Development of a construct-based risk assessment framework for genetic engineered crops

Challenges of automation and scale: Bioinformatics and the evaluation of proteins to support genetically modified product safety assessments

Bioinformatic analyses of protein sequences play an important role in the discovery and subsequent safety assessment of insect control proteins in Genetically Modified (GM) crops. Due to the rapid adoption of high-throughput sequencing methods over the last decade, the number of protein sequences in GenBank and other public databases has increased dramatically. Many of these protein sequences are the product of whole genome sequencing efforts, coupled with automated protein sequence prediction and annotation pipelines. Published genome sequencing studies provide a rich and expanding foundation of new source organisms and proteins for insect control or other desirable traits in GM products. However, data generated by automated pipelines can also confound regulatory safety assessments that employ bioinformatics. Largely this issue does not arise due to underlying sequence, but rather its annotation or associated metadata, and the downstream integration of that data into existing repositories. Observations made during bioinformatic safety assessments are described.

Genetic Transformation of Sugarcane, Current Status and Future Prospects

Sugarcane (Saccharum spp.) is a tropical and sub-tropical, vegetative-propagated crop that contributes to approximately 80% of the sugar and 40% of the world's biofuel production. Modern sugarcane cultivars are highly polyploid and aneuploid hybrids with extremely large genomes (>10 Gigabases), that have originated from artificial crosses between the two species, Saccharum officinarum and S. spontaneum. The genetic complexity and low fertility of sugarcane under natural growing conditions make traditional breeding improvement extremely laborious, costly and time-consuming. This, together with its vegetative propagation, which allows for stable transfer and multiplication of transgenes, make sugarcane a good candidate for crop improvement through genetic engineering. Genetic transformation has the potential to improve economically important properties in sugarcane as well as diversify sugarcane beyond traditional applications, such as sucrose production. Traits such as herbicide, disease and insect resistance, improved tolerance to cold, salt and drought and accumulation of sugar and biomass have been some of the areas of interest as far as the application of transgenic sugarcane is concerned. Although there have been much interest in developing transgenic sugarcane there are only three officially approved varieties for commercialization, all of them expressing insect-resistance and recently released in Brazil. Since the early 1990's, different genetic transformation systems have been successfully developed in sugarcane, including electroporation, Agrobacterium tumefaciens and biobalistics. However, genetic transformation of sugarcane is a very laborious process, which relies heavily on intensive and sophisticated tissue culture and plant generation procedures that must be optimized for each new genotype to be transformed. Therefore, it remains a great technical challenge to develop an efficient transformation protocol for any sugarcane variety that has not been previously transformed. Additionally, once a transgenic event is obtained, molecular studies required for a commercial release by regulatory authorities, which include transgene insertion site, number of transgenes and gene expression levels, are all hindered by the genomic complexity and the lack of a complete sequenced reference genome for this crop. The objective of this review is to summarize current techniques and state of the art in sugarcane transformation and provide information on existing and future sugarcane improvement by genetic engineering.

Safety evaluation of E12, W8, X17, and Y9 potatoes: Nutritional evaluation and 90-day subchronic feeding study in rats

The nutritional and health effects of four biotech potato events, E12, W8, X17, and Y9, were evaluated in a subchronic rodent feeding study. E12 contains pSIM1278 insert DNA derived from potato and designed to down regulate potato genes through RNAi. These changes result in reduced black spot and reduced acrylamide. W8, X17, and Y9 contain the DNA inserts from pSIM1278 and pSIM1678 to further reduce acrylamide and express a gene from wild potato that protects against late blight. Rats were fed diets containing 20% cooked, dried potatoes from these four events and three conventional potato varieties. Compositional analyses of the processed potatoes and the rodent diets demonstrated comparability between the four events and their respective conventional varieties. Rats consumed the diets for 90 days and were evaluated for body weight, dietary intake, clinical signs, ophthalmology, neurobehavioral parameters, clinical pathology, organ weights, gross pathology, and histopathology. No adverse effects were observed as a result of test diet consumption. These results support the conclusion that foods containing E12, W8, X17, or Y9 potatoes are as safe, wholesome and nutritious as foods from conventional potato varieties.

Familiarity in the Context of Risk Assessment of Transgenic Crops: Focus on Some Countries in the Americas

Problem formulation is the formal opening stage of a risk assessment that determines its purpose and scope and hence guides the gathering of information data. The concepts of familiarity and history of safe use are an integral part of problem formulation. These concepts do not replace the case-by-case approach and are not taken as safety standards but are valuable components of the process that shape the generation of plausible, testable risk hypotheses. The International Life Sciences Institutes in Brazil and Argentina have facilitated numerous discussions on the scientific principles for risk assessment of transgenic crops in the Latin American region in the past 5–6 years. The session held at ISBR 15th elaborated on the familiarity concept and derived tools and their role in the evolution of risk evaluation criteria. Examples of how different countries in the Americas interpret and apply these conceptual tools show that familiarity is a valuable concept, although terms are very often confused and vaguely defined. Formalizing these terms with clear definitions and scope of application in guidelines and regulatory documents would reduce ambiguity, enhance predictability, and add transparency to the evaluation processes.