title: Future tools for association mapping in crop plants.
abstract: Association mapping currently relies on the identification of genetic markers. Several technologies have been adopted for genetic marker analysis, with single nucleotide polymorphisms (SNPs) being the most popular where a reasonable quantity of genome sequence data are available. We describe several tools we have developed for the discovery, annotation, and visualization of molecular markers for association mapping. These include autoSNPdb for SNP discovery from assembled sequence data; TAGdb for the identification of gene specific paired read Illumina GAII data; CMap3D for the comparison of mapped genetic and physical markers; and BAC and Gene Annotator for the online annotation of genes and genomic sequences.
authors.affiliation: University of Queensland, Australian Centre for Plant Functional Genomics, School of Land, Crop and Food Sciences, Brisbane, Australia.
authors.forename: Chris
authors.initials: C
authors.lastname: Duran
authors.forename: Dominic
authors.initials: D
authors.lastname: Eales
authors.forename: Daniel
authors.initials: D
authors.lastname: Marshall
authors.forename: Michael
authors.initials: M
authors.lastname: Imelfort
authors.forename: Jiri
authors.initials: J
authors.lastname: Stiller
authors.forename: Paul J
authors.initials: PJ
authors.lastname: Berkman
authors.forename: Terry
authors.initials: T
authors.lastname: Clark
authors.forename: Megan
authors.initials: M
authors.lastname: McKenzie
authors.forename: Nikki
authors.initials: N
authors.lastname: Appleby
authors.forename: Jacqueline
authors.initials: J
authors.lastname: Batley
authors.forename: Kaye
authors.initials: K
authors.lastname: Basford
authors.forename: David
authors.initials: D
authors.lastname: Edwards
mesh_terms: D001483:Base Sequence; D002874:Chromosome Mapping / Q000379:methods*; D018556:Crops, Agricultural / Q000235:genetics*; D018744:DNA, Plant / Q000235:genetics; D020224:Expressed Sequence Tags; D005819:Genetic Markers / Q000235:genetics; D018745:Genome, Plant; D055106:Genome-Wide Association Study / Q000379:methods*; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA
chemical_list: D018744:DNA, Plant; D005819:Genetic Markers