Submitted to: Plant Physiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/8/2003
Publication Date: 3/1/2004
Citation: Close, T., Wanamaker, S., Caldo, R., Turner, S., Ashlock, D., Dickerson, J., Wing, R., Muehlbauer, G., Kleinhofs, A., Wise, R.P. 2004. A new resource for cereal genomics: 22k barley genechip comes of age. Plant Physiology. 134:960-968. Interpretive Summary: Triticeae grain crops (barley, wheat, and rye) are sown on 81 million acres in the United States with an average value of 9 billion dollars (USDA-NASS Agricultural Statistics, 2002, http://www.usda.gov/nass/pubs/agr02/acro02.htm). Barley (Hordeum vulgare L.) is a true diploid, and despite its large genome is well suited to genetic analysis with an extensive collection of mutants and over 150,000 accessions worldwide (http://www.ars-grin.gov/npgs/index.html; http://barley.ipk-gatersleben.de/ebdb/). Thousands of molecular markers and morphological and quantitative trait loci have been mapped, and a bacterial artificial chromosome (BAC) library covering 6.3 genome equivalents is in use throughout the world. This update provides a status report on the new publicly available 22K Affymetrix Barley1 GeneChip. We expect that this first generation array will accelerate gene discovery and the application of new knowledge to the improvement of barley and other cereal crops.
Technical Abstract: Over the course of several informal meetings at the International Plant and Animal Genome Conferences from 1998 through 2002, the barley research community came to a general consensus that a worldwide standard for parallel expression profiling was needed for small grain Triticeae crops. During this period, funding was obtained for independent and sizeable barley expressed sequence tag (EST) sequencing projects in the United States, Germany, Japan, Scotland, and Finland. By the end of 2002, these projects had produced a combined total of approximately 350,000 high-quality barley ESTs originating from 84 cDNA libraries representing various developmental stages, in addition to abiotic- and biotic-stress treatments [http://www.ncbi.nlm.nih.gov/dbEST/dbEST_summary.html]. These EST data sets constituted a major resource with which to build a platform for highly parallel transcription profiling. Beginning in January 2002 and continuing through October 2002, each project transmitted their raw EST data to the University of California, Riverside (UCR) to produce a collective resource for the purpose of designing an Affymetrix barley genome array.