title: Indel arrays: an affordable alternative for genotyping.
abstract: Natural variation and induced mutations are important resources for gene discovery and the elucidation of genetic circuits. Mapping such polymorphisms requires rapid and cost-efficient methods for genome-wide genotyping. Here we report the development of a microarray-based method that assesses 240 unique markers in a single hybridization experiment at a cost of less than US$50 in materials per line. Our genotyping array is built with 70-mer oligonucleotide elements representing insertion/deletion (indel) polymorphisms between the Arabidopsis thaliana accessions Columbia-0 (Col) and Landsberg erecta (Ler). These indel polymorphisms are recognized with great precision by comparative genomic hybridization, eliminating the need for array replicates and complex statistical analysis. Markers are present genome-wide, with an average spacing of approximately 500 kb. PCR primer information is provided for all array indels, allowing rapid single-locus inquiries. Multi-well chips allow groups of 16 lines to be genotyped in a single experiment. We demonstrate the utility of the array for accurately mapping recessive mutations, RIL populations and mixed genetic backgrounds from accessions other than Col and Ler. Given the ease of use of shotgun sequencing to generate partial genomic sequences of unsequenced species, this approach is readily transferable to non-model organisms.
authors.affiliation: FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA.
authors.forename: Neeraj
authors.initials: N
authors.lastname: Salathia
authors.forename: Hana N
authors.initials: HN
authors.lastname: Lee
authors.forename: Todd A
authors.initials: TA
authors.lastname: Sangster
authors.forename: Keith
authors.initials: K
authors.lastname: Morneau
authors.forename: Christian R
authors.initials: CR
authors.lastname: Landry
authors.forename: Kurt
authors.initials: K
authors.lastname: Schellenberg
authors.forename: Aditi S
authors.initials: AS
authors.lastname: Behere
authors.forename: Kevin L
authors.initials: KL
authors.lastname: Gunderson
authors.forename: Duccio
authors.initials: D
authors.lastname: Cavalieri
authors.forename: Georg
authors.initials: G
authors.lastname: Jander
authors.forename: Christine
authors.initials: C
authors.lastname: Queitsch
mesh_terms: D017360:Arabidopsis / Q000235:genetics; D017353:Gene Deletion; D005819:Genetic Markers / Q000235:genetics; D018745:Genome, Plant; D005838:Genotype; D016254:Mutagenesis, Insertional; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods; D011110:Polymorphism, Genetic / Q000235:genetics*; D013045:Species Specificity
chemical_list: D005819:Genetic Markers