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An AFLP-based genome-wide mapping strategy

Janny Peters UGent, Gerda Cnops UGent, Pia Neyt UGent, Johannes Zethof UGent, Karen Cornelis, Maria Van Lijsebettens UGent and Tom Gerats UGent (2004) THEORETICAL AND APPLIED GENETICS. 108(2). p.321-327
abstract
To efficiently determine the chromosomal location of phenotypic mutants, we designed a genome-wide mapping strategy that can be used in any crop for which a dense AFLP (Amplified Fragment Length Polymorphism) map is available or can be made. The AFLP technique is particularly suitable to initiate map-based cloning projects because it detects many markers per reaction. First a standard set of AFLP primer combinations that results in a framework of AFLP markers well dispersed over the genome is selected. These primer combinations are applied to a limited number of mutant individuals from a segregating population to register linkage and non-linkage of the AFLP markers to the gene-of-interest. Further delineation of the area of interest is accomplished by analyzing the remaining recombinants and additional mutant individuals with AFLP markers that lie within the identified region. We illustrate the usefulness of the method by mapping three rotunda (ron) leaf-form mutant loci of Arabidopsis thaliana and show that in the initial phase of map-based cloning projects a 400-600 kb interval can be identified for the average mutant locus within a few weeks. Once such an area is identified and before initiating the more time-consuming fine-mapping procedure, it is essential to examine publicly available databases for candidate genes and known mutants in the identified region. The 390-kb interval on chromosome 4 that harbors the ron2 mutation, also carries a known flower mutant, leunig (lug); upon crossing, the two mutants appeared to be allelic. When no such candidates are found, the mapping procedure should be continued. We present a strategy to efficiently select recombinants that can be used for fine mapping.
Please use this url to cite or link to this publication:
author
organization
year
type
journalArticle (original)
publication status
published
subject
keyword
MAP, MARKERS, CLONING, DRAFT SEQUENCE, F-2 POPULATIONS, REGULATES AGAMOUS EXPRESSION, ARABIDOPSIS-THALIANA, GENES, LEUNIG, DNA
journal title
THEORETICAL AND APPLIED GENETICS
Theor. Appl. Genet.
volume
108
issue
2
pages
321 - 327
Web of Science type
Article
Web of Science id
000188079400018
JCR category
AGRONOMY
JCR impact factor
2.981 (2004)
JCR rank
2/50 (2004)
JCR quartile
1 (2004)
ISSN
0040-5752
DOI
10.1007/s00122-003-1427-5
language
English
UGent publication?
yes
classification
A1
copyright statement
I have transferred the copyright for this publication to the publisher
id
298807
handle
http://hdl.handle.net/1854/LU-298807
date created
2005-02-17 18:06:00
date last changed
2013-10-16 14:03:14
@article{298807,
  abstract     = {To efficiently determine the chromosomal location of phenotypic mutants, we designed a genome-wide mapping strategy that can be used in any crop for which a dense AFLP (Amplified Fragment Length Polymorphism) map is available or can be made. The AFLP technique is particularly suitable to initiate map-based cloning projects because it detects many markers per reaction. First a standard set of AFLP primer combinations that results in a framework of AFLP markers well dispersed over the genome is selected. These primer combinations are applied to a limited number of mutant individuals from a segregating population to register linkage and non-linkage of the AFLP markers to the gene-of-interest. Further delineation of the area of interest is accomplished by analyzing the remaining recombinants and additional mutant individuals with AFLP markers that lie within the identified region. We illustrate the usefulness of the method by mapping three rotunda (ron) leaf-form mutant loci of Arabidopsis thaliana and show that in the initial phase of map-based cloning projects a 400-600 kb interval can be identified for the average mutant locus within a few weeks. Once such an area is identified and before initiating the more time-consuming fine-mapping procedure, it is essential to examine publicly available databases for candidate genes and known mutants in the identified region. The 390-kb interval on chromosome 4 that harbors the ron2 mutation, also carries a known flower mutant, leunig (lug); upon crossing, the two mutants appeared to be allelic. When no such candidates are found, the mapping procedure should be continued. We present a strategy to efficiently select recombinants that can be used for fine mapping.},
  author       = {Peters, Janny and Cnops, Gerda and Neyt, Pia and Zethof, Johannes and Cornelis, Karen and Van Lijsebettens, Maria and Gerats, Tom},
  issn         = {0040-5752},
  journal      = {THEORETICAL AND APPLIED GENETICS},
  keyword      = {MAP,MARKERS,CLONING,DRAFT SEQUENCE,F-2 POPULATIONS,REGULATES AGAMOUS EXPRESSION,ARABIDOPSIS-THALIANA,GENES,LEUNIG,DNA},
  language     = {eng},
  number       = {2},
  pages        = {321--327},
  title        = {An AFLP-based genome-wide mapping strategy},
  url          = {http://dx.doi.org/10.1007/s00122-003-1427-5},
  volume       = {108},
  year         = {2004},
}

Chicago
Peters, Janny, Gerda Cnops, Pia Neyt, Johannes Zethof, Karen Cornelis, Maria Van Lijsebettens, and Tom Gerats. 2004. “An AFLP-based Genome-wide Mapping Strategy.” Theoretical and Applied Genetics 108 (2): 321–327.
APA
Peters, Janny, Cnops, G., Neyt, P., Zethof, J., Cornelis, K., Van Lijsebettens, M., & Gerats, T. (2004). An AFLP-based genome-wide mapping strategy. THEORETICAL AND APPLIED GENETICS, 108(2), 321–327.
Vancouver
1.
Peters J, Cnops G, Neyt P, Zethof J, Cornelis K, Van Lijsebettens M, et al. An AFLP-based genome-wide mapping strategy. THEORETICAL AND APPLIED GENETICS. 2004;108(2):321–7.
MLA
Peters, Janny, Gerda Cnops, Pia Neyt, et al. “An AFLP-based Genome-wide Mapping Strategy.” THEORETICAL AND APPLIED GENETICS 108.2 (2004): 321–327. Print.