Abstract
BackgroundSugar beet (Beta vulgaris sp. vulgaris) crops account for about 30% of world sugar. Sugar yield is compromised by reproductive growth hence crops must remain vegetative until harvest. Prolonged exposure to cold temperature (vernalization) in the range 6°C to 12°C induces reproductive growth, leading to bolting (rapid elongation of the main stem) and flowering. Spring cultivation of crops in cool temperate climates makes them vulnerable to vernalization and hence bolting, which is initiated in the apical shoot meristem in processes involving interaction between gibberellin (GA) hormones and vernalization. The underlying mechanisms are unknown and genome scale next generation sequencing approaches now offer comprehensive strategies to investigate them; enabling the identification of novel targets for bolting control in sugar beet crops. In this study, we demonstrate the application of an mRNA-Seq based strategy for this purpose.ResultsThere is no sugar beet reference genome, or public expression array platforms. We therefore used RNA-Seq to generate the first reference transcriptome. We next performed digital gene expression profiling using shoot apex mRNA from two sugar beet cultivars with and without applied GA, and also a vernalized cultivar with and without applied GA. Subsequent bioinformatics analyses identified transcriptional changes associated with genotypic difference and experimental treatments. Analysis of expression profiles in response to vernalization and GA treatment suggested previously unsuspected roles for a RAV1-like AP2/B3 domain protein in vernalization and efflux transporters in the GA response.ConclusionsNext generation RNA-Seq enabled the generation of the first reference transcriptome for sugar beet and the study of global transcriptional responses in the shoot apex to vernalization and GA treatment, without the need for a reference genome or established array platforms. Comprehensive bioinformatic analysis identified transcriptional programmes associated with different sugar beet genotypes as well as biological treatments; thus providing important new opportunities for basic scientists and sugar beet breeders. Transcriptome-scale identification of agronomically important traits as used in this study should be widely applicable to all crop plants where genomic resources are limiting.
Highlights
Sugar beet (Beta vulgaris sp. vulgaris) crops account for about 30% of world sugar
A total of 18 out of 21 of the Arabidopsis gene homologues were present in the AraNet database and as indicated in Table 2 the associated GO terms, by collective analysis of the gene set, were enriched for plant terms including some that we considered to be consistent with reproductive growth and plant development
Results of BLASTX searches with these GA-induced genes are given in Table 4, showing that amongst the sugar beet transcripts with significant matches to known genes were included an acetoacetyl-CoA thiolase (Locus 12027), a GA-regulated gene (Locus 30091); and 3 genes encoding efflux-type pumps of the ATP-binding cassette (ABC) transporter (Locus 43376), and multidrug and toxin extrusion (MATE; Locus 54049) families of
Summary
Sugar beet (Beta vulgaris sp. vulgaris) crops account for about 30% of world sugar. Sugar yield is compromised by reproductive growth crops must remain vegetative until harvest. Prolonged exposure to cold temperature (vernalization) in the range 6°C to 12°C induces reproductive growth, leading to bolting (rapid elongation of the main stem) and flowering. A key breeding target for both autumn and spring sown crops is the suppression of cold temperature induced stem elongation (bolting) and flowering (reproductive growth) during the growing season. This is because, in sugar beet crops, prolonged exposure to cold temperatures in the range 6°C to 12°C [2], a process known as vernalization, is obligatory for the induction of reproductive growth, which requires that the plants must first bolt and flower. The key breeding strategy is to select against the early bolting gene B [4], thereby maintaining the biennial habit so that crops remain vegetative as long as temperatures do not become vernalizing during the growing season
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