 13 microsatellite loci through next-generation sequencing for the New Caledonian spider-ant Leptomyrmex pallens. Mol Biol Rep 41:1179–1187
Bohonak AJ (1999) Dispersal, gene flow, and population structure. Q Rev Biol 74:21–45
Brown JE, Stepien CA (2010) Population genetic history of the dreissenid mussel invasions: expansion patterns across North America. Biol invasions 12:3687–3710
Cao Y, Li Z, Li Q, Chen X, Chen L, Dai G (2012) Development and characterization of microsatellite loci for Fenneropenaeus penicillatus Alcock. Afr J Biotechnol 11:10831–10833
Cassista MC, Hart MW (2007) Spatial and temporal genetic homogeneity in the Arctic surfclam (Mactromeris polynyma). Mar Biol 152:569–579
Cavalli-Sforza LL, Edwards AW (1967) Phylogenetic analysis: models and estimation procedures. Evolution 21:550–570
Cheng X, Xu J, Xia S, Gu J, Yang Y, Fu J, Liu K (2009) Development and genetic mapping of microsatellite markers from genome survey sequences in Brassica napus. Theor Appl Genet 118:1121–1131
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 12:499–510
Dieringer D, Schlötterer C (2003) Microsatellite analyser (MSA): a platform independent analysis tool for large microsatellite data sets. Mol Ecol Resour 3:167–169
Excoffer L, Smouse PE, Quattro JM (1992) Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics 131:479–491
Gao X, Zheng X, Bo Q, Li Q (2016) Population genetics of the common long-armed octopus Octopus minor (Sasaki, 1920) (Cephalopoda: Octopoda) in Chinese waters based on microsatellite analysis. Biochem Syst Ecol 66:129–136
García AA, Oliver G (2008) Species discrimination in seven species of Barbatia (Bivalvia: Arcoidea) from Thailand with a redescription of B. grayana (Dunker, 1858). Raffles B Zool Suppl 18:7–23
Gong F, Zhang N, Guo H, Zhu K, Liu T, Jiang S et al (2016) Development and characterization of 23 polymorphic microsatellite markers for banana shrimp fenneropenaeus merguiensis. Conserv Genet Resour 8:9–11
Goudet J (2001) FSTAT: a program to estimate and test gene diversities and fixation indices.version 2.9.3. http://www2.unil.ch/popgen/softwares/FSTat.htm
György Z, Vouillamoz JF, Ladányi M, Pedryc A (2014) Genetic survey of Rhodiola rosea L. populations from the Swiss Alps based on SSR markers. Biochem Syst Ecol 54:137–143
Hunt A (1993) Effects of contrasting patterns of larval dispersal on the genetic connectedness of local populations of two intertidal starfish Patiriella calcar and P. exigua. MarEcol Prog Ser 92:179–186
Kalinowski ST, Taper ML, Marshall TC (2007) Revising how the computer program CERVUS accommodates genotyping error increases success in paternity assignment. Mol Ecol 16:1099–1106
Kenchington EL, Patwary MU, Zouros E, Bird CJ (2006) Genetic differentiation in relation to marine landscape in a broadcast-spawning bivalve mollusc Placopecten magellanicus). Mol Ecol 15:1781–1796
Launey S, Ledu C, Boudry P, Bonhomme F, Naciri-Graven Y (2002) Geographic structure in the European flat oyster (Ostrea edulis L.) as revealed by microsatellite polymorphism. J Hered 93:331–338
Li Q, Park C, Kijima A (2002) Isolation and characterization of microsatellite loci in the pacific abalone, Haliotis discus hannai. J Shellfish Res 21:811–815
Li S, Li Q, Yu H, Kong L, Liu S (2015) Genetic variation and population structure of the Pacific oyster Crassostrea gigas in the northwestern Pacific inferred from mitochondrial COI sequences. Fish Sci 81:1071
Ma HT, Jia CF, Yang JM, Wang F, Xue R, Han CH, Jiang HB (2015) Development of novel microsatellite markers in the Korean rockfish Sebastes schlegeli. Genet Mol Res 14:5099–5102
Martínez L, Freire R, Arias-Pérez A, Méndez J, Insua A (2015) Patterns of genetic variation across the distribution range of the cockle Cerastoderma edule, inferred from microsatellites and mitochondrial DNA. Mar Biol 162:1393–1406
Morgante M, Hanafey M, Powell W (2002) Microsatellites are preferentially associated with nonrepetitive DNA in plant genomes. Nat Genet 30:194–200
Ni L, Li Q, Kong L (2011) Microsatellites reveal fine-scale genetic structure of the Chinese surf clam Mactra chinensis.Mollusca, Bivalvia, Mactridae) in Northern China. Mar Ecol 32:488–497
Paetkau D (1999) Microsatellites obtained using strand extension: an enrichment protocol. Biotechniques 26:690–697
Peakall ROD, Smouse PE (2006) GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research. Mol Ecol Resour 6:288–295
Rajagopal S, Venugopalan V, Van der Velde G, Jenner H (2006) Greening of the coasts: a review of the Perna viridis success story. Aquat Ecol 40:273–297
Rassmann K, Schlötterer C, Tautz D (1991) Isolation of simple-sequence loci for use in polymerase chain reaction-based DNA fingerprinting. Electrophoresis 12:113–118
Rice WR (1989) Analyzing tables of statistical tests. Evolution 43:223–225
Rousset F (2008) Genepop’007: a complete re-implementation of the genepop software for Windows and Linux. Mol Ecol Resour 8:103–106
Selkoe KA, Toonen RJ (2006) Microsatellites for ecologists: a practical guide to using and evaluating microsatellite markers. Ecol Lett 9:615–629
Sokal RR, Rohlf FJ (1995) Biometry: the Principles and Practice of Statistics in Biological Research, 3rd ed. Freeman, New York
Tautz D (1989) Hypervariability of simple sequences as a general source for polymorphic DNA markers. Nucleic Acids Res 17:6463–6471
Thiel T, Michalek W, Varshney RK, Graner A (2003) Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (hordeum vulgare L). Theor Appl Genet 106:411–422
Tian Z, Zhang F, Liu H, Gao Q, Chen S (2016) Development of SSR markers for a Tibetan medicinal plant, Lancea tibetica (Phrymaceae) based on RAD sequencing. Appl Plant Sci 4:1600076
Van Oosterhout C, Hutchinson WF, Wills DP, Shipley P (2004) MICRO-CHECKER: software for identifying and correcting genotyping errors in microsatellite data. Mol Ecol Resour 4:535–538
Wang Y, Shi Y, Guo X (2009) Identification and characterization of 66 EST-SSR markers in the eastern oyster Crassostrea virginica (Gmelin). J Shellfish Res 28:227–234
Wang B, Xie X, Liu S, Wang X, Pang H, Liu Y (2017a) Development and characterization of novel microsatellite markers for the Common Pheasant (Phasianus colchicus) using RAD-sEq. Avian Res 8:4
Wang W, Ma C, Chen W, Zhang H, Kang W, Ni Y, Ma L (2017b) Population genetic diversity of Chinese sea bass.Lateolabrax maculatus. from southeast coastal regions of China based on mitochondrial COI gene sequences. Biochem Syst Ecol 71:114–120
Weber JL, May PE (1989) Abundant class of human DNA polymorphisms which can be typed using the polymerase chain reaction. J Hum Genet 44:388–396
Xue DX, Wang HY, Zhang T, Liu JX (2014) Population genetic structure and demographic history of Atrina pectinata, based on mitochondrial DNA and microsatellite markers. PLoS ONE 9:95436
Yu H, Li Q (2007) Genetic variation of wild and hatchery populations of the Pacific oyster Crassostrea gigas assessed by microsatellite markers. Mol Genet Genomics 34:1114–1122
Yu H, Gao S, Chen A, Kong L, Li Q (2015) Genetic diversity and population structure of the ark shell Scapharca broughtonii, along the coast of china based on microsatellites. Biochem Syst Ecol 58:235–241
Zhan A, Hu J, Hu X, Zhou Z, Hui M, Wang S, Bao Z (2009) Fine-scale population genetic structure of Zhikong scallop (Chlamys farreri): do local marine currents drive geographical differentiation? Mar Biotechnol 11:223–235
Zhang P, Huang XK, Wang TG, Lin SZ, Zhang LN (2011) Study on the technique of artificial reproduction and nursing of Barbatia virescens. J Shanghai Ocean Univ 6:008 (in Chinese)
Zhao Y, Wang H, Ji X, Yang Y, Zeng Y (2014) Isolation and characterization of 27 novel polymorphic microsatellite markers in oriental river prawn Macrobrachium nipponense. Conserv Genet Resour 6:293–295
Acknowledgements
This study was supported by the grants from Fundamental Research Funds for the Central Universities (201762014), and Industrial Development Project of Qingdao City (17-3-3-64-nsh).
Funding
This study was funded by Fundamental Research Funds for the Central Universities (201762014), and Industrial Development Project of Qingdao City (17-3-3-64-nsh).
Author information
Authors and Affiliations
Corresponding author
Ethics declarations
Conflict of interest
No potential conflict of interest was reported by the authors.
Electronic supplementary material
Below is the link to the electronic supplementary material.
Rights and permissions
About this article
Cite this article
Wang, L., Yu, H. & Li, Q. Development of microsatellite markers and analysis of genetic diversity of Barbatia virescens in the southern coasts of China. Genes Genom 41, 407–416 (2019). https://doi.org/10.1007/s13258-018-0769-y
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s13258-018-0769-y