Molecular and Analytical Methodological Development
With the advent of second generation sequencing machines, marker development for non-model species has become significantly more achievable. Of all the second generation sequencing approaches, the GS-FLX Roche (454 Life Sciences, Branford, CT, USA) initially holds the most promise due to the larger average fragment size that can be obtained as compared with its competitors.
Mike Gardner (michael.gardner@flinders.edu.au) is coordinating projects on this sequencing platform for the development of microsatellite and anonymous nuclear markers. We are also investigating other potential uses for this technology.
Relevant publications:
Gardner MG, Fitch AJ, Bertozzi T, Lowe AJ (2011) Rise of the machines - recommendations for ecologists when using second generation sequencing for microsatellite development. Molecular Ecology Resources. Published online, doi: 10.1111/j.1755-0998.2011.03037.x
Lowe AJ, Harris SA, Ashton P (2004) Ecological Genetics: Design, Analysis and Application. Blackwells, Oxford. 326 pp. Received highly complimentary reviews in Trends in Ecology and Evolution (Dhondt AA, 2004, 19: 292-293), Heredity, Annals of Botany.
Cavers S, Degen B, Caron H, Hardy O, Lemes M, Gribel R, Margis R, Salgueiro F, Lowe AJ (2005) Optimal sampling strategy for estimation of spatial genetic structure in tree populations. Heredity 95: 281-289.
Kremer A, Caron H, Cavers S, Colpaert N, Gheysen L, Gribel R, Lemes M, Lowe A, Margis R, Navarro C, Salgueiro F (2005) Monitoring genetic diversity in tropical trees with multilocus dominant markers. Heredity 95: 274-280.
Microsatellite and molecular marker development
Wells JA, Gardner MG, Lowe AJ (2007) Development of eight polymorphic microsatellites for an Australasian rainforest tree species, Cryptocarya mackinnoniana (Lauraceae). Molecular Ecology Notes 7: 981-983.
Lowe AJ, Moule C, Trick M, Edwards KJ (2004) Efficient large-scale development of microsatellites for marker and mapping applications in Brassica crop species. Theoretical and Applied Genetics. 108: 1103-1112.
Squirrell J, Hollingsworth PM, Woodhead M, Russell J, Lowe AJ, Gibby M, Powell W (2003) How much effort is required to isolate nuclear microsatellites from plants? Molecular Ecology 12: 1339-1348.
Lowe AJ, Russell JR, Powell W, Dawson IK (1998) Identification and characterization of nuclear, cleaved amplified polymorphic sequences (CAPS) loci in Irvingia gabonensis and I. wombolu, indigenous fruit trees of west and central Africa. Molecular Ecology. 7: 1771-1788.
