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TECHNICAL ADVANCE: Indel arrays: an affordable alternative for genotyping
Author(s) -
Salathia Neeraj,
Lee Ha.,
Sangster Todd A.,
Morneau Keith,
Landry Christian R.,
Schellenberg Kurt,
Behere Aditi S.,
Gunderson Kevin L.,
Cavalieri Duccio,
Jander Georg,
Queitsch Christine
Publication year - 2007
Publication title -
the plant journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.058
H-Index - 269
eISSN - 1365-313X
pISSN - 0960-7412
DOI - 10.1111/j.1365-313x.2007.03194.x
Subject(s) - indel , genotyping , biology , genetics , computational biology , indel mutation , genome , dna microarray , locus (genetics) , reference genome , molecular inversion probe , genotype , gene , single nucleotide polymorphism , gene expression
Summary 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 (L er ). 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 L er . 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.