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    Microsatellite marker development based on next-generation sequencing for the smooth marron (Cherax cainii, Austin) and cross-species amplification in other Cherax species.

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    Author
    Loughnan, SR; Beheregaray, LB; Robinson, NA
    Date
    2015-08-25
    Source Title
    BMC Research Notes
    Publisher
    Springer Science and Business Media LLC
    University of Melbourne Author/s
    Robinson, Nicholas
    Affiliation
    School of BioSciences
    Metadata
    Show full item record
    Document Type
    Journal Article
    Citations
    Loughnan, S. R., Beheregaray, L. B. & Robinson, N. A. (2015). Microsatellite marker development based on next-generation sequencing for the smooth marron (Cherax cainii, Austin) and cross-species amplification in other Cherax species.. BMC Res Notes, 8 (1), pp.370-. https://doi.org/10.1186/s13104-015-1345-z.
    Access Status
    Open Access
    URI
    http://hdl.handle.net/11343/259200
    DOI
    10.1186/s13104-015-1345-z
    Open Access at PMC
    http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4547429
    Abstract
    BACKGROUND: The smooth marron, Cherax cainii is an important freshwater crustacean species for aquaculture and for a local wild fishery. C. tenuimanus, commonly known as the hairy marron is under threat from environmental impacts and genetic introgression from C. cainii that is hampering the survival of wild C. tenuimanus stocks. Marron are endemic to the south-west of Western Australia and C. tenuimanus is restricted to only the Margaret River. RESULTS: To isolate microsatellite sequences, shotgun 454 pyrosequencing was performed resulting in 184,981 DNA sequence reads. Following screening for microsatellites, 8799 putative microsatellite loci were detected and PCR primers were designed for 968 of these. Ten microsatellite loci were screened in 30 captive C. cainii individuals with eight loci producing unambiguous results. The average number of alleles per locus was 4.7 and average H e was 0.474. Following an analysis of relatedness, 79% of captive dyads were assigned as unrelated. Utilising C. quadricarinatus and C. destructor, cross-species amplification tests were conducted and amplification was achieved at four of the eight loci. CONCLUSIONS: Using next-generation sequencing methods, eight polymorphic microsatellite loci were developed from C. cainii, with potential for cross amplification in other Cherax species. The markers can be utilised for studies of natural genetic stock structure and for monitoring relatedness levels and genetic variation in both wild and captive populations.

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