Marker development for the genetic study of natural variation in Arabidopsis thaliana.
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.
Nemri
Adnane
A
Sainsbury Laboratory, Norwich NR4 7UH, UK. adnane.nemri@tsl.ac.uk
Neff
Michael M
MM
Burrell
Michael
M
Jones
Jonathan D G
JD
Studholme
David J
DJ
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*
D017931:DNA Primers; D018744:DNA, Plant; D005819:Genetic Markers