A method for estimating and comparing population genetic variation using random amplified polymorphic DNA (RAPD) profiling is presented. An analysis of molecular variance (AMOVA) is extended to accomodate phenotypic molecular data in diploid populations in Hardy-Weinberg equilibrium or with an assumed degree of selfing. We present a two step strategy: 1) Estimate RAPD site frequencies without preliminary assumptions on the unknown population structure, then perform significance testing for population substructuring.2) If population structure is evident from the first step, use this data to calculate better estimates for RAPD site frequencies and sub-population variance components. A nonparametric test for the homogeneity of molecular variance (HOMOVA) is also presented. This test was designed to statistically test for differences in intrapopulational molecular variances (heteroscedasticity among populations). These theoretical developments are applied to a RAPD data set in Vucciniwn mucrocurpon (American cranberry) using small sample sizes. where a gradient of molecular diversity is found between central and marginal populations.The AMOVA and HOMOVA methods provide flexible population analysis tools when using data from RAPD or other DNA methods that provide many polymorphic markers with or without direct allelic data.

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The green fluorescent protein (GFP) from the jellyfish Aequorea victoria has proven to be a powerful tool in plant genetic transformation studies. This paper reviews the history and the progression of the expression of GFP variants in transgenic plants. The distinguishing features of the most useful GFPs, such as those including the S65T chromophore mutation and those with dual excitation peaks, are discussed. The review also focuses on the utility of GFP as a visual selectable marker in aiding the plant transformation process; GFP has been more important in monocot transformation compared with dicot transformation. Finally, the potential utility of new fluorescent proteins is speculated upon.

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