A New Resource for Cereal Genomics: 22K Barley GeneChip Comes of Age

Abstract

In recent years, access to complete genomic sequences, coupled with rapidly accumulating data related to RNA and protein expression patterns, has made it possible to determine comprehensively how genes contribute to complex phenotypes. However, for major crop plants, publicly available, standard platforms for parallel expression analysis have been limited. We report the conception and design of the new publicly available, 22K Barley1 GeneChip probe array, a model for plants without a fully sequenced genome. Array content was derived from worldwide contribution of 350,000 high-quality ESTs from 84 cDNA libraries, in addition to 1,145 barley (Hordeum vulgare) gene sequences from the National Center for Biotechnology Information nonredundant database. Conserved sequences expressed in seedlings of wheat (Triticum aestivum), oat (Avena strigosa), rice (Oryza sativa), sorghum (Sorghum bicolor), and maize (Zea mays) were identified that will be valuable in the design of arrays across grasses. To enhance the usability of the data, BarleyBase, a MIAME-compliant, MySQL relational database, serves as a public repository for raw and normalized expression data from the Barley1 GeneChip probe array. Interconnecting links with PlantGDB and Gramene allow BarleyBase users to perform gene predictions using the 21,439 non-redundant Barley1 exemplar sequences or cross-species comparison at the genome level, respectively. We expect that this first generation array will accelerate hypothesis generation and gene discovery in disease defense pathways, responses to abiotic stresses, development, and evolutionary diversity in monocot plants.

Differentially expressed genes during malting and correlation with malting quality phenotypes in barley (Hordeum vulgare L.)

“…A barley microarray containing more than 22,792 probe sets representing approximately 21,439 barley genes has been developed (Close et al 2004). We used the barley gene chip array to conduct transcript proWling of genes that are diVerentially expressed during malting in barley and then correlated diVerentially expressed genes with malting quality phenotypes.…”

A high-density transcript linkage map of barley derived from a single population

“…Haruna Nijo is the recurrent parent in each of the 10 new RCSL populations developed at Okayama University (Sato, unpublished Single population derived barley transcript map K Sato et al constructed from both Haruna Nijo (Saisho et al, 2007) and H602 (Sato, unpublished). Haruna Nijo is the basis of a new TILLING system comprised of 10 000 individuals (Sato, unpublished (Close et al, 2004). Haruna Nijo was used to develop the first comprehensive set of barley full-length cDNAs (5006 clones) (http://www.shigen.nig.ac.jp/ barley/).…”

“…Extensive, qualitycontrolled barley EST information is available in the HarvEST (http://harvest.ucr.edu/) database. These resources were also used to develop the Affymetrix Barley 1 GeneChip (Close et al, 2004), a platform for large-scale expression analysis (Druka et al, 2006).…”

Expression Profiles in Barley Microspore Embryogenesis

“…The stress pretreatment consisted of incubating the anthers in a medium containing 0.7 M mannitol, 40 mM CaCl 2 and 8g/l agarose, for four days at 25°C in the dark (Cistué et al 2003). The recently developed Barley1 GeneChip (Close et al 2004) was used for this study, thus enabling the analysis of more than 22,000 genes simultaneously.…”

“…In this chapter we show an analysis of gene expression profiling associated with mannitol stress pretreatment, obtained by using the Barley1 GeneChip (Close et al 2004).…”