Plant & Animal Genomes XIV Conference

January 14-18, 2006
Town & Country Convention Center
San Diego, CA

The Maize Full-Length cDNA Project

Yeisoo Yu¹ , Karl Haller² , HyeRan Kim¹ , Dave Kudrna¹ , Kristi Collura¹ , Wolfgang Golser¹ , Teri R. Mueller¹ , Jennifer Currie¹ , Darren Morrow³ , John Fernandes³ , Rod Wing¹ , Virginia Walbot³ , Cari Soderlund²

¹  Arizona Genomics Institute, Department of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA

²  Arizona Genomics Computational Laboratory, Department of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA

³  Department of Biological Sciences, Stanford University, 855 California Ave., Palo Alto, CA 94304, USA

Maize is the most important US crop and a complete genome sequence will be available in the next 3 years. Thus the availability of full-length (FL) cDNA sequences becomes crucial for accurate annotation and future functional characterization of the genes. NSF funded maize full-length cDNA project will finish approximately 30,000 FLcDNAs, focusing on reproductive development and stress-induced transcripts. A full-length cDNA library in a Gateway-compatible backbone was built using RNA from 13 organs types (from inflorescence primordia to immature seeds), highly enriched for full-length transcripts by cap and tail selection, and then normalized to increase representation of rare transcripts. The second cDNA library from embryo, scutellum and 7-day seedlings with stress inducer treatments will be made following the same methods. 30,000 candidate FLcDNA clones for full-length sequencing will be selected based on (1) 360,000 5' and 3' Expressed Sequence Tag (EST) assemblies generated in this project by aligning to publicly available ESTs, FLcDNAs and genomic sequences of rice and maize, and (2) hybridization of RNA from specific reproductive stages to oligo-microarray and high density filter 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 information derived from this project will be used to better understand gene regulatory networks involved in plant reproduction and environmental stresses leading to higher yielding and broader adaptive crop plants to feed future generations. Maize full-lengthcDNA project will also help to train teachers and young scientists from underrepresented groups in the art of scientific investigation and discovery through outreach efforts.