Genome scale analysis of vernalization and gibberellin responses in sugar beet shoot apices

Sugar beet crop plants require vernalization (prolonged exposure to cold temperature) for the induction of reproductive growth, a process that is initiated in the shoot apical meristem. Gibberellin plant hormones are known to interact with vernalization although the underlying mechanisms are not known. Here we report an mRNA-Seq based strategy to investigate these processes at genome-scale. Since there is no public reference genome for sugar beet, we first produced a sugar beet reference transcriptome by de novo assembly of 6.6Gb sequence generated from shoot apex mRNA, which had in excess of 75% coverage when compared with the 17,186 ESTs in the public sugar beet gene index. Moreover, we identified 7468 long transcripts (>500bp) with no match thus representing a likely 40% increase in the number of known sugar beet genes. We next used the new reference transcriptome to perform RNA-Seq-based digital gene expression profiling using shoot apex mRNA samples from the C600 sugar beet line and the cultivar Roberta both with and without GA treatment, and also vernalized C600 samples with and without GA. Subsequent bioinformatic analyses identified transcriptional programmes associated with genotypic difference and experimental treatment of biological samples. Further, batch analysis allowed rapid identification of transcripts with dynamic expression profiles in response to both vernalization and GA treatment, which suggested previously unsuspected roles for a FRUITFUL-like MADS box protein in vernalization and efflux transporters in the response to gibberellin respectively. Finally, our strategy for genome-scale identification of agronomically important traits in sugar beet should be widely applicable to other important crop plants.