Czech J. Genet. Plant Breed., 2005, 41(4):144-152 | DOI: 10.17221/3660-CJGPB

The Barley Microarray. A Community Vision and Application to Abiotic Stress

T J. Close

Department of Botany & Plant Sciences, University of California, Riverside, CA, USA

A microarray chip representing approximately 20 000 barley unigenes was produced as part of a USA project entitled "An integrated physical and expression map of barley for Triticeae improvement". The content of the chip was derived from more than 400 000 barley "Expressed Sequence Tag" (EST) sequences received from cooperators inUSA,Germany,Australia,Japan,Scotland, andFinland, plus about 1000 sequences retrieved from the GenBank nr database or GrainGenes. All EST sequences were trimmed to high quality regions, contaminants were identified and removed, and the remaining information was compiled using the CAP3 assembly program. A "stringent" assembly (paralogs separated) contained about 53 000 "unigenes" (the sum of contigs plus singletons), among which about 50% had reliable 3' ends and were therefore suitable for chip content. From these, probe sets were designed and the "Barley1" chip fabricated by Affymetrix. Complete details on the content of the barley microarray, and enhanced probe-set annotations, can be obtained using the software HarvEST:Barley, available from http://harvest.ucr.edu. The availability of an Affymetrix barley microarray has facilitated the study of gene expression on a large scale. Replicated experiments have revealed commonalities and differences between responses to abiotic stresses, and inherent differences between barley genotypes. The design and a brief summary of the results of drought stress experiments are stated.

Keywords: genomics; ESTs; microarray; abiotic stress

Published: December 31, 2005  Show citation