Development of metabolic engineering approaches to regulate the content of total phenolics, antiradical activity and organic acids in callus cultures of the highbush blueberry (Vaccinium corymbosum L.)

Blueberry (Vaccinium corymbosum L.) is increasingly cultivated to produce high quality berries for consumption and potential applications in medicine, nutrition and as industrial precursors. Seasonal availability sets limitations on chemical compound isolation from cultivated plants. Biotechnological solutions, such as tissue cultures and metabolic engineering, can provide sufficient amounts of plant material with reasonably high metabolite levels, which may be adjusted by different strategies. Here, we describe our approach to modifying total phenolic content (TPC), antiradical activity (ARA) and amounts of selected organic acids in in vitro cultures of two varieties of V. corymbosum by varying the growth media. TPC, ARA and acid levels were determined in mature leaves of field-grown plants and in stable callus cultures derived from leaves of varieties ‘Bluecrop’ and ‘Duke’ grown on Murashige-Skoog (MS) and Woody plant (WP) media supplemented with varying concentrations and combinations of different plant growth hormones. TPC varied from 83 mg g -1 dry weight (DW) to 142 mg g -1 DW in leaves of ‘Bluecrop’ and ‘Duke’, respectively, and correlated with their ARA with ‘Duke’ at the lead. For callus cultures the highest ARA, as well as the highest TPC of 94 mg g -1 DW was observed in ‘Bluecrop’ grown on WP medium with 2,4-dichlorophenoxyacetic acid (2,4-D). High level of quinic acid was found in the mature leaves of all tested varieties, while callus cultures exhibited relative increase in amounts of malic, succinic and citric acids instead. Oxalic acid was found only in callus cultures

Towards whole genome association genetic scans in barley

In crop plants, the potential of association mapping, with the objective of estimating the position of genes conferring a specific trait or phenotype using linkage disequilibrium (LD) between alleles of genetically mapped markers, has recently become a focus of considerable interest. One major attraction of association genetics is the potential to locate genes responsible for a wide range of traits in a single sample population using pre-existing phenotypic data that has been collected during crop improvement and cultivar registration programs. This study testify to the potential of exploiting whole genome LD-scans to locate genes controlling key biological traits in cultivated barley. We are currently increasing the density of markers, particularly those with a MAF >0.1, by developing two further pilot OPAs, which in due course will be compressed into two commercially available platforms for high throughput low cost genotyping in cultivated barley. In the immediate future these will be used in large association genetic studies in the UK and US involving approximately 4000 barley genotypes with the aim of realising the potential for whole genome association genetic scans in cultivated barley

Scientific Opinion on a request from the European Commission related to the prolongation of prohibition of the placing on the market of genetically modified oilseed rape event GT73 for import, processing and feed uses in Austria

Following a request from the European Commission, the Panel on Genetically Modified Organisms of the European Food Safety Authority (EFSA GMO Panel) evaluated the documentation provided by Austria to support the prolongation of the safeguard clause measure prohibiting the placing on the market of the genetically modified oilseed rape event GT73 for import, processing and feed uses in Austria. The EFSA GMO Panel assessed whether the submitted documentation comprised new scientific information that would change or invalidate the conclusions of its previous risk assessments on oilseed rape GT73. The EFSA GMO Panel also considered the relevance of the concerns raised by Austria in the light of the most recent data published in the scientific literature. The authorised uses of oilseed rape GT73 exclude cultivation, but data on gene flow, persistence and invasiveness derived from cultivation were considered as a worst case, representing conditions where exposure and potential impact are expected to be the highest, to assess possible environmental impacts resulting from seed import spills. In the documentation provided by Austria and in the scientific literature, the EFSA GMO Panel could not identify new scientific evidence that indicates that the import, processing and feed uses of oilseed rape GT73 in the EU pose a significant and imminent risk to the environment. The EFSA GMO Panel does not consider the occurrence of occasional feral oilseed rape GT73 plants, pollen dispersal and consequent cross-pollination as environmental harm in itself. In conclusion, the EFSA GMO Panel considers that, based on the documentation supplied by Austria and a review of recent scientific literature, there is no specific scientific evidence in terms of risk to the environment that would support the notification of a safeguard clause measure under Article 23 of Directive 2001/18/EC nor its prolongation, and that would invalidate its previous risk assessments of oilseed rape GT73

Scientific Opinion on a request from the European Commission for the assessment of the new scientific elements supporting the prolongation of prohibition of the placing on the market of maize MON 863 for food and feed purposes in Austria

Austria notified the European Commission of its new scientific elements justifying the prolongation for three additional years of the implementation of a national safeguard measure prohibiting the placing on the market of genetically modified maize MON 863 in Austria. Subsequently, the European Commission asked the European Food Safety Authority (EFSA) to assess the new scientific information supporting the prolongation of the prohibition. Having considered the information provided by Austria and all relevant scientific publications, the EFSA Panel on Genetically Modified Organisms (GMO Panel) concluded that the new scientific elements submitted by the Austrian Authorities do not lead EFSA to reconsider the conclusions in its opinions on maize MON 863

New algorithm improves fine structure of the barley consensus SNP map

<p>Abstract</p> <p>Background</p> <p>The need to integrate information from multiple linkage maps is a long-standing problem in genetics. One way to visualize the complex ordinal relationships is with a directed graph, where each vertex in the graph is a bin of markers. When there are no ordering conflicts between the linkage maps, the result is a directed acyclic graph, or DAG, which can then be linearized to produce a consensus map.</p> <p>Results</p> <p>New algorithms for the simplification and linearization of consensus graphs have been implemented as a package for the R computing environment called DAGGER. The simplified consensus graphs produced by DAGGER exactly capture the ordinal relationships present in a series of linkage maps. Using either linear or quadratic programming, DAGGER generates a consensus map with minimum error relative to the linkage maps while remaining ordinally consistent with them. Both linearization methods produce consensus maps that are compressed relative to the mean of the linkage maps. After rescaling, however, the consensus maps had higher accuracy (and higher marker density) than the individual linkage maps in genetic simulations. When applied to four barley linkage maps genotyped at nearly 3000 SNP markers, DAGGER produced a consensus map with improved fine structure compared to the existing barley consensus SNP map. The root-mean-squared error between the linkage maps and the DAGGER map was 0.82 cM per marker interval compared to 2.28 cM for the existing consensus map. Examination of the barley hardness locus at the 5HS telomere, for which there is a physical map, confirmed that the DAGGER output was more accurate for fine structure analysis.</p> <p>Conclusions</p> <p>The R package DAGGER is an effective, freely available resource for integrating the information from a set of consistent linkage maps.</p

Large scale analysis of positional effects of single-base mismatches on microarray gene expression data

<p>Abstract</p> <p>Background</p> <p>Affymetrix GeneChips utilize 25-mer oligonucleotides probes linked to a silica surface to detect targets in solution. Mismatches due to single nucleotide polymorphisms (SNPs) can affect the hybridization between probes and targets. Previous research has indicated that binding between probes and targets strongly depends on the positions of these mismatches. However, there has been substantial variability in the effect of mismatch type across studies.</p> <p>Methods</p> <p>By taking advantage of naturally occurring mismatches between rhesus macaque transcripts and human probes from the Affymetrix U133 Plus 2 GeneChip, we collected the largest 25-mer probes dataset with single-base mismatches at each of the 25 positions on the probe ever used in this type of analysis.</p> <p>Results</p> <p>A mismatch at the center of a probe led to a greater loss in signal intensity than a mismatch at the ends of the probe, regardless of the mismatch type. There was a slight asymmetry between the ends of a probe: effects of mismatches at the 3' end of a probe were greater than those at the 5' end. A cross study comparison of the effect of mismatch types revealed that results were not in good agreement among different reports. However, if the mismatch types were consolidated to purine or pyrimidine mismatches, cross study conclusions could be generated.</p> <p>Conclusion</p> <p>The comprehensive assessment of the effects of single-base mismatches on microarrays provided in this report can be useful for improving future versions of microarray platform design and the corresponding data analysis algorithms.</p

Assessment of genetically modified maize MIR604 for renewal authorisation under Regulation (EC) No 1829/2003 (application EFSA‐GMO‐RX‐013)

Following the submission of application EFSA‐GMO‐RX‐013 under Regulation (EC) No 1829/2003 from Syngenta Crop Protection NV/SA, the EFSA Panel on Genetically Modified Organisms (GMO) was asked to deliver a scientific risk assessment on the data submitted in the context of the renewal of authorisation application for the insect‐resistant genetically modified maize MIR604, for food and feed uses, excluding cultivation within the EU. The data received in the context of this renewal application contained post‐market environmental monitoring reports, a systematic search and evaluation of literature, updated bioinformatic analyses, and additional documents or studies performed by or on behalf of the applicant. The GMO Panel assessed these data for possible new hazards, modified exposure or new scientific uncertainties identified during the authorisation period and not previously assessed in the context of the original application. Under the assumption that the DNA sequence of the event in maize MIR604 considered for renewal is identical to the corrected sequence of the originally assessed event, the GMO Panel concludes that there is no evidence in renewal application EFSA‐GMO‐RX‐013 for new hazards, modified exposure or scientific uncertainties that would change the conclusions of the original risk assessment on maize MIR604

Statement complementing the EFSA Scientific Opinion on application (EFSA‐GMO‐NL‐2009‐75) for placing on the market of genetically modified oilseed rape Ms8 × Rf3 × GT73 and subcombinations, which have not been authorised previously (i.e. Ms8 × GT73 and Rf3 × GT73) independently of their origin, for food and feed uses, import and processing, with the exception of isolated seed protein for food, under Regulation (EC) No 1829/2003), taking into consideration additional information

The EFSA Panel on Genetically Modified Organisms (GMO) previously assessed oilseed rape Ms8 × Rf3 × GT73 and its subcombinations Ms8 × GT73 and Rf3 × GT73 according to the scope as defined in the application EFSA‐GMO‐NL‐2009‐75, and was not in the position to complete the safety assessment of products rich in protein, such as rapeseed protein isolates or products of this nature in animal feeding. Following a mandate from the European Commission, the GMO Panel assessed a 28‐day toxicity study in mice with the glyphosate oxidoreductase (GOXv247) protein, provided to complement information related to application EFSA‐GMO‐NL‐2009‐75 for the placing on the market of oilseed rape Ms8 × Rf3 × GT73 and its subcombinations Ms8 × GT73 and Rf3 × GT73, for food and feed uses, import and processing, with the exception of isolated seed protein for food. The 28‐day toxicity study on Escherichia coli‐ produced GOXv247 protein did not show adverse effects in mice, at the gavage doses up to 1000 mg/kg body weight (bw) per day. Taking into account its previous assessment on EFSA‐GMO‐NL‐2009‐75 and the outcome of the 28‐day toxicity study in mice with the GOXv247 protein provided in this mandate, the GMO Panel, based on a weight of evidence approach, concludes that food and feed containing, consisting and produced from genetically modified oilseed rape Ms8 × Rf3 × GT73 and its sub combinations Ms8 × GT73 and Rf3 × GT73, are as safe as its conventional counterpart, according to the scope as defined in the application EFSA‐GMO‐NL‐2009‐75

Assessment of genetically modified maize MON 88017 for renewal authorisation under Regulation (EC) No 1829/2003 (application EFSA‐GMO‐RX‐014)

Following the submission of application EFSA‐GMO‐RX‐014 under Regulation (EC) No 1829/2003 from Monsanto Company the Panel on Genetically Modified Organisms of the European Food Safety Authority was asked to deliver a scientific risk assessment on the data submitted in the context of the renewal of authorisation application for the insect‐resistant and herbicide‐tolerant genetically modified maize MON 88017, for food and feed uses, excluding cultivation within the EU. The data received in the context of this renewal application contained post‐market environmental monitoring reports, a systematic search and evaluation of literature, updated bioinformatic analyses, and additional documents or studies performed by or on behalf of the applicant. The GMO Panel assessed these data for possible new hazards, modified exposure or new scientific uncertainties identified during the authorisation period and not previously assessed in the context of the original application. Under the assumption that the DNA sequence of the event in maize MON 88017 considered for renewal is identical to the sequence of the originally assessed event, the GMO Panel concludes that there is no evidence in renewal application EFSA‐GMO‐RX‐014 for new hazards, modified exposure or scientific uncertainties that would change the conclusions of the original risk assessment on maize MON 88017