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GrainGenes Reference Report: PPS-134-960

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Reference	PPS-134-960
Title	A new resource for cereal genomics: 22K barley GeneChip comes of age
Journal	Plant Physiology
Year	2004
Volume	134
Pages	960-968
Author	Close TJ [ Show all 10 ]
Abstract	Summary: 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
External Databases	Pubmed: 15020760
Keyword	[ Hide all but 1 of 53 ] abiotic abiotic stress age avena strigosa barley biotechnology cdna cdna library complexes conserved sequences crop plants cross-species database defense defense pathways dhn genes discovery disease diversity evolutionary expression analysis expression pattern gene gene prediction gene sequence generation genome genomics hordeum hordeum vulgare library maize map model monocot oat oligonucleotide arrays oryza oryza sativa phenotype prediction protein protein expression responses rice saccharomyces cerevisiae seedling sequence sorghum sorghum bicolor stress triticum zea

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