Abstract
Genomic elucidation and mapping of novel organisms requires the generation of large genetic resources. In this study, 253 novel and polymorphic microsatellite loci were isolated and characterized for the saltwater crocodile (Crocodylus porosus) by constructing libraries enriched for microsatellite DNA. All markers were evaluated on animals obtained from Darwin Crocodile Farm in the Northern Territory, Australia, and are intended for future use in the construction of a genetic-linkage map for the saltwater crocodile. The 253 loci yielded an average of 4.12 alleles per locus, and those selected for mapping had an average polymorphic information content (PIC) of 0.425.
This is a preview of subscription content, log in via an institution to check access.
References
Brownstein M, Carpenter J, Smith J (1996) Modulation of non-templated nucleotide addition by Taq polymerase: primer modifications that facilitate genotyping. BioTechniques 20:1004–1010
Davis L, Glenn T, Strickland D et al (2002) Microsatellite DNA analyses support an east-west phylogeographic split of American alligator populations. J Exp Zool (Mol Dev Evol) 294:352–372
Dessauer H, Glenn T, Densmore L (2002) Studies on the molecular evolution of the Crocodylia: footprints in the sands of time. J Exp Zool (Mol Dev Evol) 294:302–311
Dever J, Densmore L (2001) Microsatellites in Moreleti’s crocodile (Crocodylus moreletti) and their utility in addressing crocodilian population genetics. J Herpetol 35:541–544
Dever J, Strauss R, Rainwater T et al (2002) Genetic diversity, population subdivision and gene flow in wild populations of Morelet’s crocodile (Crocodylus moreletii) in Belize, Central America. Copeia 2002:1078–1091
Don R, Cox P, Wainwright B, Baker K, Mattick J (1991) ‘Touchdown’ PCR to circumvent spurious priming during gene amplification. Nucleic Acids Res 19:4008
Fitzsimmons N, Tanksley S, Forstner M et al (2001) Microsatellite markers for Crocodylus: new genetic tools for population genetics, mating system studies and forensics. In: Grigg J, Seebacher F, Franlin C (eds) Crocodilian biology and evolution. Surrey Beatty and Sons, Chipping Norton, Australia, pp 51–57
Fitzsimmons N, Buchan J, Lam P et al (2002) Identification of purebred Crocodylus siamensis for reintroduction in Vietnam. J Exp Zool (Mol Dev Evol) 294:373–381
Glenn T, Schable N (2005) Isolating microsatellite DNA loci. In: Zimmer E, Roalson E (eds) Methods in enzymology 395, molecular evolution: producing the biochemical data, part B. Academic Press, San Diego
Glenn T, Stephan W, Dessauer H, Braun M (1996) Allelic diversity in alligator microsatellites loci is negatively correlated with GC content of flanking sequences and evolutionary conservation of PCR amplifiability. Mol Biol Evol 13:1151–1154
Glenn T, Dessauer H, Braun M (1998) Characterisation of microsatellite DNA loci in American Alligators. Copeia 1998:591–601
Isberg S, Chen Y, Barker S, Moran C (2004) Analysis of microsatellites and parentage testing in saltwater crocodiles. J Hered 95(5):445–449
Isberg S, Johnston S, Chen Y, Moran C (2006) First evidence of higher female recombination in a species with temperature-dependent sex determination: the saltwater crocodile. J Hered 97(6):599–602
Kalinowski S, Taper M, Marshall T (2007) Revising how the computer program CERVUS accommodates genotyping error increases success in paternity assignment. Mol Ecol 16:1099–1006
Sambrook J, Fritsch E, Maniatis T (1989) Molecular cloning: a laboratory manual, 2nd edn. Cold Spring Harbor Laboratory Press, USA
Shuelke M (2000) An economic method for fluorescent labeling of PCR fragments. Nat Biotechnol 18:233–234
Verdade L, Zucoloto R, Coutinho L (2002) Microgeographic variation in Caiman latirostris. J Exp Zool (Mol Dev Evol) 294:387–396
Zucoloto R, Verdade L, Coutinho L (2002) Microsatellite DNA Library for Caiman latirostris. J Exp Zool (Mol Dev Evol) 294:346–351
Zucoloto R, Villela P, Verdade L, Coutinho L (2006) Cross-species microsatellite amplification in South American Caimans (Caiman spp and Paleosuchus palpebrosus). Genet Mol Biol 29(1):75–79
Acknowledgements
This research was supported by Rural Industries Research and Development Corporation grant US-139A to the University of Sydney, and US Department of Energy award DE-FC09-07SR22506 to the University of Georgia. All research took place at the University of Sydney, Australia, and the Savannah River Ecology Laboratory (SREL), of the University of Georgia, USA. Tissue samples were provided by Darwin Crocodile Farm, NT, Australia. Capture, handling and blood sampling of crocodiles was approved by Australian Animal Ethic Committee, permit No. N00/8-2005/3/4177.
Disclaimer
This report was prepared as an account of work sponsored by an agency of the United States Government. Neither the United States Government nor any agency thereof, nor any of their employees, makes any warranty, express or implied, or assumes any legal liability or responsibility for the accuracy, completeness, or usefulness of any information, apparatus, product, or process disclosed, or represents that its use would not infringe privately owned rights. Reference herein to any specific commercial product, process, or service by trade name, trademark, manufacturer, or otherwise does not necessarily constitute or imply its endorsement, recommendation, or favoring by the United States Government or any agency thereof. The views and opinions of authors expressed herein do not necessarily state or reflect those of the United States Government or any agency thereof.
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Miles, L.G., Isberg, S.R., Moran, C. et al. 253 Novel polymorphic microsatellites for the saltwater crocodile (Crocodylus porosus). Conserv Genet 10, 963–980 (2009). https://doi.org/10.1007/s10592-008-9600-7
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s10592-008-9600-7