Microarray Resources for Maize Research

University Of Arizona, Tucson AZ

Investigators

Abstract

Maize is the most economically important crop in the US and the premier organism for addressing fundamental biological questions in monocots, especially the cereals, which contribute 70% of humanity's diet. The robust scientific community combined with the extensive genetic and genomic tools available and accumulating, make maize an excellent experimental system. This project will provide a low cost, comprehensive, public sector microarray resource for expression analysis in the important crop plant maize (Zea mays L.). Objectives are: 1) Continue producing maize cDNA amplicon arrays as needed by users. 2) Produce an array with 70-mer oligonucleotides representing the >30,000 identifiable unique maize genes, which should allow better discrimination among gene duplicates (common in maize) relative to cDNA arrays. Provide community with arrays and a hybridization service using a minimal cost recovery model. 3) Provide a website to disseminate project information and provide all expression data generated by this project within a project-specific relational database Zeamage, for Zea mays Gene Expression Database, with links to rice and maize genome annotation. 4) Perform expression profiling with a subset of maize tissues to provide a baseline of data and detailed protocols for the community. 5) Utilize flexible Nimblegen system to experimentally refine oligonucleotide design for the next generation of 70-mer arrays to achieve better discrimination among gene family members and gene duplications. The availability of low cost arrays and hybridization services provided by this project will enable a much larger number of investigators to apply global gene expression profiling to their specific applied or fundamental research programs on maize. Importantly, as ALL the data will be quickly available within a public database, investigators at institutions that do not have the resources to perform the experiments themselves will have access to the data. In addition to training postdoctoral associates and undergraduate students, several outreach components to train a broad community of researchers to the latest in expression profiling technology will be carried out. These activities include holding biannual three-day hands-on microarray workshops, holding half-day workshops at annual meetings, hosting visiting scientists at our facilities, and developing a interactive website and other mechanisms for communication with end-users. Deliverables Accessible from http://www.tigr.org: 1) Maize cDNA amplicon arrays. 2) Oligonucleotide arrays for at least >30,000 unique maize genes. 3) A hybridization service. 4) Zeamage database containing expression profiles for a subset of maize tissues, detailed protocols, with links to rice and maize genome annotation.