Transcriptomics of the developing wheat Karyopsis

Crop improvement through traditional breeding programs is a time consuming process with little control over the outcome, often resulting in undesired phenotypes. By comparison, directed gene selection and or manipulation potentially offer more reliable outcomes. To carry out gene selection or manipulations we first need to correlate function with gene sequences. To quantitatively analyze genome-wide gene expression profiles to aid the functional annotation of the hexaploid wheat (Triticum aestivum) transcriptome we have employed Serial Analysis of Gene Expression (SAGE). The ability of SAGE to identify low-abundance transcripts will ultimately pave the way to novel gene discovery and identify subtle differences in gene expression between closely related individuals. Using this high-throughput technology we have been able to analyze gene expression during wheat seed development. SAGE libraries have been constructed on whole karyopses at six time points including 2DPA (days post Anthesis), 8DPA, 14DPA, 20DPA, 30DPA with the end point being mature dry seed. Currently 20,000 nucleotide “tags” from each library have been sequenced and BLASTED against multiple databases including GENBANK and TIGR for identification. Clustering of known sequences has revealed patterns of gene expression during development with further sequencing providing more reliable quantitation. The analysis of SAGE libraries on fractionated tissues including pericarp, endosperm and embryo has provided a snapshot of the temporo-spatial pattern of gene expression. Shortfalls in the procedure that may limit the degree of representation of a library (including the lack of NlaIII sites) are also addressed.