| Predicting the size of the progeny mapping population required to positionally clone a gene. | |
MedLine Citation:
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PMID: 17565938 Owner: NLM Status: MEDLINE |
Abstract/OtherAbstract:
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A key frustration during positional gene cloning (map-based cloning) is that the size of the progeny mapping population is difficult to predict, because the meiotic recombination frequency varies along chromosomes. We describe a detailed methodology to improve this prediction using rice (Oryza sativa L.) as a model system. We derived and/or validated, then fine-tuned, equations that estimate the mapping population size by comparing these theoretical estimates to 41 successful positional cloning attempts. We then used each validated equation to test whether neighborhood meiotic recombination frequencies extracted from a reference RFLP map can help researchers predict the mapping population size. We developed a meiotic recombination frequency map (MRFM) for approximately 1400 marker intervals in rice and anchored each published allele onto an interval on this map. We show that neighborhood recombination frequencies (R-map, >280-kb segments) extracted from the MRFM, in conjunction with the validated formulas, better predicted the mapping population size than the genome-wide average recombination frequency (R-avg), with improved results whether the recombination frequency was calculated as genes/cM or kb/cM. Our results offer a detailed road map for better predicting mapping population size in diverse eukaryotes, but useful predictions will require robust recombination frequency maps based on sampling more progeny. |
Authors:
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Stephen J Dinka; Matthew A Campbell; Tyler Demers; Manish N Raizada |
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Publication Detail:
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Type: Journal Article; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, Non-P.H.S. Date: 2007-06-11 |
Journal Detail:
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Title: Genetics Volume: 176 ISSN: 0016-6731 ISO Abbreviation: Genetics Publication Date: 2007 Aug |
Date Detail:
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Created Date: 2007-08-24 Completed Date: 2007-12-06 Revised Date: 2013-06-06 |
Medline Journal Info:
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Nlm Unique ID: 0374636 Medline TA: Genetics Country: United States |
Other Details:
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Languages: eng Pagination: 2035-54 Citation Subset: IM |
Affiliation:
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Department of Plant Agriculture, University of Guelph, 50 Stone Road, Guelph, Ontario, Canada. |
Export Citation:
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| MeSH Terms | |
Descriptor/Qualifier:
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Chromosome Mapping
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methods*,
statistics & numerical data Cloning, Molecular / methods Genes, Plant Genetic Techniques Mathematics Meiosis / genetics Models, Genetic Oryza sativa / genetics Recombination, Genetic* |
| Comments/Corrections | |
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