Document Detail


Predicting the size of the progeny mapping population required to positionally clone a gene.
MedLine Citation:
PMID:  17565938     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
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:
Stephen J Dinka; Matthew A Campbell; Tyler Demers; Manish N Raizada
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Publication Detail:
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:
Title:  Genetics     Volume:  176     ISSN:  0016-6731     ISO Abbreviation:  Genetics     Publication Date:  2007 Aug 
Date Detail:
Created Date:  2007-08-24     Completed Date:  2007-12-06     Revised Date:  2013-06-06    
Medline Journal Info:
Nlm Unique ID:  0374636     Medline TA:  Genetics     Country:  United States    
Other Details:
Languages:  eng     Pagination:  2035-54     Citation Subset:  IM    
Affiliation:
Department of Plant Agriculture, University of Guelph, 50 Stone Road, Guelph, Ontario, Canada.
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MeSH Terms
Descriptor/Qualifier:
Chromosome Mapping / methods*,  statistics & numerical data
Cloning, Molecular / methods
Genes, Plant
Genetic Techniques
Mathematics
Meiosis / genetics
Models, Genetic
Oryza sativa / genetics
Recombination, Genetic*
Comments/Corrections

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine


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