Maize Full-Length cDNA Project

University Of Arizona, Tucson AZ

Investigators

Abstract

Full-length complementary DNA (FLcDNA) sequences are crucial for accurate annotation and future functional characterization of the genes in the maize genome. This project will generate approximately 30,000 FLcDNA sequences focusing on reproductive development and stress-induced transcripts. A commercial library in a Gateway-compatible backbone built using RNA from 13 organs types (from inflorescence primordia to immature seeds), highly enriched for full-length cDNA representation by cap and tail selection, will be normalized to increase representation of rare transcripts. A new library from additional floral developmental stages, embryo, scutellum, and 7-day seedlings with stress inducer treatments will be made using the same methods. Candidate clones for finishing will be picked based on (1) 360,000 5' and 3' Expressed Sequence Tag (EST) assemblies generated in this project by alignment to publicly available ESTs, FLcDNAs and genomic sequences of rice and maize, and (2) hybridization of RNA from specific reproductive stages to 360,000 filter-arrayed clones in order to enrich rare transcripts. Iterative primer walking will be employed on each candidate FLcDNA, and a transposon method will also be utilized to complete finish larger insert and difficult clones with phred 40 quality. The outcomes from the project to be delivered to the community include: (1) 360,000 5' and 3' ESTs from 180,000 presumptive FLcDNAs, (2) 30,000 FLcDNA clones and sequences, and (3) FLcDNA annotation, including available stage-specificity of expression and possible mapping information, and a web-based genome browser. The maize FLcDNA resources will have a wide variety of potential uses from functional studies towards understanding gene evolution during cereal diversification, and exploration of gene regulatory networks involved in plant reproduction and environmental stresses. Availability of project outcomes A web-based display will be created at http://www.genome.arizona.edu to provide access to the project results and project progress. All biological resources including clones, amplified libraries, and high-density filters will also make publicly available through BAC/EST resource center at Arizona Genomics Institute (www.genome.arizona.edu/order).