Skip to main content
Log in

Development of the new microsatellite multiplex PCR panel and genetic variation of farmed snakeskin gourami, Trichopodus pectoralis

  • Published:
Aquaculture International Aims and scope Submit manuscript

Abstract

Genetically distinct populations have been used to found genetically diverse base populations, which are a prerequisite for successful selective breeding programs. Genetic markers are very useful in this regard as a tool for characterization of genetic diversity. In the present study, a panel of eight multiplex microsatellite primers was developed and seven of them were used to assess genetic diversity of farmed snakeskin gourami, which have been domesticated for more than 30 years. The microsatellites developed showed number of alleles per locus (A) of 3 to 22 alleles, expected heterozygosity (He) range of 0.328–0.923, and Polymorphic Information Content (PIC) range of 0.227–0.915. Four farmed populations of snakeskin gourami (n = 50 fish/population) possessed moderate genetic diversity (FST = 0.056; pairwise FST = − 0.047–0.041; genetic distance = 0.034–0.087), with all but one population pair significantly different as revealed by pairwise FST. Population structuring assigned the studied populations to two clusters. Genetic variation within populations was characterized, with average number of alleles/locus of 6.7–8.0 and expected heterozygosity of 0.65–0.68. Effective population size ranged from 13.2 to 37.7. Our study was the first to report a multiplex microsatellite panel for snakeskin gourami, and it showed genetic distinction among farmed stocks of this species.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Fig. 1
Fig. 2
Fig. 3

Similar content being viewed by others

References

  • Aho T, Ronn J, Piironen J, Bjorklund M (2006) Impact of effective population size on genetic diversity in hatchery reared brown trout (Salmo trutta L) population. Aquaculture 253:244–248

    Article  Google Scholar 

  • Abebe AS, Mikko S, Johansson AM (2015) Genetic diversity of five local Swedish chicken breeds detected by microsatellite markers. PLoS One 10(4):e0120580. https://doi.org/10.1371/journal.pone.0120580

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Allendorf FW, Luikart G (2007) Conservation and the genetics of populations. Blackwell, London

    Google Scholar 

  • Allendorf FW, Phelps SR (1980) Loss of genetic variation in a hatchery stock of cutthroat trout. Trans Am Fish Soc 109:537–543

    Article  Google Scholar 

  • Ariede RB, Freitas MV, Hata ME, Matrochirico-Filho VA, Utsunomia R, Mendonça FF, Foresti F, Porto-Foresti F, Hashimoto DT (2018) Development of microsatellite markers using next-generation sequencing for the fish Colossoma macropomum. Mol Biol Rep 45:9–18

    Article  CAS  PubMed  Google Scholar 

  • Argue BJ, Arce SM, Lotz JM, Moss SM (2002) Selective breeding of Pacific white shrimp (Litopenaeus vannamei) for growth and resistance to Taura Syndrome Virus. Aquaculture 204:447–460

    Article  Google Scholar 

  • Bentsen HB, Eknath AE, Palada-de Vera M, Danting JC, Bolivar HL, Rye RA, Dionisio EE, Longalong FM, Circa AV, Tayamen MM, Gjerd B (1998) Genetic improvement of farmed tilapias: growth performance in a complete diallel cross experiment with eight strains of Oreochromis niloticus. Aquaculture 160:145–173

    Article  Google Scholar 

  • Botstein D, White RL, Skolnick M, Davis RW (1980) Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am J Hum Genet 32:314–331

    CAS  PubMed  PubMed Central  Google Scholar 

  • Cavalli-Sforza LL, Edwards AW (1967) Phylogenetic analysis: models and estimation procedures. Evolution 21:550–570

    Article  CAS  PubMed  Google Scholar 

  • Chatchaiphan S, Thaithungchin C, Koonawootrittriron S, Na-Nakorn U (2019) Responses to mass selection in a domesticated population of snakeskin gourami, Trichopodus pectoralis, Regan 1910, and confounding effects from stocking densities. Aquaculture 498:181–186

    Article  Google Scholar 

  • Chistiakov DA, Hellemans B, Volckaert FAM (2006) Microsatellites and their genomic distribution, evolution, function and applications: a review with special reference to fish genetics. Aquaculture 255:1–29

    Article  CAS  Google Scholar 

  • Gonçalves RA, Santos CHA, Leitão CSS, Souza EMS, Almeida-Val VMF (2018) Genetic basis of Colossoma macropomum broodstock: perspectives for an improvement program. J World Aquacult Soc. https://doi.org/10.1111/jwas.12564

    Article  Google Scholar 

  • Coughlan J, Imsland AK, Galvin PT, Fitzgerals RD, Noevdal G, Cross TF (1998) Microsatellite DNA variation in wild populations and farmed strains of turbot from Ireland and Norway: a preliminary study. J Fish Biol 52:916–922

    Article  CAS  Google Scholar 

  • Cunningham EP, Dooley JJ, Splan RK, Bradley DG (2001) Microsatellite diversity, pedigree relatedness and the contribution of founder lineages to thoroughbred horses. Anim Genet 32:360–364

    Article  CAS  PubMed  Google Scholar 

  • DeWoody JA, Avise JC (2000) Microsatellite variation in marine, freshwater and anadromous fishes compared with other animals. J Fish Biol 56:461–473

    Article  CAS  Google Scholar 

  • Do C, Waples RS, Peel D, Macbeth GM, Tillet BJ, Ovenden JR (2014) NeEstimator V2: re-implementation of software for the estimation of contemporary effective population size (Ne) from genetic data. Mol Ecol Resour 14(1):209–214. https://doi.org/10.1111/1755-0998.12157

    Article  CAS  PubMed  Google Scholar 

  • Earl DA (2012) Structure Harvester v0.6.93. Available at http://users.soe.ucsc.edu/~dearl/software/struct_harvest/ Accessed 1 October 2019.

  • Edwards KJ, Barker JHA, Daly A, Jones C, Karp A (1996) Microsatellite libraries enriched for several microsatellite sequences in plants. Biotechniques 20:758–760

    Article  CAS  PubMed  Google Scholar 

  • Edwards YJK, Elgar G, Clark MS, Bishop MJ (1998) The identification and characterization of microsatellites in the compact genome of the Japanese pufferfish, Fugu rubripes: perspectives in functional and comparative genomic analyses. J Mol Biol 278:843–854

    Article  CAS  PubMed  Google Scholar 

  • Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 14:2611–2620

    Article  CAS  PubMed  Google Scholar 

  • Excoffier L, Laval G, Schneider S (2006) Arlequin ver 3.1 An integrated software package for population genetics data analysis. Computational and molecular population genetic lab, University of Bern, Bern, Switzerland.

  • Falconer DS, Mackay TFC (eds) (1996) Introduction to quantitative genetics (4th ed). Pearson, Essex

    Google Scholar 

  • Felsenstein J (2005) PHYLIP (Phylogeny Inference Package) version 3.65. http://evolution.genetics.washington.edu/phylip.html. Cited 5 Jan 2019

  • Food and Agriculture Organization of the United States (2019) FishStatJ software for fishery statistical time series. http://www.fao.org/fishery. Cited 5 Jan 2019

  • Frankham R, Gilligan DM, Morris DR, Briscoe DA (2001) Inbreeding and extinction: effects of purging. Conserv Genet 2:279–284

    Article  Google Scholar 

  • Froese R, Pauly D (2018) FishBase World Wide Web electronic publication. http://www.fishbase.org. Cited 6 Jun 2018

  • Garza JC, Freimer B (1996) Homoplasy for size at microsatellite loci in humans and chimpanzees. Genome Res 6:211–217

    Article  CAS  PubMed  Google Scholar 

  • Gjedrem T, Gjøen HM, Gjerde B (1991) Genetic origin of Norwegian farmed Atlantic salmon. Aquaculture 98:41–50

    Article  Google Scholar 

  • Govindaraj M, Vetriventhan M, Srinivasan M (2015) Importance of genetic diversity assessment in crop plants and its recent advances: an overview of its analytical perspectives. Genet Res Int. https://doi.org/10.1155/2015/431487

    Article  Google Scholar 

  • Goudet J (1995) FSTAT (Version 1.2): a computer program to calculate F-statistics. J Hered 86:485–486

    Article  Google Scholar 

  • Gregory TR (2019) Animal genome size database. http://www.genomesize.com. Cited 5 Dec 2018

  • Guo SW, Thompson EA (1992) Performing the exact test of Hardy–Weinberg proportions for multiple alleles. Biometrics 48:361–372

    Article  CAS  PubMed  Google Scholar 

  • Guo L, Zhang N, Yang JW, Guo HY, Zhu KC, Liu BS, Liu TT, Zhang DC (2018) Comprehensive assessment of the genetic diversity and population structure of cultured populations of golden pompano, Trachinotus ovatus (Linnaeus, 1758), by microsatellites. Aquac Int 26(6):1445–1457

    Article  Google Scholar 

  • Hochberg Y (1988) A sharper Bonferroni procedure for multiple tests of significance. Biometrika 75:800–802

    Article  Google Scholar 

  • Hubisz M, Falush D, Stephens M, Pritchard JK (2009) Inferring weak population structure with the assistance of sample group information. Mol Ecol Resour 9:1322–1332

    Article  PubMed  PubMed Central  Google Scholar 

  • Indrambarya B (1980) Pla Salid. In: A Lecture at the Royal Society Available via DIALOG. http://ag-ebook.lib.ku.ac.th/ebooks/2011/2011-002-0147/index.html. Cited 21 Dec 2018

  • Indrambarya B (1983) Pla Salid. In: A Lecture at the Royal Society Available via DIALOG. http://ag-ebook.lib.ku.ac.th/ebooks/2011/2011-002-0147/index.html. Cited 21 Dec 2018

  • 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

    Article  PubMed  Google Scholar 

  • Koolboon U, Koonawootrittriron S, Kamolrat W, Na-Nakorn U (2014) Effects of parental strains and heterosis of the hybrid between Clarias macrocephalus and Clarias gariepinus. Aquaculture 424–425:131–139

    Article  Google Scholar 

  • Koressaar T, Remm M (2007) Enhancements and modifications of primer design program. Primer3 Bioinformatics 23(10):1289–1291

    Article  CAS  PubMed  Google Scholar 

  • Kohlmann K, Kersten P, Flajshans M (2005) Microsatellite-based genetic variability and differentiation of domesticated, wild and feral common carp (Cyprinus carpio L.) populations. Aquaculture 247:253–266

    Article  CAS  Google Scholar 

  • Liu ZJ, Cordes FJ (2004) DNA marker technology and their applications in aquaculture genetics. Aquaculture 238:1–37

    Article  CAS  Google Scholar 

  • Na-Nakorn U, Yashiro R, Wachirachaikarn A, Pansaen N (2010) Novel microsatellites for multiplex PCRs of the Humpback grouper, Cromileptes altivelis (Valenciennes, 1828), and application for broodstock management. Aquaculture 306:57–62

    Article  CAS  Google Scholar 

  • Oosterhout CV, Hutchinson WF, Wills DPM, Shipley P (2004) MICRO-CHECKER: software for identifying and correcting genotyping errors in microsatellite data. Mol Ecol Notes 4:535–538

    Article  CAS  Google Scholar 

  • Pathak A, Singh RK, Mohindra V, Lal KK, Barman AS, Jena JK (2018) Development and characterization of novel microsatellite markers in great snakehead, Channa marulia (Hamilton, 1822). Meta Gene 18:143–148

    Article  Google Scholar 

  • Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959

    CAS  PubMed  PubMed Central  Google Scholar 

  • Raymond M, Rousset F (1995) An exact test for population differentiation. Evolution 49:1280–1283

    Article  PubMed  Google Scholar 

  • Reed DH, Frankham R (2001) How closely correlated are molecular and quantitative measures of genetic variation? A meta-analysis. Evolution 55(6):1095–1103

    Article  CAS  PubMed  Google Scholar 

  • Rice WR (1989) Analyzing tables of statistical tests. Evolution 43:223–225

    Article  PubMed  Google Scholar 

  • Rueda EC, Sommer J, Scarabotti P, Markariani R, Ortí G (2011) Isolation and characterization of polymorphic microsatellite loci in the migratory freshwater fish Prochilodus lineatus (Characiformes: Prochilodontidae). Conserv Genet Resour 3:681–684

    Article  Google Scholar 

  • Sahu BP, Shoo L, Joshi CG, Mohanty P, Sundaray JK, Jayasankar P, Das P (2014) Isolation and characterization of polymorphic microsatellite loci in Indian major carp, Catla catla using next-generation sequencing platform. Biochem Syst Ecol 57:357–362

    Article  CAS  Google Scholar 

  • Sekino M, Hara M, Taniguchi N (2002) Loss of microsatellite and mitochondrial DNA variabilities in hatchery strains of Japanese flounder Paralichthys olivaceus. Aquaculture 213:101–122

    Article  CAS  Google Scholar 

  • Serapion J, Kucuktas H, Feng J, Liu Z (2004) Bioinformatic mining of type I microsatellites from expressed sequence tags of channel catfish (Ictalurus punctatus). Mar Biotechnol 6:364–377

    Article  CAS  Google Scholar 

  • Sonesson AK, Woolliams JA, Meuwissen THE (2005) 6. Kinship, relationship and inbreeding. In: Gjedrem T (ed) Selection and breeding programs in aquaculture. Springer, Dordrecht, pp 73–87

    Chapter  Google Scholar 

  • Sutthakiet O, Koonawootrittriron S, Chatchaiphan S, Thaitungchin C, Na-Nakorn U (2019) Genetic parameters of a snakeskin gourami (Trichopodus pectoralis, Regan 1910) base population created from crossing three hatchery stocks. Aquaculture. https://doi.org/10.1016/j.aquaculture.2019.734358

    Article  CAS  Google Scholar 

  • Taggart JB, Hynes RA, Prodöhl PA, Ferguson A (1992) A simplified protocol for routine total DNA isolation from salmonid fishes. J Fish Biol 40:963–965

    Article  CAS  Google Scholar 

  • Tomljanović T, Treer T, Ćubrić VČ, Safne T, Šprem N, Piria M, Matulić D, Safner R, Aničić I (2013) Microsatellite-based genetic variability and differentiation of hatchery and feral common carp Cyprinus Carpio L. (Cyprinidae, Cypriniformes) populations in Croatia. Arch Biol Sci 65(2):577–584

    Article  Google Scholar 

  • Untergasser A, Cutcutache I, Koressaar T, Ye J, Faircloth BC, Remm M, Rozen SG (2012) Primer3–new capabilities and interfaces. Nucleic Acids Res 40(15):e115. https://doi.org/10.1093/nar/gks596

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Vandeputte M, Haffray P (2014) Parentage assignment with genomic markers: a major advance for understanding and exploitating genetic variation of quantitative traits in farmed aquatic animals. Front Genet 5(432):1–8. https://doi.org/10.3389/fgene.2014.00432

    Article  CAS  Google Scholar 

  • Wachirachaikarn A, Na-Nakorn N (2019) Genetic diversity of the North African catfish hatchery stocks in Thailand. ScienceAsia 45:301–308

    Article  Google Scholar 

  • Wachirachaikarn A, Rungsin W, Srisapoome P, Na-Nakorn U (2009) Crossing of African catfish (Clarias gariepinus) strains based on strain selection using genetic diversity data. Aquaculture 290:53–60

    Article  Google Scholar 

  • Wachirachaikarn A, Prakoon W, Nguyen TTT, Prompakdee W, Na-Nakorn U (2011) Loss of genetic variation of Phalacronotus bleekeri (Günther, 1864) in the hatchery stocks revealed by newly developed microsatellites. Aquaculture 321:298–302

    Article  Google Scholar 

  • Wright S (1978) Variability Within and Among Natural Populations. In: Evolution and the genetics of population, 4th edn. University of Chicago Press, Chicago, p 590

    Google Scholar 

  • Yeh FC, Yang RC, Boyle T (1999) POPGENE Version1.31 Microsoft Window-Based software for population genetics analysis. http://www.ualberta.ca/~fyeh/index.htm. Cited 1 December 2019

  • Zhu F, Zhang L-J, Yin S-W, Zhang H-W, Hou X-Y, Hu Y-L, Luo J (2014) Genetic diversity and variation in wild populations of dark sleeper (Odontobutis potamophila) in China inferred with microsatellite markers. Biochem Syst Ecol 57:40–47

    Article  CAS  Google Scholar 

Download references

Funding

This work was supported by Thailand Research Fund and Betagro Science Center Co. Ltd. (Contract No. DPG5980003; Distinguished Research Professor TRF FY 2016) awarded to UN.

We thank the following people: the farm owners for allowing us to collect fin-clipped samples of snakeskin gourami; Assist. Prof. Chareerat Mongkolsiriwatana, Research Unit of Genetic Technology and Applications, Department of Science, Faculty of Liberal Arts and Science for providing AW with facilities to conduct all microsatellite works; Mr.Chatchai Thaithungchin for his assistance in sample collection; and Mr. David John Anderson who provided English editing of the manuscript. Finally, we expressed the sincere thanks to the anonymous referees for their invaluable comments that significantly improved our manuscript.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Uthairat Na-Nakorn.

Ethics declarations

Conflict of Interest

The authors declare that they have no conflict of interest.

Ethical approval

All of the protocols were approved by the Kasetsart University Animal Ethics Committee -ID ACKU 61-FIS-004.

Additional information

Publisher’s note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Wachirachaikarn, A., Sutthakiet, O., Senanan, W. et al. Development of the new microsatellite multiplex PCR panel and genetic variation of farmed snakeskin gourami, Trichopodus pectoralis. Aquacult Int 28, 751–765 (2020). https://doi.org/10.1007/s10499-019-00492-1

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10499-019-00492-1

Keywords

Navigation