Research Trends and Challenges of Using CRISPR/Cas9 for Improving Rice Productivity

Nowadays, rice production faces significant challenges due to population pressure, global climate change, and outbreak of various pests and diseases. Breeding techniques used to improve rice traits include mutant breeding, cross breeding, heterogeneity, transformation, molecular markers, genome-wide association study (GWAS), and so on. Since the recently developed CRISPR/Cas9 technology can directly target a specific part of a desired gene to induce mutation, it can be used as a powerful means to expand genetic diversity of crops and develop new varieties. So far, CRISPR/Cas9 technology has been used for improving rice characteristics such as high yield, good quality, abundant nutrition, pest and disease resistance, herbicide resistance, and biotic and abiotic stress resistance. This review highlights the mechanisms and optimization of the CRISPR system and its application to rice crop, including resistance to biotic and abiotic stresses, and improved rice quality and yield.

Towards progressive regulatory approaches for agricultural applications of animal biotechnology

Traditional breeding techniques, applied incrementally over thousands of years, have yielded huge benefits in the characteristics of agricultural animals. This is a result of significant, measurable changes to the genomes of those animal species and breeds. Genome editing techniques may now be applied to achieve targeted DNA sequence alterations, with the potential to affect traits of interest to production of agricultural animals in just one generation. New opportunities arise to improve characteristics difficult to achieve or not amenable to traditional breeding, including disease resistance, and traits that can improve animal welfare, reduce environmental impact, or mitigate impacts of climate change. Countries and supranational institutions are in the process of defining regulatory approaches for genome edited animals and can benefit from sharing approaches and experiences to institute progressive policies in which regulatory oversight is scaled to the particular level of risk involved. To facilitate information sharing and discussion on animal biotechnology, an international community of researchers, developers, breeders, regulators, and communicators recently held a series of seven virtual workshop sessions on applications of biotechnology for animal agriculture, food and environmental safety assessment, regulatory approaches, and market and consumer acceptance. In this report, we summarize the topics presented in the workshop sessions, as well as discussions coming out of the breakout sessions. This is framed within the context of past and recent scientific and regulatory developments. This is a pivotal moment for determination of regulatory approaches and establishment of trust across the innovation through-chain, from researchers, developers, regulators, breeders, farmers through to consumers.

VIGE: virus-induced genome editing for improving abiotic and biotic stress traits in plants

Agricultural production is hampered by disease, pests, and environmental stresses. To minimize yield loss, it is important to develop crop cultivars with resistance or tolerance to their respective biotic and abiotic constraints. Transformation techniques are not optimized for many species and desirable cultivars may not be amenable to genetic transformation, necessitating inferior cultivar usage and time-consuming introgression through backcrossing to the preferred variety. Overcoming these limitations will greatly facilitate the development of disease, insect, and abiotic stress tolerant crops. One such avenue for rapid crop improvement is the development of viral systems to deliver CRISPR/Cas-based genome editing technology to plants to generate targeted beneficial mutations. Viral delivery of genomic editing constructs can theoretically be applied to span the entire host range of the virus utilized, circumventing the challenges associated with traditional transformation and breeding techniques. Here we explore the types of viruses that have been optimized for CRISPR/Cas9 delivery, the phenotypic outcomes achieved in recent studies, and discuss the future potential of this rapidly advancing technology.

Induced Breeding of Freshwater Fishes and Cost Benefit Analysis of a Selected Fish Hatchery in Jashore, Bangladesh

An investigation was carried out to know the induced breeding techniques of some firewater fish species such as rui (Labeo rohita), catla (Catla catla), silver carp (Hypophthalmichthys molitrix), grass carp (Ctenopharyngodon idella), common carp (Cyprinus carpio), bighead carp (Hypophthalmichthys nobilis), sharpunti (Puntius sarana) and bata (Labeo bata) at Ma Fatima Fish Hatchery in Chanchra, Jashore, Bangladesh. The cost-benefit analysis was also performed on this hatchery for three months from May to July, 2016. The brood fishes purchased from different local sources were used for spawning. The hatchery mainly practiced induced breeding by maintaining proper age and weight of brood stock during spawning. The ranges of fertilization and hatching rates of the experimental fishes were 80.04±1.44 % to 94.35±0.54% and 75.34±3.49% to 88.68±2.76%, respectively. Total spawn production was 960, 862 and 734 kg, and the total revenue income from spawn sell was BDT 2,883,500, 2,355,100 and 1,844,800 (BDT 85 = 1 US$) in May, June and July, respectively. Estimated capital cost was BDT 87,90,000, while the operating costs were BDT 1,810,650; 1,555,105 and 1,267,680 in May, June and July, respectively. The calculated cost-benefit ratios in May, June and July were 1.59, 1.51 and 1.46, respectively. The hatchery got the highest net profit of BDT (Bangladeshi Taka) 1,041,906 in May due to the highest production and higher price of spawn, and the lowest profit of BDT 546,176 was obtained in July. So, May was found to be the peak breeding month of Ma Fatima Hatchery. The estimated cost-benefit ratio indicated that the spawn production through induced breeding techniques was profitable for the hatchery owners.

Salt and Water Stress Responses in Plants

Climate change-driven ecological disturbances have a great impact on freshwater availability which hampers agricultural production. Currently, drought and salinity are the two major abiotic stress factors responsible for the reduction of crop yields worldwide. Increasing soil salt concentration decreases plant water uptake leading to an apparent water limitation and later to the accumulation of toxic ions in various plant organs which negatively affect plant growth. Plants are autotrophic organisms that function with simple inorganic molecules, but the underlying pathways of defense mechanisms are much more complex and harder to unravel. However, the most promising strategy to achieve sustainable agriculture and to meet the future global food demand, is the enhancement of crop stress tolerance through traditional breeding techniques and genetic engineering. Therefore, it is very important to better understand the tolerance mechanisms of the plants, including signaling pathways, biochemical and physiological responses. Although, these mechanisms are based on a well-defined set of basic responses, they can vary among different plant species.

Somatic Embryogenesis in Vitis for Genome Editing: Optimization of Protocols for Recalcitrant Genotypes

New Plant Breeding Techniques (NPBTs) protocols have been developed to produce new grape varieties with improved quantitative and qualitative characteristics. Reliable transformation protocols for grapes are based on the generation/induction of embryogenic callus cells that are then transformed. Varieties such as Italia have proven to be very recalcitrant to regeneration via somatic embryogenesis. In this work, the development of a protocol for improved production of embryogenic calluses is described. Two sterilization protocols were tested: (a) a lower active chlorine concentration for a longer time (LS); and (b) a higher chlorine concentration for a shorter time (HS), in combination with the absence or presence of citric acid in the growing substrate in the first growth media. The embryogenic calluses formation in Chardonnay, a cv. with a high embryogenic response, was significantly higher in presence of citric acid in the initial growing substrate regardless of the sterilization protocol. In Aglianico, a cv. with a lower embryogenic response, no significant differences were observed. Instead, in a recalcitrant cv. as Italia, we obtained a 13-fold increase in embryogenic calluses formation performing sterilization of flowers with the HS protocol compared to LS.

Essentially derived varieties in the era of new breeding techniques

The current study sets out to analyse the concept of "essentially derived variety" (EDV) envisaged by the plant variety protection regime when new breeding techniques (NBTs) are employed in the development of new plant varieties. The use of NBTs to develop new plant varieties has grown rapidly over the last years because of their ease of use and their high efficiency. NBT varieties are mono-parental and retain most of the genome of the initial variety, thus most of its essential characteristics. The problem arises when the initial variety used as the source of genetic variation is a variety protected by a plant variety right. In this case, the question is whether the EDV concept should apply to the second variety obtained by NBTs and what can break the EDV chain. It must be noted that the EDV concept has revolutionised the plant variety protection system since it introduced the principle of "limited dependence" as an exception to the general independence principle governing this system. Therefore, as it is an exception, it should be interpreted rigorously.

Genetics and Genomics of Fusarium Wilt of Chilies: A Review

Hot pepper (Capsicum annum L.) is a major spice crop and is used worldwide for its nutritional value. In the field, its plant is susceptible to various fungal diseases, including fusarium wilt, caused by soil-borne fungus Fusarium oxysporum f. sp. capsici, which can survive in the soil for several years. The infected plant can be recognized by the yellowing of older leaves and downward curling of apical shoots, followed by plant wilting and ultimately the death of the plant. The resistance mechanism in plants is controlled by a single dominant gene, and conventional plant breeding techniques are used to develop a wilt-resistant germplasm. Non-conventional techniques such as gene pyramiding and expression enhancement of antifungal genes could be used to shorten the time to develop resistance against fusarium wilt in hot peppers. In this review, we discuss different aspects of the disease and the molecular basis of resistance in chili/hot pepper plants. Furthermore, this review covers the scope of conventional and non-conventional breeding strategies and different management approaches used to tackle the disease.

The Generic Risks and the Potential of SDN-1 Applications in Crop Plants

The use of site-directed nucleases (SDNs) in crop plants to alter market-oriented traits is expanding rapidly. At the same time, there is an on-going debate around the safety and regulation of crops altered with the site-directed nuclease 1 (SDN-1) technology. SDN-1 applications can be used to induce a variety of genetic alterations ranging from fairly ‘simple’ genetic alterations to complex changes in plant genomes using, for example, multiplexing approaches. The resulting plants can contain modified alleles and associated traits, which are either known or unknown in conventionally bred plants. The European Commission recently published a study on new genomic techniques suggesting an adaption of the current GMO legislation by emphasizing that targeted mutagenesis techniques can produce genomic alterations that can also be obtained by natural mutations or conventional breeding techniques. This review highlights the need for a case-specific risk assessment of crop plants derived from SDN-1 applications considering both the characteristics of the product and the process to ensure a high level of protection of human and animal health and the environment. The published literature on so-called market-oriented traits in crop plants altered with SDN-1 applications is analyzed here to determine the types of SDN-1 application in plants, and to reflect upon the complexity and the naturalness of such products. Furthermore, it demonstrates the potential of SDN-1 applications to induce complex alterations in plant genomes that are relevant to generic SDN-associated risks. In summary, it was found that nearly half of plants with so-called market-oriented traits contain complex genomic alterations induced by SDN-1 applications, which may also pose new types of risks. It further underscores the need for data on both the process and the end-product for a case-by-case risk assessment of plants derived from SDN-1 applications.

Advances in breeding techniques for durable Septoria tritici blotch (STB) resistance in cereals

Septoria tritici blotch (STB), caused by the hemibiotrophic fungus Zymoseptoria tritici, is one of the most important foliar diseases of winter cereal crops. Recent advances are helping to understand the genetic basis and architecture of resistance to STB. To date, at least 22 genes for qualitative resistance and over 200 quantitative trait loci (QTL) for quantitative resistance have been identified in cereals. This knowledge is enabling cereal breeding programs to develop varieties with more durable resistance to STB. This chapter reviews recent research on genetic resistance loci and breeding strategies based on both conventional and biotechnology-based breeding approaches (molecular marker/genomic-assisted breeding, genetic transformation, and gene-editing) to achieve achieving durable resistance to STB infection and minimise grain yield losses.