An Integrated Physical-Genetic Framework In Mimulus, A Model Plant System For Ecological Genomics
Jeffrey Tomkins, Director, Clemson University Genomics Institute, Dept. Genetics & Biochemistry
24 Mar 2006
Plants in the genus Mimulus have served as model system for ecological and evolutionary studies for over 50 years. Genomic regions contributing to reproductive barriers and adaptive differences between species have been identified by QTL mapping in two different groups of Mimulus species. Further progress on understanding the molecular genetic basis of adaptation and speciation requires the development of comparative genomic tools for these species. High information content fingerprinting (HICF) technique was used to construct physical maps for both M. guttatus and M. lewisii. Two BAC libraries of M. guttatus, constructed with restriction enzymes HindIII and BstyI, and one HindIII BAC library of M. lewisii have been fingerprinted (36,864 BACs from each library). A semi-automated pipeline was developed for data processing and analysis with the software applications ABI Data Collection v2.0, ABI GeneMapper v3.7, GenoProfiler v1.1, and FPC v8.0. A total of 60,189 (85%) clones from both M. guttatus BAC libraries were used for contig construction after filtering the dataset in the GenoProfiler program. The contig assembly, using a tolerance of 3 and a cutoff value of e-50, produced 2,232 contigs containing 49,357 clones (82% of total clones used for FPC) with an average Sulston score of 0.92. The first release of the M. guttatus WebFPC is available at http://www.genome.clemson.edu./projects/mimulus/. The data analysis of the fingerprinted HindIII BAC library for M. lewisii is in progress. From the initial assemblies, 5,000 clones for each species will be rearrayed into minimum tile libraries for further studies. To integrate the genetic and physical maps, approximately 1,000 STS markers will be anchored to all three Mimulus BAC libraries using an overgo probe pooling strategy. At present, 115 gene-based markers have been anchored and added to the FPC data.