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Plant Physiol, December 2000, Vol. 124, pp. 1483-1492
A Simple Procedure for the Analysis of Single Nucleotide
Polymorphisms Facilitates Map-Based Cloning in
Arabidopsis1
Eliana
Drenkard,
Brent G.
Richter,2
Steve
Rozen,
Lisa
M.
Stutius,
Nathaniel A.
Angell,
Michael
Mindrinos,
Raymond J.
Cho,
Peter J.
Oefner,
Ronald W.
Davis, and
Frederick M.
Ausubel*
Department of Genetics, Harvard Medical School, and Department of
Molecular Biology, Massachusetts General Hospital, Boston,
Massachusetts 02114 (E.D., B.G.R., N.A.A., F.M.A.); Whitehead Institute
for Biomedical Research, 9 Cambridge Center, Cambridge, Massachusetts
02142 (S.R.); Harvard College, Cambridge, Massachusetts 02138 (L.M.S.);
and Departments of Biochemistry (M.M., R.J.C., P.J.O., R.W.D) and
Genetics (R.W.D), Stanford University School of Medicine, Stanford,
California 94305
We developed a modified allele-specific PCR procedure for assaying
single nucleotide polymorphisms (SNPs) and used the procedure (called
SNAP for single-nucleotide amplified polymorphisms) to generate 62 Arabidopsis mapping markers. SNAP primers contain a single base pair
mismatch within three nucleotides from the 3' end of one allele (the
specific allele) and in addition have a 3' mismatch with the
nonspecific allele. A computer program called SNAPER was used to
facilitate the design of primers that generate at least a 1,000-fold
difference in the quantity of the amplification products from the
specific and nonspecific SNP alleles. Because SNAP markers can be
readily assayed by electrophoresis on standard agarose gels and because
a public database of over 25,000 SNPs is available between the
Arabidopsis Columbia and Landsberg erecta ecotypes, the
SNAP method greatly facilitates the map-based cloning of Arabidopsis
genes defined by a mutant phenotype.
1
This work was supported by the National Science
Foundation (grant no. MCB-9729599).
2
Present address: Genomics Collaborative Inc., 99 Erie
Street, Cambridge, MA 02139.
*
Corresponding author; e-mail ausubel{at}frodo.mgh.harvard.edu;
fax 617-726-5949.
© 2000 American Society of Plant Physiologists
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