Enabling Genome Editing for Enhanced Agricultural Sustainability

Agricultural sustainability encompasses environmental, social, and economic aspects, all of which are continually shifting due changing environmental pressures and societal expectations. A range of strategies are required to address these challenges, and these include the use of innovation and adoption of the best available practices and technologies. Advances in biotechnologies, including genome editing, and their application in plant breeding and research are expected to provide a range of benefits that contribute to all aspects of agricultural sustainability. However, adoption of these technologies needs to be supported by proportionate, coherent, forward-looking, and adaptable policies and regulatory approaches. In this Perspective, we reflect on the regulatory challenges associated with commercialising a transgenic crop, and developments thus far in providing regulatory clarity for genome edited crops. We aim to demonstrate that much remains to be done to shift towards a more proportionate and enabling approach before the potential benefits of genome edited crops can be realised. The implications of precautionary and disproportionate regulation are also discussed.

Regulation of Synthetic Biology: Developments Under the Convention on Biological Diversity and Its Protocols

The primary international forum deliberating the regulation of "synthetic biology" is the Convention on Biological Diversity (CBD), along with its subsidiary agreements concerned with the biosafety of living modified organisms (LMOs; Cartagena Protocol on Biosafety to the CBD), and access and benefit sharing in relation to genetic resources (Nagoya Protocol to the CBD). This discussion has been underway for almost 10 years under the CBD agenda items of "synthetic biology" and "new and emerging issues relating to the conservation and sustainable use of biological diversity," and more recently within the scope of Cartagena Protocol topics including risk assessment and risk management, and "digital sequence information" jointly with the Nagoya Protocol. There is no internationally accepted definition of "synthetic biology," with it used as an umbrella term in this forum to capture "new" biotechnologies and "new" applications of established biotechnologies, whether actual or conceptual. The CBD debates are characterized by polarized views on the adequacy of existing regulatory mechanisms for "new" types of LMOs, including the scope of the current regulatory frameworks, and procedures and tools for risk assessment and risk mitigation and/or management. This paper provides an overview of international developments in biotechnology regulation, including the application of the Cartagena Protocol and relevant policy developments, and reviews the development of the synthetic biology debate under the CBD and its Protocols, including the major issues expected in the lead up to and during the 2020 Biodiversity Conference.

A first genome assembly of the barley fungal pathogen Pyrenophora teres f. teres

Background

Pyrenophora teres f. teres is a necrotrophic fungal pathogen and the cause of one of barley's most important diseases, net form of net blotch. Here we report the first genome assembly for this species based solely on short Solexa sequencing reads of isolate 0-1. The assembly was validated by comparison to BAC sequences, ESTs, orthologous genes and by PCR, and complemented by cytogenetic karyotyping and the first genome-wide genetic map for P. teres f. teres.

Results

The total assembly was 41.95 Mbp and contains 11,799 gene models of 50 amino acids or more. Comparison against two sequenced BACs showed that complex regions with a high GC content assembled effectively. Electrophoretic karyotyping showed distinct chromosomal polymorphisms between isolates 0-1 and 15A, and cytological karyotyping confirmed the presence of at least nine chromosomes. The genetic map spans 2477.7 cM and is composed of 243 markers in 25 linkage groups, and incorporates simple sequence repeat markers developed from the assembly. Among predicted genes, non-ribosomal peptide synthetases and efflux pumps in particular appear to have undergone a P. teres f. teres-specific expansion of non-orthologous gene families.

Conclusions

This study demonstrates that paired-end Solexa sequencing can successfully capture coding regions of a filamentous fungal genome. The assembly contains a plethora of predicted genes that have been implicated in a necrotrophic lifestyle and pathogenicity and presents a significant resource for examining the bases for P. teres f. teres pathogenicity.