Genomeless genomics in crop improvement

The DNA sequencing of the entire nuclear genomes from Arabidopsis, rice and poplar has facilitated the broad-adoption of contemporary research techniques that extend far beyond the study of individual genes. New post-genomic technologies such as microarray based genome-scale gene expression profiling and proteome analysis are absolutely dependent on deep sequence coverage of the gene-space, but have an immense potential to drive the research community in exciting new directions. Facets of many crop genomes currently preclude them from complete sequencing, but the broadest adoption of post-genomic technologies is essential to make in-roads in plant biotechnology and crop improvement. A variety of technologies are available that can be used to establish a genomics foothold in even the most recalcitrant of crop plant species. In this review we address the fundamental technologies that are being widely adopted within the crop-plant research community to gain such a foothold. By considering primarily the expressed sequence tag resources, we have explored how even moderately simple genomic resources may be exploited in molecular marker development, candidate gene selection and microarray-based gene expression profiling.