Key Molecular and Metabolic Processes Used for Genetic Engineering to Improve Freezing Tolerance in Cereals

It has been estimated recently that cereals are harvested on 700 million hectares (Mha) worldwide (Dunwell, 2014), and also that, due to low temperature damage, worldwide losses in crop production amount to about US$2 billion each year (Sanghera et al., 2011). In spite of the urgent need for more cold- or frost-tolerant cereal varieties, classical breeding programmes have shown limited progress in improving freezing tolerance (Thomashow, 1999). This lack of success is due mainly to the fact that the physiological process, i.e. the cold acclimation that leads to the development of freezing tolerance, is quite a complex quantitative trait. However, the deeper insight provided by different ‘omics’ technologies has made possible knowledge-based engineering of more stress-resistant plants; while the recent developments in cereal transformation methodology offer the technology to realize these aims. Since many recently published book chapters and reviews summarize our current knowledge on plant abiotic stress tolerance, this chapter focuses particularly on freezing tolerance, especially in cereals

High-throughput Agrobacterium-mediated barley transformation

<p>Abstract</p> <p>Background</p> <p>Plant transformation is an invaluable tool for basic plant research, as well as a useful technique for the direct improvement of commercial crops. Barley (<it>Hordeum vulgare</it>) is the fourth most abundant cereal crop in the world. It also provides a useful model for the study of wheat, which has a larger and more complex genome. Most existing barley transformation methodologies are either complex or have low (<10%) transformation efficiencies.</p> <p>Results</p> <p>A robust, simple and reproducible barley transformation protocol has been developed that yields average transformation efficiencies of 25%. This protocol is based on the infection of immature barley embryos with <it>Agrobacterium </it>strain AGL1, carrying vectors from the pBract series that contain the <it>hpt </it>gene (conferring hygromycin resistance) as a selectable marker. Results of large scale experiments utilising the <it>luc </it>(firefly luciferase) gene as a reporter are described. The method presented here has been used to produce hundreds of independent, transgenic plant lines and we show that a large proportion of these lines contain single copies of the <it>luc </it>gene.</p> <p>Conclusion</p> <p>This protocol demonstrates significant improvements in both efficiency and ease of use over existing barley transformation methods. This opens up opportunities for the development of functional genomics resources in barley.</p

Characterising standard genetic parts and establishing common principles for engineering legume and cereal roots

Plant synthetic biology and cereal engineering depends on the controlled expression of transgenes of interest. Most engineering in plant species to date has relied heavily on the use of a few, well-established constitutive promoters to achieve high levels of expression; however, the levels of transgene expression can also be influenced by the use of codon optimisation, intron-mediated enhancement and varying terminator sequences. Most of these alternative approaches for regulating transgene expression have only been tested in small-scale experiments, typically testing a single gene of interest. It is therefore difficult to interpret the relative importance of these approaches and to design engineering strategies that are likely to succeed in different plant species, particularly if engineering multi-genic traits where the expression of each transgene needs to be precisely regulated. Here we present data on the characterisation of 46 promoters and 10 terminators in Medicago truncatula, Lotus japonicus, Nicotiana benthamiana and Hordeum vulgare, as well as the effects of codon optimisation and intron-mediated enhancement on the expression of two transgenes in H. vulgare. We have identified a core set of promoters and terminators of relevance to researchers engineering novel traits in plant roots. In addition, we have shown that combining codon optimisation and intron-mediated enhancement increases transgene expression and protein levels in barley. Based on our study, we recommend a core set of promoters and terminators for broad use, and also propose a general set of principles and guidelines for those engineering cereal species

The status under EU Law of Organisms developed through novel genomic techniques

In a ruling on 25 July 2018, the Court of Justice of the European Union concluded that organisms obtained by means of techniques/methods of mutagenesis constitute GMOs in the sense of Directive 2001/18, and that organisms obtained by means of techniques/methods of directed mutagenesis are not excluded from the scope of the Directive. Following the ruling, there has been much debate about the possible wider implications of the ruling. In October 2019, the Council of the European Union requested the European Commission to submit, in light of the CJEU ruling, a study regarding the status of novel genomic techniques under Union Law. For the purpose of the study, the Commission initiated stakeholder consultations early in 2020. Those consultations focused on the technical status of novel genomic techniques. This article aims to contribute to the discussion on the legal status of organisms developed through novel genomic techniques, by offering some historical background to the negotiations on the European Union (EU) GMO Directives as well as a technical context to some of the terms in the Directive, and by analysing the ruling. The article advances that (i) the conclusion that organisms obtained by means of techniques/methods of mutagenesis constitute GMOs under the Directive means that the resulting organisms must comply with the GMO definition, ie the genetic material of the resulting organisms has been altered in a way that does not occur naturally by mating and/or natural recombination; (ii) the conclusion that organisms obtained by means of techniques/methods of directed mutagenesis were not intended to be excluded from the scope of the Directive is not inconsistent with the negotiation history of the Directive; (iii) whether an organism falls under the description of “obtained by means of techniques/methods of directed mutagenesis” depends on whether the genetic material of the resulting organisms has been altered in a way that does not occur naturally by mating and/or natural recombination. Finally, the article offers an analysis of the EU GMO definition, concluding that for an organism to be a GMO in the sense of the Directive, the technique used, as well as the genetic alterations of the resulting organism, must be considered

Exploring the metabolic and physiological roles of HQT in S. lycopersicum by gene editing

The most abundant phenolic compound in Solanaceous plants is chlorogenic acid (CGA), which possesses protective properties such as antimicrobial and antioxidant activities. These properties are particularly relevant when plants are under adverse conditions, such as pathogen attack, excess light, or extreme temperatures that cause oxidative stress. Additionally, CGA has been shown to absorb UV-B light. In tomato and potato, CGA is mainly produced through the HQT pathway mediated by the enzyme hydroxycinnamoyl-CoA:quinate hydroxycinnamoyl transferase. However, the absence of natural or induced mutants of this gene has made it unclear whether other pathways contribute to CGA production and accumulation. To address this question, we used CRISPR technology to generate multiple knock-out mutant lines in the tomato HQT gene. The resulting slhqt plants did not accumulate CGA or other caffeoylquinic acids (CQAs) in various parts of the plant, indicating that CQA biosynthesis depends almost entirely on the HQT pathway in tomato and, likely, other Solanaceous crops. We also found that the lack of CGA in slhqt plants led to higher levels of hydroxycinnamoyl-glucose and flavonoids compared to wild-type plants. Gene expression analysis revealed that this metabolic reorganization was partly due to flux redirection, but also involved modulation of important transcription factor genes that regulate secondary metabolism and sense environmental conditions. Finally, we investigated the physiological role of CGA in tomato and found that it accumulates in the upper epidermis where it acts as a protector against UV-B irradiation

Overexpression of Two Upstream Phospholipid Signaling Genes Improves Cold Stress Response and Hypoxia Tolerance, but Leads to Developmental Abnormalities in Barley

Phosphatidylinositol transfer protein (PITP) and phosphatidylinositol 4 kinase (PI4K) are upstream regulatory elements of the phospholipid signaling pathway. PITP and PI4K over expressing transgenic barley lines were developed and studied. We revealed that the over expression of the PITP and PI4K genes increased stress tolerance during hypoxic cold stress, but not during salinity stress, and differences were also found in the level of frost tolerance. On the other hand, we ralised that the over expression of these upstream signaling elements led to more phenotypic abnormalities than in other transgenic studies working with effector genes or even transcription factors. We hypothesize that this high level of abnormalities are the consequence of the modulation of a very upstream signal transduction pathway elements

Attribution of neuropsychiatric symptoms and prioritisation of evidence in the diagnosis of neuropsychiatric lupus:a mixed method study

OBJECTIVE: Neuropsychiatric lupus (NPSLE) is challenging to diagnose. Many neuropsychiatric symptoms, such as headache and hallucinations, cannot be verified by tests or clinician assessment. We investigated prioritisations of methods for diagnosing NPSLE and attributional views.METHODS: Thematic and comparative analyses were used to investigate how clinicians prioritise sources of evidence from a 13-item list, and explore discordances in clinician and patient perspectives on attribution.RESULTS: We identified high levels of variability and uncertainty in clinicians' assessments of neuropsychiatric symptoms in SLE patients. In attributional decisions, clinicians (surveys n = 400, interviews n = 50) ranked clinicians' assessments above diagnostic tests (many of which they reported were often unenlightening in NPSLE). Clinicians ranked patient opinion of disease activity last, and 46% of patients reported never/rarely having been asked if their SLE was flaring, despite experienced patients often having "attributional insight". SLE Patients (surveys n = 676, interviews n = 27) estimated higher attributability of neuropsychiatric symptoms to the direct effects of SLE on the nervous system than clinicians (p &lt; 0.001 for all symptoms excluding mania), and 24% reported that their self-assessment of disease activity was never/rarely concordant with their clinicians. Reports of misattributions were common, particularly of non-verifiable diffuse symptoms. Terminology differed between clinicians and influenced attribution estimates.CONCLUSION: NPSLE diagnostic tests and clinician assessments have numerous limitations, particularly in detecting diffuse neuropsychiatric symptoms that can be directly attributable and benefit from immunosuppression. Our findings suggest that incorporating patient attributional insights-although also subject to limitations-may improve attribution decision-making. Consensus regarding terminology and interpretations of "direct attributability" is required.</p

Speed breeding in growth chambers and glasshouses for crop breeding and model plant research

‘Speed breeding’ (SB) shortens the breeding cycle and accelerates crop research through rapid generation advancement. SB can be carried out in numerous ways, one of which involves extending the duration of plants’ daily exposure to light, combined with early seed harvest, to cycle quickly from seed to seed, thereby reducing the generation times for some long-day (LD) or day-neutral crops. In this protocol, we present glasshouse and growth chamber–based SB approaches with supporting data from experimentation with several crops. We describe the conditions that promote the rapid growth of bread wheat, durum wheat, barley, oat, various Brassica species, chickpea, pea, grass pea, quinoa and Brachypodium distachyon. Points of flexibility within the protocols are highlighted, including how plant density can be increased to efficiently scale up plant numbers for single-seed descent (SSD). In addition, instructions are provided on how to perform SB on a small scale in a benchtop growth cabinet, enabling optimization of parameters at a low cost

Speed breeding is a powerful tool to accelerate crop research and breeding

The growing human population and a changing environment have raised significant concern for global food security, with the current improvement rate of several important crops inadequate to meet future demand1. This slow improvement rate is attributed partly to the long generation times of crop plants. Here, we present a method called ‘speed breeding’, which greatly shortens generation time and accelerates breeding and research programmes. Speed breeding can be used to achieve up to 6 generations per year for spring wheat (Triticum aestivum), durum wheat (T. durum), barley (Hordeum vulgare), chickpea (Cicer arietinum) and pea (Pisum sativum), and 4 generations for canola (Brassica napus), instead of 2–3 under normal glasshouse conditions. We demonstrate that speed breeding in fully enclosed, controlled-environment growth chambers can accelerate plant development for research purposes, including phenotyping of adult plant traits, mutant studies and transformation. The use of supplemental lighting in a glasshouse environment allows rapid generation cycling through single seed descent (SSD) and potential for adaptation to larger-scale crop improvement programs. Cost saving through light-emitting diode (LED) supplemental lighting is also outlined. We envisage great potential for integrating speed breeding with other modern crop breeding technologies, including high-throughput genotyping, genome editing and genomic selection, accelerating the rate of crop improvement