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1.
Epigenomic features of DNA G-quadruplexes and their roles in regulating rice gene transcription.
Feng, Y, Tao, S, Zhang, P, Sperti, FR, Liu, G, Cheng, X, Zhang, T, Yu, H, Wang, XE, Chen, C, et al
Plant physiology. 2022;(3):1632-1648
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Abstract
A DNA G-quadruplex (G4) is a non-canonical four-stranded nucleic acid structure involved in many biological processes in mammals. The current knowledge on plant DNA G4s, however, is limited; whether and how DNA G4s impact gene expression in plants is still largely unknown. Here, we applied a protocol referred to as BG4-DNA-IP-seq followed by a comprehensive characterization of DNA G4s in rice (Oryza sativa L.); we next integrated dG4s (experimentally detectable G4s) with existing omics data and found that dG4s exhibited differential DNA methylation between transposable element (TE) and non-TE genes. dG4 regions displayed genic-dependent enrichment of epigenomic signatures; finally, we showed that these sites displayed a positive association with expression of DNA G4-containing genes when located at promoters, and a negative association when located in the gene body, suggesting localization-dependent promotional/repressive roles of DNA G4s in regulating gene transcription. This study reveals interrelations between DNA G4s and epigenomic signatures, as well as implicates DNA G4s in modulating gene transcription in rice. Our study provides valuable resources for the functional characterization or bioengineering of some of key DNA G4s in rice.
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2.
Green revolution to grain revolution: Florigen in the frontiers.
Dash, PK, Rai, R
Journal of biotechnology. 2022;:38-46
Abstract
Burgeoning human population dents, globally, the brimming buffer stock as well as gain in food grain production. However, an imminent global starvation was averted through precise scientific intervention and pragmatic policy changes in the 1960s and was eulogized as the "Green Revolution". Miracle rice and wheat obtained through morphometric changes in the ideotype of these two crops yielded bumper harvest that nucleated in Asia and translated into Latin America. The altered agronomic traits in these two crops were the result of tinkering with the phyto-hormone "Gibberellin'. Recently, another plant hormone 'Cytokinin' has gained prominence for its involvement in the grain revolution in rice and other field crops. Suo moto homeostasis of CK by the cytokinin oxidase enzyme governs the cardinal shoot apical meristem that produces new flowering primordia thereby enhancing grain number. Similarly, the flowering hormone 'Florigen' impacts sympodia formation, flowering, and fruit production in tomato. The role of heterozygosity induced heterosis by florigen in revolutionizing tomato production and cellular homeostasis of CK by CK oxidising enzyme (CKX) in enhancing rice production has been path-breaking. This review highlights role of phytohormones in grain revolution and crop specific fine-tuning of gibberellins, cytokinins and florigen to accomplish maximum yield potential in field crops.
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3.
Developing climate-resilient crops: improving plant tolerance to stress combination.
Rivero, RM, Mittler, R, Blumwald, E, Zandalinas, SI
The Plant journal : for cell and molecular biology. 2022;(2):373-389
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Abstract
Global warming and climate change are driving an alarming increase in the frequency and intensity of different abiotic stresses, such as droughts, heat waves, cold snaps, and flooding, negatively affecting crop yields and causing food shortages. Climate change is also altering the composition and behavior of different insect and pathogen populations adding to yield losses worldwide. Additional constraints to agriculture are caused by the increasing amounts of human-generated pollutants, as well as the negative impact of climate change on soil microbiomes. Although in the laboratory, we are trained to study the impact of individual stress conditions on plants, in the field many stresses, pollutants, and pests could simultaneously or sequentially affect plants, causing conditions of stress combination. Because climate change is expected to increase the frequency and intensity of such stress combination events (e.g., heat waves combined with drought, flooding, or other abiotic stresses, pollutants, and/or pathogens), a concentrated effort is needed to study how stress combination is affecting crops. This need is particularly critical, as many studies have shown that the response of plants to stress combination is unique and cannot be predicted from simply studying each of the different stresses that are part of the stress combination. Strategies to enhance crop tolerance to a particular stress may therefore fail to enhance tolerance to this specific stress, when combined with other factors. Here we review recent studies of stress combinations in different plants and propose new approaches and avenues for the development of stress combination- and climate change-resilient crops.
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4.
Expanding Gene-Editing Potential in Crop Improvement with Pangenomes.
Tay Fernandez, CG, Nestor, BJ, Danilevicz, MF, Marsh, JI, Petereit, J, Bayer, PE, Batley, J, Edwards, D
International journal of molecular sciences. 2022;(4)
Abstract
Pangenomes aim to represent the complete repertoire of the genome diversity present within a species or cohort of species, capturing the genomic structural variance between individuals. This genomic information coupled with phenotypic data can be applied to identify genes and alleles involved with abiotic stress tolerance, disease resistance, and other desirable traits. The characterisation of novel structural variants from pangenomes can support genome editing approaches such as Clustered Regularly Interspaced Short Palindromic Repeats and CRISPR associated protein Cas (CRISPR-Cas), providing functional information on gene sequences and new target sites in variant-specific genes with increased efficiency. This review discusses the application of pangenomes in genome editing and crop improvement, focusing on the potential of pangenomes to accurately identify target genes for CRISPR-Cas editing of plant genomes while avoiding adverse off-target effects. We consider the limitations of applying CRISPR-Cas editing with pangenome references and potential solutions to overcome these limitations.
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Outstanding Questions on the Beneficial Role of Silicon in Crop Plants.
Shivaraj, SM, Mandlik, R, Bhat, JA, Raturi, G, Elbaum, R, Alexander, L, Tripathi, DK, Deshmukh, R, Sonah, H
Plant & cell physiology. 2022;(1):4-18
Abstract
Silicon (Si) is widely accepted as a beneficial element for plants. Despite the substantial progress made in understanding Si transport mechanisms and modes of action in plants, several questions remain unanswered. In this review, we discuss such outstanding questions and issues commonly encountered by biologists studying the role of Si in plants in relation to Si bioavailability. In recent years, advances in our understanding of the role of Si-solubilizing bacteria and the efficacy of Si nanoparticles have been made. However, there are many unknown aspects associated with structural and functional features of Si transporters, Si loading into the xylem, and the role of specialized cells like silica cells and compounds preventing Si polymerization in plant tissues. In addition, despite several 1,000 reports showing the positive effects of Si in high as well as low Si-accumulating plant species, the exact roles of Si at the molecular level are yet to be understood. Some evidence suggests that Si regulates hormonal pathways and nutrient uptake, thereby explaining various observed benefits of Si uptake. However, how Si modulates hormonal pathways or improves nutrient uptake remains to be explained. Finally, we summarize the knowledge gaps that will provide a roadmap for further research on plant silicon biology, leading to an exploration of the benefits of Si uptake to enhance crop production.
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Rice functional genomics: decades' efforts and roads ahead.
Chen, R, Deng, Y, Ding, Y, Guo, J, Qiu, J, Wang, B, Wang, C, Xie, Y, Zhang, Z, Chen, J, et al
Science China. Life sciences. 2022;(1):33-92
Abstract
Rice (Oryza sativa L.) is one of the most important crops in the world. Since the completion of rice reference genome sequences, tremendous progress has been achieved in understanding the molecular mechanisms on various rice traits and dissecting the underlying regulatory networks. In this review, we summarize the research progress of rice biology over past decades, including omics, genome-wide association study, phytohormone action, nutrient use, biotic and abiotic responses, photoperiodic flowering, and reproductive development (fertility and sterility). For the roads ahead, cutting-edge technologies such as new genomics methods, high-throughput phenotyping platforms, precise genome-editing tools, environmental microbiome optimization, and synthetic methods will further extend our understanding of unsolved molecular biology questions in rice, and facilitate integrations of the knowledge for agricultural applications.
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Seed priming with non-ionizing physical agents: plant responses and underlying physiological mechanisms.
Bera, K, Dutta, P, Sadhukhan, S
Plant cell reports. 2022;(1):53-73
Abstract
Seed priming has long been explored as an effective value-added potential technique that results in improved germination, reduced seedling emergence time, shortened crop duration, increased stress tolerance and eventually increased higher grain production. However, the wider applicability of water or chemical-based conventional methods of seed priming is often restricted considering its deleterious effects on post-treatment storability or agricultural pollution due to the persistence of chemicals in plant systems or in the environment. In this context, the utilization of physical methods of seed priming for enhancing plant productivity has created a new horizon in the domain of seed technology. Being eco-friendly and cost-effective approaches, priming with extra-terrestrial or physical agents such as ionizing radiation such as X-rays and gamma rays and non-ionizing radiation such as ultrasonic wave, magnetic field, microwaves, and infrared light offers many advantages along with ensuring enhanced production over conventional methods. Ultraviolet radiations, bridging between ionizing and non-ionizing radiation, are important electromagnetic waves that would also be an effective priming agent. Non-ionizing radiation has certain biological advantages over ionizing radiation since it does not generate charged ions while passing through a subject, but has enough energy to cause biological effects. Extensive research works to study the effects of various non-ionizing physical priming methods are required before their wider exploitation in agriculture. With this background, this review aims to highlight the current understanding of non-ionizing physical methods of seed priming and its applicability to combat present-day challenges to achieve agro-ecological resilience.
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8.
Recent Advances in Plant Nanoscience.
Zhang, Q, Ying, Y, Ping, J
Advanced science (Weinheim, Baden-Wurttemberg, Germany). 2022;(2):e2103414
Abstract
Plants have complex internal signaling pathways to quickly adjust to environmental changes and harvest energy from the environment. Facing the growing population, there is an urgent need for plant transformation and precise monitoring of plant growth to improve crop yields. Nanotechnology, an interdisciplinary research field, has recently been boosting plant yields and meeting global energy needs. In this context, a new field, "plant nanoscience," which describes the interaction between plants and nanotechnology, emerges as the times require. Nanosensors, nanofertilizers, nanopesticides, and nano-plant genetic engineering are of great help in increasing crop yields. Nanogenerators are helping to develop the potential of plants in the field of energy harvesting. Furthermore, the uptake and internalization of nanomaterials in plants and the possible effects are also worthy of attention. In this review, a forward-looking perspective on the plant nanoscience is presented and feasible solutions for future food shortages and energy crises are provided.
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9.
Deciphering the Epigenetic Alphabet Involved in Transgenerational Stress Memory in Crops.
Mladenov, V, Fotopoulos, V, Kaiserli, E, Karalija, E, Maury, S, Baranek, M, Segal, N, Testillano, PS, Vassileva, V, Pinto, G, et al
International journal of molecular sciences. 2021;(13)
Abstract
Although epigenetic modifications have been intensely investigated over the last decade due to their role in crop adaptation to rapid climate change, it is unclear which epigenetic changes are heritable and therefore transmitted to their progeny. The identification of epigenetic marks that are transmitted to the next generations is of primary importance for their use in breeding and for the development of new cultivars with a broad-spectrum of tolerance/resistance to abiotic and biotic stresses. In this review, we discuss general aspects of plant responses to environmental stresses and provide an overview of recent findings on the role of transgenerational epigenetic modifications in crops. In addition, we take the opportunity to describe the aims of EPI-CATCH, an international COST action consortium composed by researchers from 28 countries. The aim of this COST action launched in 2020 is: (1) to define standardized pipelines and methods used in the study of epigenetic mechanisms in plants, (2) update, share, and exchange findings in epigenetic responses to environmental stresses in plants, (3) develop new concepts and frontiers in plant epigenetics and epigenomics, (4) enhance dissemination, communication, and transfer of knowledge in plant epigenetics and epigenomics.
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Chromosome doubling methods in doubled haploid and haploid inducer-mediated genome-editing systems in major crops.
Hooghvorst, I, Nogués, S
Plant cell reports. 2021;(2):255-270
Abstract
The doubled haploid technique aims to generate pure inbred lines for basic research and as commercial cultivars. The doubled haploid technique first generates haploid plants and is followed by chromosome doubling, which can be separated in time or overlapped, depending the procedure for each species. For a long time, much effort has been focused on haploid production via androgenesis, gynogenesis, or parthenogenesis. The obtention of haploid plants has frequently required more optimization and has lagged behind research and improvements in chromosome doubling methods. Nevertheless, chromosome doubling has recently been of renewed interest to increase the rates and efficiency of doubled haploid plant production through trialing and optimizing of different procedures. New antimitotic compounds and application methods are being studied to ensure the success of chromosome doubling once haploid material has been regenerated. Moreover, a haploid inducer-mediated CRISPR/Cas9 genome-editing system is a breakthrough method in the production of haploid plant material and could be of great importance for species where traditional haploid regeneration methods have not been successful, or for recalcitrant species. In all cases, the new deployment of this system will demand a suitable chromosome doubling protocol. In this review, we explore the existing doubled haploid and chromosome doubling methods to identify opportunities to enhance the breeding process in major crops.