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Bioinformatics and Computational Biology Summer Institute |
Research Projects for Fellows, June 20 - August 6, 2005
P11: Transforming Genetic Map Locations into Predicted Cytological Coordinates using Recombination Nodule Frequencies
| Title: | Transforming Genetic Map Locations into Predicted Cytological Coordinates using Recombination Nodule Frequencies |
| Mentors: | Dr. Carolyn Lawrence and Trent Seigfried |
| Description: | The maize genome is soon to be sequenced, enabling researchers to begin to investigate how those data relate to the architecture of the maize chromosome complement. How are the chromosomes arranged? Is it possible to relate the genetic and cytological maps to the assembled genome sequence? Are there sequences present at centromeres that signal the cell to construct kinetochores, the machines that ensure proper chromosome segregation to occur, at the correct site? More complex questions can be asked, and at some point the full complement of the genome can be related to its function, both within the cell and to the plant as a whole. Convergence of traditional biological investigation with genome content and organization is currently lacking. This represents a new area of research that will open up once a complete genome sequence and a method for searching through the whole of the data are in place. Even without a complete sequence available, it is possible to begin work toward integrating the genetic and physical (e.g., cytological and sequence-based contig fingerprint) maps so that gaps between the assembled genome sequence contigs might be estimated and to further our understanding of how these data are interrelated. For maize, Anderson and others have demonstrated that the positions of genetic loci can be translated into cytological map positions via a conversion that uses recombination nodule frequencies along the structure of pachytene chromosomes. A new tool (see the listed web resource) can accomplish this conversion, but loci that are near one another (i.e., within approximately 3 cM of each other on a genetic map) cannot resolved using the conversion directly. It should be possible to better resolve these positions if the conversion equations are refined, and it is possible that the conversions also can be applied to other organisms than maize for which adequate recombination nodule data exists (i.e., tomato and mouse). Because the mouse genome is fully sequenced, it should be possible to determine whether genetic and cytological coordinates can be related to base pair distances directly, which would give some idea of whether the same could be done for maize to determine the number of base pairs between sequence contigs for which genetic and/or cytological map placement is known. The student who chooses to work on this project will be responsible for creating data infiles for the tomato and mouse and for refining the conversion tool itself so that it is not specific to maize data. The student also will determine whether the conversion equations can be improved so that the precision with which it predicts cytological locations is not limited by the 0.2 micrometer limitations imposed by the data collection procedure described in the materials and methods section of the earlier Anderson et al. reference listed below. |
| Web Resources: | http://shrimp1.zool.iastate.edu/cmrn2/ |
| References: | Anderson L, Doyle GG, Brigham B, Carter JV, Hooker K, Lai A, Rice ME, & Stack S (2003) High-resolution crossover maps for each bivalent of Zea mays using recombination nodules. Genetics 165 (2):849-865 Anderson L, Salameh N, Bass HW, Harper LC, Cande WZ, Weber G, & Stack S (2004) Integrating genetic linkage maps with pachytene chromosome structure in maize. Genetics 166 (4):1923-1933 |