ABSTRACT
Genome analysis offers large-scale discovery opportunities and new tools for plant biology disciplines, including genetics, plant physiology, plant biochemistry and metabolism, and breeding. High-throughput sequencing and expression analysis create the opportunities to link phenotypes and traits through expression analysis. Recent achievements in crop biotechnology and technological advances primarily driven by the human genome projects have catapulted genome-scale plant gene discovery and gene function characterization. Plant genomics efforts have been launched within both the public and private communities. In concordance with the rapid acceleration in large-scale expressed sequence tags (ESTs) (Newman et al., 1994) and genomic DNA sequencing projects of Arabidopsis (https://genome-www3.stanford.edu/cgi-bin/webdriver? Mlva1=atdb_agi_total), rice (Sasaki and Burr, 1998), and other plant species, plant genome researchers have clearly recognized the need for instruments in functional genomics. The EST and genomic DNA sequence data provide a solid foundation for large-scale functional characterization of individual genes as well as whole plant genomes using syntenic approaches and comparative genomics strategies. Technology platforms for plant functional genomics include transcript profiling (Baldwin et al., 1999; Kehoe et al., 1999), gene disruptions by T-DNA insertion and transposon mutagenesis (Hirsch et al., 1998; Koes et al., 1995; McKinney et al., 1995; Smith et al., 1996), and gene silencing by infection of plant viruses carrying the target DNA sequences (Settles and Byrne, 1998). Transcript profiling provides the capability for genome functional relationships by illuminating the association of genes and function in complex processes. The amenability of transcript profiling to automation schemes using high-performance robotics and informatics analytical processes promises to be an indispensable link in the understanding of how genomes function and how complex processes have evolved.
