A simple procedure for the analysis of single nucleotide polymorphisms facilitates map-based cloning in Arabidopsis.

Journal Article (Journal Article)

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.

Full Text

Duke Authors

Cited Authors

  • Drenkard, E; Richter, BG; Rozen, S; Stutius, LM; Angell, NA; Mindrinos, M; Cho, RJ; Oefner, PJ; Davis, RW; Ausubel, FM

Published Date

  • December 2000

Published In

Volume / Issue

  • 124 / 4

Start / End Page

  • 1483 - 1492

PubMed ID

  • 11115864

Pubmed Central ID

  • PMC1539302

International Standard Serial Number (ISSN)

  • 0032-0889

Digital Object Identifier (DOI)

  • 10.1104/pp.124.4.1483


  • eng

Conference Location

  • United States