Michael G. K. Jones

Cocoa pod borer is the most serious and damaging pest of cocoa in Southeast Asia. Annually, crop production losses due to cocoa pod borer (CPB) damages are about 5–20%. Occasionally, total loss in production can be due to CPB damages. Chemical insecticide spraying is the usual method employed in the plantations. This resulted in chemical residues that are not biodegradable found on the plants and cocoa beans. Therefore, alternative approaches to managing CPB need to be explored. This chapter describes the use of RNA interference (RNAi) technology to manage CPB. Several genes involved in vital metabolic processes of the insect have been identified via bioinformatics. Feeding the insects with the dsRNA causes increased insect mortality. Analysis using quantitative PCR confirmed the suppression of the target genes.

New breeding technologies (NBTs) such as genome editing have the potential to revolutionize the landscape of agricultural biotechnology. With their precision, cost, and time efficiency, NBTs can help tackle issues including food security and climate change. As is the case with other frontier technologies, the successful adoption of NBTs is directly linked to the global regulatory architecture. Presently, the fate of NBTs is mired in regulatory uncertainty, perpetuated by a trans-Atlantic divide, with some countries reviewing their existing biosafety frameworks. The debate is centered on the basic definitions of biotechnology products, the kinds of triggers used, and the possibility of excluding some variants of NBTs. The regulatory divide has also created nontrade barriers affecting the ability of developing countries to benefit from NBTs adequately. There are related contentious issues such as the role of socioeconomic factors in regulations and achieving a science-based risk assessment regime. The fragmented international regulatory regime, notably the Cartagena Protocol on Biosafety, has posed many impediments to harmonization and has been unable to generate consensus among states. While many countries, including Australia, Argentina, and Brazil, have opted to review existing legislation, the European Union has taken a highly conservative approach toward NBTs, declaring them similar to genetically modified organisms (GMOs). This outcome is unfavorable not only for building toward harmonization but has also reduced member states’ ability to develop and benefit from NBTs. Distinguishing NBTs from previous methods of plant breeding is not only scientifically accurate but also crucial for their democratized commercialization. Developing countries that are dependent on agricultural trade will suffer if existing regulatory regimes are not changed. Furthermore, social acceptance of NBTs is also a significant determinant of their success.

Australia has a well-developed system for the regulation of genetically manipulated (GM) and gene-edited (GEd) organisms, including grains and horticultural crop plants. The aim is to protect the health and safety of people and the environment by identifying any risks posed by gene technology. It is based on two Commonwealth legislative acts, the Gene Technology (GT) Act 2000 and the Gene Technology Regulations 2001, with corresponding State and Territory laws. The GT Act included establishing the Office of the Gene Technology Regulator (OGTR), which is overseen by the Gene Technology Regulator, who takes advice and consults with a range of bodies, and is responsible for ensuring the monitoring and compliance of the GT legislation. There have been a series of reviews of the National Gene Technology Scheme to modernize and future-proof it in response to new scientific developments. Following a consultative review process (2016–2019), to address national policy on the products of various new GEd technologies (including site-directed nucleases: SDN-1, SDN-2, SDN-3 and olignucleotide-directed mutagenesis—ODM), in October 2019 the decision was released to deregulate SDN-1 products not generated via transgenic approaches, but not those which used SDN-2, ODM or SDN-3 technologies, which remain captured as GMOs. Thus only products of SDN-1 technology which do not contain any externally introduced DNA bases can be grown in the same way as products of conventional breeding activities.

In New Zealand, GM and GEd organisms are regulated by the Hazardous Substances and New Organisms (HSNO) Act 1996 administered by the Environmental Protection Agency (EPA). In an initial determination in 2012, the EPA determined that organisms produced using GEd methods, where no foreign DNA remained in the edited plant, were not GMOs. However, in 2014, following an appeal to this decision by the Sustainability Council of New Zealand Trust (Sustainability Council) in the High Court, the determination of the presiding judge was to overturn the EPA’s decision. Thus the current status of all GEd products in New Zealand is that they are regulated as GMOs.

Nonliving food products of GM or GEd technology are overseen by Food Standards Australia New Zealand (FSANZ); the Australia New Zealand Food Standards Code applies to GM and GEd foods. FSANZ is currently reviewing its position on GEd foods, and at present considers applications for GEd food on a case-by-case basis.

Plant-parasitic nematodes are found in most places in the world. The most prevalent ones have a broad host range, so wherever they are located, whether in a backyard garden or on a commercial farm, they are likely to be pests. For this reason, readily accessible, relatively inexpensive, and environmentally friendly methods of control have been sought and applied to control many species of these pests. One such control strategy is organic amendments, of which many types have been demonstrated as a potentially successful method for controlling different types of plant nematodes. This chapter discusses the biochemical and molecular mechanisms underlying the efficacy of organic amendments, the direct effects of active compounds, and the indirect adverse impact on various aspects of the life cycle of different plant-parasitic nematodes. Caveats in interpreting data on the applications of organic amendments to control nematodes and other factors that may dictate their efficacy are also discussed.

Nematodes are ecologically ubiquitous and include free living and parasites of almost all organisms. They have simple wormlike bodies, are highly adaptable, and display the ability to locate, invade, and manipulate host physiology in parasitic forms. Free-living nematodes play a role in maintaining ecosystems by feeding on dead matter or microbes, while parasitic nematodes cost billions of dollars by affecting human and animal health and crop production. Various control methods are being developed to control parasitic nematodes including chemicals/drugs, biological agents, and in the case of plants, plant breeding for resistance and transgenic plants. Depending on the situation, different control methods often have limitations, and a strategy aiming to confer maximum control with the use of minimum resources can be feasible depending on the approach and extent of infestation.

The biology of migratory plant parasitic nematodes has been less studied than that of the sedentary endoparasites. The damage they cause is less obvious, their presence and number are more difficult to quantify and they are difficult organisms to study. Nevertheless, they are economically serious pests of many crops, from wheat and barley grown in low rainfall areas to horticultural crops (e.g. Lilium longiflorum) and tropical crops such as coffee, banana and sugarcane. The most studied migratory nematodes are the root lesion nematodes, Pratylenchus spp., the burrowing nematode Radopholus similis and the rice root nematode Hirschmanniella oryzae. In the life cycle of migratory nematodes apart from the egg, all stages of juveniles and adults are motile and can enter and leave host roots. They do not induce the formation of a permanent feeding site, but feed from individual host cells. They create pathways for entry of other root pathogens, often resulting in lesions, stunted roots, yellowing of leaves and plants showing symptoms of water stress, leading to yield loss and decreased quality of produce. In terms of genetic plant defences, no major genes for resistance to migratory nematodes have been found, and resistance breeding is usually based on QTL analysis and marker-assisted selection to combine the best minor resistance genes. Feeding damage reduces root function, and root damage and necrotic lesions the nematodes cause can then make them leave the root and seek others to parasitise. Infestation induces classical plant defence responses and changes in host metabolism which reflects the damage they cause, although detailed studies are lacking. New genomic resources are becoming available to study migratory endoparasites, and the knowledge gained can contribute to improved understanding of their interactions with hosts. Notably transcriptomes of Pratylenchus coffeae, Pratylenchus thornei, Pratylenchus zeae, R. similis and H. oryzae and the first genomic sequence, for P. coffeae, are now available. From these data, some candidate effector genes required for parasitism have been identified: many effectors similar to those found in sedentary endoparasites are present, with the exception of those thought to be involved in formation of feeding sites induced by the sedentary parasites. Belowground defence, in the form of enhanced resistance to migratory parasites, may also be achieved by transgenic expression of modified cysteine protease inhibitors (cystatins), anti-root invasion peptides and host-induced gene silencing (RNAi) strategies, demonstrating that migratory nematodes are amenable to control by these technologies. New more environmentally friendly nematicides, combined with better biological control agents, can be applied or used in seed coatings in integrated pest management approaches to defend roots from attack by migratory nematodes.

Viruses have traditionally been seen as pathogens of plants and animals. Recent research has shown that most viruses induce no pathology in natural plant hosts and in some cases they may be of benefit in reducing damage from both biotic and abiotic stressors. New technologies are revealing that viruses are far more abundant and diverse than previously known, and unexpected roles as symbionts and as sources of genetic raw material for evolution are informing a new appreciation of the roles plant viruses play in nature.

Of all the economically important plant parasitic nematodes, root-knot nematodes (Meloidogyne species) are amongst the most widespread, the best recognized and most widely studied. This is partly because infected roots develop galls where the nematodes feed, which with severe infection give roots a ‘knotted’ appearance. They have a remarkably wide host range, and are ubiquitous especially in tropical and sub-tropical regions of the world. Juveniles move through the soil rhizosphere and locate host roots, in which they migrate intercellularly to pro-vascular cells to form a feeding site. Here, in response to nematode secretions, they re-program the development of about 6 cells into ‘giant cells’, which provide them with the nourishment needed for them to complete their life cycle of about 4–5 weeks. Giant cells form by repeated mitosis without cytokinesis, and so become multi-nucleate. Wall ingrowths typical of transfer cells develop both where giant cell walls contact vascular elements and between neighbouring giant cells. These amplify the surface area of the cell membrane and enable solutes and water to enter the cells, and to move between giant cells in response to nematode feeding. The developing giant cells become filled with cytoplasm, prominent amoeboid nuclei, mitochondria and small vacuoles, and appear to be very active metabolically. Giant cell development is accompanied with a host of changes in gene expression, cytoskeleton changes, plant hormone changes and structural changes. The delicate interaction between the nematode and its associated giant cells is mediated via feeding tubes, derived from nematode gland secretions, which act as an ultrafilter and pressure regulator. As the infective worm-like J2 larvae develop via 3 moults to reach the adult stage, they swell and adult females become spherical, and lays eggs into a gelatinous matrix. Most root-knot nematodes reproduce by mitotic parthenogenesis, although facultative meiotic parthenogenesis also occurs (e.g. in M. hapla). The availability of new molecular technologies that enable detailed study of gene expression and regulation in giant cells, and new genomic technologies applied both to host and nematode pathogen, is leading to rapid advances in understanding host-pathogen interactions of this important plant pest species.