Validation of a novel associative transcriptomics pipeline in Brassica oleracea: identifying candidates for vernalisation response.

Background: Associative transcriptomics has been used extensively in Brassica napus to enable the rapid identification of markers correlated with traits of interest. However, within the important vegetable crop species, Brassica oleracea, the use of associative transcriptomics has been limited due to a lack of fixed genetic resources and the difficulties in generating material due to self-incompatibility. Within Brassica vegetables, the harvestable product can be vegetative or floral tissues and therefore synchronisation of the floral transition is an important goal for growers and breeders.

CRISPR-Cas9-Mediated Gene Editing of Genes Impair Glucoraphanin Accumulation of in the Field.

Discoveries in model plants grown under optimal conditions can provide important directions for crop improvement. However, it is important to verify whether results can be translated to crop plants grown in the field. In this study, we sought to study the role of in the regulation of aliphatic glucosinolate (A-GSL) biosynthesis and associated sulfur metabolism in field-grown with the use of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-Cas9 gene-editing technology.

Comparative transcriptomics reveals desynchronisation of gene expression during the floral transition between Arabidopsis and cultivars.

Comparative transcriptomics can be used to translate an understanding of gene regulatory networks from model systems to less studied species. Here, we use RNA-Seq to determine and compare gene expression dynamics through the floral transition in the model species and the closely related crop . We find that different curve registration functions are required for different genes, indicating that there is no single common 'developmental time' between Arabidopsis and .

Magnesium and calcium overaccumulate in the leaves of a schengen3 mutant of Brassica rapa.

Magnesium (Mg) and calcium (Ca) are essential mineral nutrients poorly supplied in many human food systems. In grazing livestock, Mg and Ca deficiencies are costly welfare issues. Here, we report a Brassica rapa loss-of-function schengen3 (sgn3) mutant, braA.

Total FLC transcript dynamics from divergent paralogue expression explains flowering diversity in Brassica napus.

Flowering time is a key adaptive and agronomic trait. In Arabidopsis, natural variation in expression levels of the floral repressor FLOWERING LOCUS C (FLC) leads to differences in vernalization. In Brassica napus there are nine copies of FLC.

Natural variation in autumn expression is the major adaptive determinant distinguishing Arabidopsis FLC haplotypes.

In winter is registered during vernalization through the temperature-dependent repression and epigenetic silencing of floral repressor . Natural Arabidopsis accessions show considerable variation in vernalization. However, which aspect of the repression mechanism is most important for adaptation to different environments is unclear.

The oilseed rape developmental expression resource: a resource for the investigation of gene expression dynamics during the floral transition in oilseed rape.

Background: Transcriptome time series can be used to track the expression of genes during development, allowing the timing, intensity, and dynamics of genetic programmes to be determined. Furthermore, time series analysis can reveal causal relationships between genes, leading to an understanding of how the regulatory networks are rewired during development. Due to its impact on yield, a developmental transition of agricultural interest in crops is the switch from vegetative to floral growth.

QTL-seq identifies BnaFT.A02 and BnaFLC.A02 as candidates for variation in vernalization requirement and response in winter oilseed rape (Brassica napus).

Winter, spring and biennial varieties of Brassica napus that vary in vernalization requirement are grown for vegetable and oil production. Here, we show that the obligate or facultative nature of the vernalization requirement in European winter oilseed rape is determined by allelic variation at a 10 Mbp region on chromosome A02. This region includes orthologues of the key floral regulators FLOWERING LOCUS C (BnaFLC.

Spatio-temporal expression dynamics differ between homologues of flowering time genes in the allopolyploid Brassica napus.

Polyploidy is a recurrent feature of eukaryotic evolution and has been linked to increases in complexity, adaptive radiation and speciation. Within angiosperms such events have occurred repeatedly in many plant lineages. Here we investigate the retention and spatio-temporal expression dynamics of duplicated genes predicted to regulate the floral transition in Brassica napus (oilseed rape, OSR).

Absence of warmth permits epigenetic memory of winter in Arabidopsis.

Plants integrate widely fluctuating temperatures to monitor seasonal progression. Here, we investigate the temperature signals in field conditions that result in vernalisation, the mechanism by which flowering is aligned with spring. We find that multiple, distinct aspects of the temperature profile contribute to vernalisation.

Introducing the Brassica Information Portal: Towards integrating genotypic and phenotypic Brassica crop data.

The Brassica Information Portal (BIP) is a centralised repository for brassica phenotypic data. The site hosts trait data associated with brassica research and breeding experiments conducted on brassica crops, that are used as oilseeds, vegetables, livestock forage and fodder and for biofuels. A key feature is the explicit management of meta-data describing the provenance and relationships between experimental plant materials, as well as trial design and trait descriptors.

COOLAIR Antisense RNAs Form Evolutionarily Conserved Elaborate Secondary Structures.

There is considerable debate about the functionality of long non-coding RNAs (lncRNAs). Lack of sequence conservation has been used to argue against functional relevance. We investigated antisense lncRNAs, called COOLAIR, at the A.

Nucleotide polymorphism affecting FLC expression underpins heading date variation in horticultural brassicas.

Variation in flowering time and response to overwintering has been exploited to breed brassica vegetables that can be harvested year-round. Our knowledge of flowering time control now enables the investigation of the molecular basis of this important variation. Here, we show that a major determinant of heading date variation in Brassica oleracea is from variation in vernalization response through allelic variation at FLOWERING LOCUS C.

Seasonal shift in timing of vernalization as an adaptation to extreme winter.

The requirement for vernalization, a need for prolonged cold to trigger flowering, aligns reproductive development with favorable spring conditions. In Arabidopsis thaliana vernalization depends on the cold-induced epigenetic silencing of the floral repressor locus FLC. Extensive natural variation in vernalization response is associated with A.

Brassica oleracea and B. napus.

With the accelerating advances in genetics and genomics research in Arabidopsis and Brassica, transformation technologies are now routinely being exploited to elucidate gene function as well as contributing to the development of novel enhanced crops. When a researcher's desired goal is simply to modify or introduce candidate genes into a Brassica, the availability of easy-to-follow protocols and knowledge of readily transformable genotypes becomes a valuable resource. In this chapter we outline a basic A.

Remembering the prolonged cold of winter.

Plants have to cope with constantly changing conditions and need to respond to environmental stresses and seasonal changes in temperature and photoperiod. Alignment of their development with particular seasons requires memory mechanisms and an ability to integrate noisy temperature signals over long time scales. An increasingly well understood example of how seasonal changes influence development is vernalization, the acceleration of flowering by prolonged cold.

Functional alleles of the flowering time regulator FRIGIDA in the Brassica oleracea genome.

Background: Plants adopt different reproductive strategies as an adaptation to growth in a range of climates. In Arabidopsis thaliana FRIGIDA (FRI) confers a vernalization requirement and thus winter annual habit by increasing the expression of the MADS box transcriptional repressor FLOWERING LOCUS C (FLC). Variation at FRI plays a major role in A.

Major-effect alleles at relatively few loci underlie distinct vernalization and flowering variation in Arabidopsis accessions.

We have explored the genetic basis of variation in vernalization requirement and response in Arabidopsis accessions, selected on the basis of their phenotypic distinctiveness. Phenotyping of F2 populations in different environments, plus fine mapping, indicated possible causative genes. Our data support the identification of FRI and FLC as candidates for the major-effect QTL underlying variation in vernalization response, and identify a weak FLC allele, caused by a Mutator-like transposon, contributing to flowering time variation in two N.

Pharma-Planta: road testing the developing regulatory guidelines for plant-made pharmaceuticals.

Significant advances over the last few years have seen plant-made pharmaceuticals (PMPs) move from the exploratory research phase towards clinical trials, with the first commercial products for human use expected to reach the market by 2009. Europe has yet to witness the commercial application of PMP technology, although at least one product has begun phase II clinical trials with others following close behind. These emerging products are set to challenge the complex and overlapping regulations that currently govern GM plants and 'conventional' pharmaceutical production.

Brassica oleracea.

A better understanding of the genetic basis underlying the genotype dependence of Brassica oleracea transformation is enabling researchers to distinguish between recalcitrant and successful candidate genotypes for routine transformation. In this chapter we outline an A. tumefaciens-mediated transformation method for B.

Molecular farming for new drugs and vaccines. Current perspectives on the production of pharmaceuticals in transgenic plants.

The European Union Framework 6 Pharma–Planta Consortium