THE RESPONSE OF BARLEY TO DROUGHT, LOW TEMPERATURE, SALINITY AND ABA: AS GLEANED FROM THE BARLEY1 GENECHIP

¹ Department of Botany & Plant Sciences, University of California, Riverside, California, 92521-0124, USA

² USDA-ARS, US Salinity Laboratory, University of California, Riverside, California, 92507-4617, USA

³ Department of Botany, University of Agriculture, Faisalabad, 38040, Pakistan

A microarray chip representing approximately 21,500 barley unigenes has been produced as part of a USDA-IFAFS 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 EST sequences received from cooperators in USA, Germany, Japan, Scotland, and Finland, plus about 1,000 sequences retrieved by Roger Wise and co-workers at Iowa State University from the GenBank nr database. All EST sequences were trimmed to high quality regions, contaminants were identified and removed, and the remaining information was compiled using CAP3. A “stringent” assembly (paralogs separated) contained a total of about 53,000 “unigenes” (the sum of contigs plus singletons), among which about 50% had reliable 3’ ends. From these sequences with reliable 3’ ends the Barley1 chip content was defined. Probe sets were then designed and the chip fabricated by Affymetrix. The availability of this barley microarray has made it possible to examine barley gene expression on a large scale. Using data from this chip, together with Affymetrix MAS, Silicon Genetics Genespring and HarvEST:Barley (harvest.ucr.edu) software, we analyzed biologically triplicated experiments. We identified overlaps and differences in gene expression between drought stress, low temperature, salinity stress and ABA treatment. Expression patterns of several genes detected by the Barley1 chip were validated by RT-PCR.