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Genemapper
Genemapper Fragment Analysis provides genotyping by microsatellite analysis, AFLPs and loss of heterogeneity. The 5-color system allows the researcher to use 4 fluorescent-labeled primers to multiplex several genomes in the same well. At minimum, 4 genotypes can be determined per sample in less than an hour for about $120 (96 samples in a 96-well plate). Multiplexing different products with the same color can double or even quadruple the number of genotypes per sample (due to resolution of different-sized products with one base resolution).
Here are some examples of how Genemapper Fragment Analysis can be used.
Identifying populations
In the McPheron lab, microsatellite markers are being used to identify populations of Anastrepha obliqua (Diptera: Tephritidae) which is a pest of mango and citrus as well as other fruits. Its geographic range stretches from the southern tier states of the United States down to Brazil and includes the islands in the Caribbean. Current strategies for controlling this pest include conventional as well as sterile insect technique. This study looks at population-level variation as a function of spatial, temporal, and host-association. Genotyping through fragment analysis data is being used to show that population structure is thus due to host association and spatial attributes.
Investigating population structure
Iliana Baum's lab uses newly-developed tri- and tetra- nucleotide repeat microsatellite markers to investigate population structure in Caribbean Elkhorn Coral (Acropora palmata) and Pacific Lobe Coral (Porites lobata). Research focuses on the development and application of molecular tools to understand the influence of biogeography, population structure, and mating patterns on the survival and evolution of corals and other marine organisms. Fluorescent-labeled primers are used in PCR reactions and the labeled products are analyzed using the 3730XL sequencer. Up to four markers are run in a single multiplex reaction, greatly increasing throughput and efficiency. Thus, 384 genotypes can be determined in less than one hour for this project.
Distinguishing between genotypes
Jonathan Lynch's lab is using SSR markers to distinguish between genotypes in common bean multilines. These multilines are made by mixing seeds from multiple genotypes before planting. The bean genotypes are contrasting in root architecture, which affects their adaptation to soil stresses such as low phosphorus and drought. These molecular techniques will allow the study of below-ground competition and reproductive success by analyzing DNA from root and yield samples. The end result will be the determination of which genotypes are associated with better adaptation and reproductive success.