title: Marker development for the genetic study of natural variation in Arabidopsis thaliana.
abstract: We report AtPRIMER, an application that automates the discovery of new polymorphic markers between ecotypes of Arabidopsis thaliana. On specifying two ecotypes and the genomic region of interest, the script retrieves all corresponding single nucleotide polymorphisms (SNPs) and generates CAPS and/or dCAPS PCR primer sequences. We show that AtPRIMER accurately found specific polymorphic markers for our linkage mapping project. AtPRIMER will therefore be useful for efficient marker development with high density and specificity.
authors.affiliation: Sainsbury Laboratory, Norwich NR4 7UH, UK. adnane.nemri@tsl.ac.uk
authors.forename: Adnane
authors.initials: A
authors.lastname: Nemri
authors.forename: Michael M
authors.initials: MM
authors.lastname: Neff
authors.forename: Michael
authors.initials: M
authors.lastname: Burrell
authors.forename: Jonathan D G
authors.initials: JD
authors.lastname: Jones
authors.forename: David J
authors.initials: DJ
authors.lastname: Studholme
mesh_terms: D000465:Algorithms; D017360:Arabidopsis / Q000235:genetics*; D001483:Base Sequence; D004252:DNA Mutational Analysis / Q000379:methods; D017931:DNA Primers / Q000235:genetics*; D018744:DNA, Plant / Q000235:genetics*; D005819:Genetic Markers / Q000235:genetics*; D014644:Genetic Variation / Q000235:genetics*; D008969:Molecular Sequence Data; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D017931:DNA Primers; D018744:DNA, Plant; D005819:Genetic Markers