Formerly the "Center for Desert Agriculture"

Recent Submissions

  • Synthetic Directed Evolution in Plants: Unlocking Trait Engineering and Improvement

    Gundra, Sivakrishna Rao; Jiang, Wenjun; Mahfouz, Magdy M. (Synthetic Biology, Oxford University Press (OUP), 2021-09-08) [Article]
    ABSTRACT Genetic variation accelerates adaptation and resilience and enables the survival of species to their changing environment. Increasing the genetic diversity of crop species is essential to improve their yield and enhance food security. Synthetic directed evolution (SDE) employs localized sequence diversification (LSD) of gene sequence and selection pressure to evolve gene variants with better fitness, improved properties, and desired phenotypes. Recently, CRISPR-Cas dependent and independent technologies have been applied for LSD to mediate synthetic evolution in diverse species, including plants. SDE holds excellent promise to discover, accelerate, and expand the range of traits of value in crop species. Here, we highlight the efficient SDE approaches for the LSD of plant genes, selection strategies, and critical traits for targeted improvement. We discuss the potential of emerging technologies, including CRISPR-Cas base editing, retron editing, EvolvR, and prime editing, to establish efficient SDE in plants. Moreover, we cover CRISPR-Cas independent technologies, including T7 polymerase editor for continuous evolution. We highlight the key challenges and potential solutions of applying SDE technologies to improve plant traits of value.
  • Multiple strategies of plant colonization by beneficial endophytic Enterobacter sp. SA187

    Synek, Lukas; Rawat, Anamika; L'Haridon, Floriane; Weisskopf, Laure; Saad, Maged; Hirt, Heribert (Environmental Microbiology, Wiley, 2021-09-01) [Article]
    Although many endophytic plant growth-promoting rhizobacteria have been identified, relatively little is still known about the mechanisms by which they enter plants and promote plant growth. The beneficial endophyte Enterobacter sp. SA187 was shown to maintain productivity of crops in extreme agricultural conditions. Here we present that roots of its natural host (Indigofera argentea), alfalfa, tomato, wheat, barley and Arabidopsis are all efficiently colonized by SA187. Detailed analysis of the colonization process in Arabidopsis showed that colonization already starts during seed germination, where seed-coat mucilage supports SA187 proliferation. The meristematic zone of growing roots attracts SA187, allowing epiphytic colonization in the elongation zone. Unlike primary roots, lateral roots are significantly less epiphytically colonized by SA187. Root endophytic colonization was found to occur by passive entry of SA187 at lateral-root bases. However, SA187 also actively penetrates the root epidermis by enzymatic disruption of plant cell wall material. In contrast to roots, endophytic colonization of shoots occurs via stomata, whereby SA187 can actively re-open stomata similarly to pathogenic bacteria. In summary, several entry strategies were identified that allow SA187 to establish itself as a beneficial endophyte in several plant species, supporting it's use as a plant growth-promoting bacterium in agriculture systems. This article is protected by copyright. All rights reserved.
  • Plant genome engineering from lab to field—a Keystone Symposia report

    Cable, Jennifer; Ronald, Pamela C.; Voytas, Daniel; Zhang, Feng; Levy, Avraham A.; Takatsuka, Ayumu; Arimura, Shin-ichi; Jacobsen, Steven E.; Toki, Seiichi; Toda, Erika; Gao, Caixia; Zhu, Jian-Kang; Boch, Jens; Van Eck, Joyce; Mahfouz, Magdy M.; Andersson, Mariette; Fridman, Eyal; Weiss, Trevor; Wang, Kan; Qi, Yiping; Jores, Tobias; Adams, Tom; Bagchi, Rammyani (Annals of the New York Academy of Sciences, Wiley, 2021-08-25) [Article]
    Facing the challenges of the world's food sources posed by a growing global population and a warming climate will require improvements in plant breeding and technology. Enhancing crop resiliency and yield via genome engineering will undoubtedly be a key part of the solution. The advent of new tools, such as CRIPSR/Cas, has ushered in significant advances in plant genome engineering. However, several serious challenges remain in achieving this goal. Among them are efficient transformation and plant regeneration for most crop species, low frequency of some editing applications, and high attrition rates. On March 8 and 9, 2021, experts in plant genome engineering and breeding from academia and industry met virtually for the Keystone eSymposium "Plant Genome Engineering: From Lab to Field" to discuss advances in genome editing tools, plant transformation, plant breeding, and crop trait development, all vital for transferring the benefits of novel technologies to the field.
  • Quinoa Phenotyping Methodologies: An International Consensus

    Stanschewski, Clara; Rey, Elodie; Fiene, Gabriele; Craine, Evan; Wellman, Gordon; Melino, Vanessa J.; Patiranage, Dilan; Johansen, Kasper; Schmöckel, Sandra; Bertero, Daniel; Oakey, Helena; Colque-Little, Carla; Afzal, Irfan; Raubach, Sebastian; Miller, Nathan; Streich, Jared; Amby, Daniel; Emrani, Nazgol; Warmington, Mark; Mousa, Magdi; Wu, David; Jacobson, Daniel; Andreasen, Christian; Jung, Christian; Murphy, Kevin; Bazile, Didier; Tester, Mark A.; on behalf of the Quinoa Phenotyping Consortium (Plants, MDPI AG, 2021-08-24) [Article]
    Quinoa is a crop originating in the Andes but grown more widely and with the genetic potential for significant further expansion. Due to the phenotypic plasticity of quinoa, varieties need to be assessed across years and multiple locations. To improve comparability among field trials across the globe and to facilitate collaborations, components of the trials need to be kept consistent, including the type and methods of data collected. Here, an internationally open-access framework for phenotyping a wide range of quinoa features is proposed to facilitate the systematic agronomic, physiological and genetic characterization of quinoa for crop adaptation and improvement. Mature plant phenotyping is a central aspect of this paper, including detailed descriptions and the provision of phenotyping cards to facilitate consistency in data collection. High-throughput methods for multi-temporal phenotyping based on remote sensing technologies are described. Tools for higher-throughput post-harvest phenotyping of seeds are presented. A guideline for approaching quinoa field trials including the collection of environmental data and designing layouts with statistical robustness is suggested. To move towards developing resources for quinoa in line with major cereal crops, a database was created. The Quinoa Germinate Platform will serve as a central repository of data for quinoa researchers globally.
  • CRISPR-Based Crop Improvements: A Way Forward to Achieve Zero Hunger

    Ahmad, Shakeel; Tang, Liqun; Shahzad, Rahil; Mawia, Amos Musyoki; Rao, Gundra Sivakrishna; Jamil, Shakra; Wei, Chen; Sheng, Zhonghua; Shao, Gaoneng; Wei, Xiangjin; Hu, Peisong; Mahfouz, Magdy M.; Hu, Shikai; Tang, Shaoqing (Journal of Agricultural and Food Chemistry, American Chemical Society (ACS), 2021-07-21) [Article]
    Zero hunger is one of the sustainable development goals set by the United Nations in 2015 to achieve global food security by 2030. The current harvest of crops is insufficient; feeding the world's population and meeting the goal of zero hunger by 2030 will require larger and more consistent crop production. Clustered regularly interspaced short palindromic repeats-associated protein (CRISPR-Cas) technology is widely used for the plant genome editing. In this review, we consider this technology as a potential tool for achieving zero hunger. We provide a comprehensive overview of CRISPR-Cas technology and its most important applications for food crops' improvement. We also conferred current and potential technological breakthroughs that will help in breeding future crops to end global hunger. The regulatory aspects of deploying this technology in commercial sectors, bioethics, and the production of transgene-free plants are also discussed. We hope that the CRISPR-Cas system will accelerate the breeding of improved crop cultivars compared with conventional breeding and pave the way toward the zero hunger goal.
  • Pre-mRNA alternative splicing as a modulator for heat stress response in plants

    Ling, Yu; Mahfouz, Magdy M.; Zhou, Shuangxi (Trends in Plant Science, Elsevier BV, 2021-07) [Article]
    The molecular responses of plants to the important abiotic stress, heat stress (HS), have been extensively studied at the transcriptional level. Alternative splicing (AS) is a post-transcriptional regulatory process in which an intron-containing gene can generate more than one mRNA variant. The impact of HS on the premRNA splicing process has been reported in various eukaryotes but seldom discussed in-depth, especially in plants. Here, we review AS regulation in response to HS in different plant species. We discuss potential molecular mechanisms controlling heat-inducible AS regulation in plants and hypothesize that AS regulation participates in heat-priming establishment and HS memory maintenance. We propose that the pre-mRNA splicing variation is an important regulator of plant HS responses (HSRs).
  • Robust, Long-Term, and Exceptionally Sensitive Microneedle-Based Bioimpedance Sensor for Precision Farming

    Bu Khamsin, Abdullah; Moussi, Khalil; Tao, Ran; Lubineau, Gilles; Blilou, Ikram; Salama, Khaled N.; Kosel, Jürgen (Advanced Science, Wiley, 2021-06-17) [Article]
    Precision farming has the potential to increase global food production capacity whilst minimizing traditional inputs. However, the adoption and impact of precision farming are contingent on the availability of sensors that can discern the state of crops, while not interfering with their growth. Electrical impedance spectroscopy offers an avenue for nondestructive monitoring of crops. To that end, it is reported on the deployment of impedimetric sensors utilizing microneedles (MNs) that can be used to pierce the waxy exterior of plants to obtain sensitive impedance spectra in open-air settings with an average relative noise value of 3.83%. The sensors are fabricated using a novel micromolding and release method that is compatible with UV photocurable and thermosetting polymers. Assessments of the quality of the MNs under scanning electron microscopy show that the replication process is high in fidelity to the original design of the master mold and that it can be used for upward of 20 replication cycles. The sensor's performance is validated against conventional planar sensors for obtaining the impedance values of Arabidopsis thaliana. As a change is detected in impedance due to lighting and hydration, this raises the possibility for their widespread use in precision farming.
  • G3BPs in Plant Stress

    Abulfaraj, Aala A.; Hirt, Heribert; Rayapuram, Naganand (Frontiers in Plant Science, Frontiers Media SA, 2021-06-10) [Article]
    The sessile nature of plants enforces highly adaptable strategies to adapt to different environmental stresses. Plants respond to these stresses by a massive reprogramming of mRNA metabolism. Balancing of mRNA fates, including translation, sequestration, and decay is essential for plants to not only coordinate growth and development but also to combat biotic and abiotic environmental stresses. RNA stress granules (SGs) and processing bodies (P bodies) synchronize mRNA metabolism for optimum functioning of an organism. SGs are evolutionarily conserved cytoplasmic localized RNA-protein storage sites that are formed in response to adverse conditions, harboring mostly but not always translationally inactive mRNAs. SGs disassemble and release mRNAs into a translationally active form upon stress relief. RasGAP SH3 domain binding proteins (G3BPs or Rasputins) are “scaffolds” for the assembly and stability of SGs, which coordinate receptor mediated signal transduction with RNA metabolism. The role of G3BPs in the formation of SGs is well established in mammals, but G3BPs in plants are poorly characterized. In this review, we discuss recent findings of the dynamics and functions of plant G3BPs in response to environmental stresses and speculate on possible mechanisms such as transcription and post-translational modifications that might regulate the function of this important family of proteins.
  • Polycomb-dependent differential chromatin compartmentalization determines gene coregulation in Arabidopsis

    Huang, Ying; Sircar, Sanchari; Ramirez-Prado, Juan Sebastian; Manza-Mianza, Deborah; Antunez-Sanchez, Javier; Brik-Chaouche, Rim; Rodriguez-Granados, Natalia; An, Jing; Bergounioux, Catherine; Mahfouz, Magdy M.; Hirt, Heribert; Crespi, Martin; Concia, Lorenzo; Barnech, Fredy; Amiard, Simon; Probst, Aline V; Gutierrez-Marcos, Jose; Ariel, Federico; Raynaud, Cecile; Latrasse, David; Benhamed, Moussa (Genome research, Cold Spring Harbor Laboratory, 2021-06-04) [Article]
    In animals, distant H3K27me3-marked Polycomb targets can establish physical interactions forming repressive chromatin hubs. In plants, growing evidence suggests that H3K27me3 act directly or indirectly to regulate chromatin interactions, although how this histone modification modulates 3D chromatin architecture remains elusive. To decipher the impact of the dynamic deposition of H3K27me3 on the Arabidopsis thaliana nuclear interactome, we combined genetics, transcriptomics and alternative 3D epigenomic approaches. By analyzing mutants defective for histone H3K27 methylation or demethylation we uncovered the crucial role of this chromatin mark in short- and previously unnoticed long-range chromatin loop formation. We found that a reduction in H3K27me3 led to a decrease in the interactions within Polycomb-associated repressive domains. Regions with lower H3K27me3 levels in the H3K27 methyltransferase clf mutant established new interactions with regions marked with H3K9ac – a histone modification associated with active transcription, thus indicating that a reduction in H3K27me3 levels induces a global reconfiguration of chromatin architecture. Altogether, our results reveal that the 3D genome organization is tightly linked to reversible histone modifications that govern chromatin interactions. Consequently, nuclear organization dynamics shapes the transcriptional reprogramming during plant development and places H3K27me3 as a key feature in the coregulation of distant genes.
  • A protoplast-based bioassay to quantify strigolactone activity in arabidopsis using strigoquant

    Braguy, Justine; Samodelov, Sophia L.; Andres, Jennifer; Ochoa-Fernandez, Rocio; Al-Babili, Salim; Zurbriggen, Matias D. (Springer US, 2021-05-25) [Book Chapter, Protocol]
    Understanding the biological background of strigolactone (SL) structural diversity and the SL signaling pathway at molecular level requires quantitative and sensitive tools that precisely determine SL dynamics. Such biosensors may be also very helpful in screening for SL analogs and mimics with defined biological functions. Recently, the genetically encoded, ratiometric sensor StrigoQuant was developed and allowed the quantification of the activity of a wide concentration range of SLs. StrigoQuant can be used for studies on the biosynthesis, function and signal transduction of this hormone class. Here, we provide a comprehensive protocol for establishing the use of StrigoQuant in Arabidopsis protoplasts. We first describe the generation and transformation of the protoplasts with StrigoQuant and detail the application of the synthetic SL analogue GR24. We then show the recording of the luminescence signal and how the obtained data are processed and used to assess/determine SL perception.
  • NAC Transcription Factors ATAF1 and ANAC055 Negatively Regulate Thermomemory in Arabidopsis

    Alshareef, Nouf Owdah Hameed; Woo, Yong; de Werk, Tobias; Kamranfar, Iman; Mueller-Roeber, Bernd; Tester, Mark A.; Balazadeh, Salma; Schmöckel, Sandra M.; Annapurna Devi Allu3 (Research Square Platform LLC, 2021-05-17) [Preprint]
    Pre-exposing (priming) plants to mild, non-lethal elevated temperature improves their tolerance to a later higher-temperature stress (triggering stimulus), which is of great ecological importance. ‘Thermomemory’ is maintaining this tolerance for an extended period of time. NAM/ATAF1/2/CUC2 (NAC) proteins are plant-specific transcription factors (TFs) that modulate responses to abiotic stresses, including heat stress (HS). Here, we investigated the potential role of NACs for thermomemory. We determined the expression of 104 Arabidopsis NAC genes after priming and triggering heat stimuli, and found ATAF1 expression is strongly induced right after priming and declines below control levels thereafter during thermorecovery. Knockout mutants of ATAF1 show better thermomemory than wild type, revealing a negative regulatory role. Differential expression analyses of RNA-seq data from ATAF1 overexpressor, ataf1 mutant and wild-type plants after heat priming revealed five genes that might be priming-associated direct targets of ATAF1: AT2G31260 (ATG9), AT2G41640 (GT61), AT3G44990 (XTH31), AT4G27720 and AT3G23540. Based on co-expression analyses applied to the aforementioned RNA-seq profiles, we identified ANAC055 to be transcriptionally co-regulated with ATAF1. Like ataf1, anac055 mutants show improved thermomemory, revealing a potential co-control of both NAC TFs over thermomemory. Our data reveals a core importance of two NAC transcription factors, ATAF1 and ANAC055, for thermomemory.
  • The Seed Development Factors TT2 and MYB5 Regulate Heat Stress Response in Arabidopsis

    Jacob, Pierre; Brisou, Gwilherm; Dalmais, Marion; Thévenin, Johanne; van der Wal, Froukje; Latrasse, David; Suresh Devani, Ravi; Benhamed, Moussa; Dubreucq, Bertrand; Boualem, Adnane; Lepiniec, Loic; Immink, Richard G. H.; Hirt, Heribert; Bendahmane, Abdelhafid (Genes, MDPI AG, 2021-05-15) [Article]
    HEAT SHOCK FACTOR A2 (HSFA2) is a regulator of multiple environmental stress responses required for stress acclimation. We analyzed HSFA2 co-regulated genes and identified 43 genes strongly co-regulated with HSFA2 during multiple stresses. Motif enrichment analysis revealed an over-representation of the site II element (SIIE) in the promoters of these genes. In a yeast 1-hybrid screen with the SIIE, we identified the closely related R2R3-MYB transcription factors TT2 and MYB5. We found overexpression of MYB5 or TT2 rendered plants heat stress tolerant. In contrast, tt2, myb5, and tt2/myb5 loss of function mutants showed heat stress hypersensitivity. Transient expression assays confirmed that MYB5 and TT2 can regulate the HSFA2 promoter together with the other members of the MBW complex, TT8 and TRANSPARENT TESTA GLABRA 1 (TTG1) and that the SIIE was involved in this regulation. Transcriptomic analysis revealed that TT2/MYB5 target promoters were enriched in SIIE. Overall, we report a new function of TT2 and MYB5 in stress resistance and a role in SIIE-mediated HSFA2 regulation.
  • CRISPR/Cas systems versus plant viruses: engineering plant immunity and beyond

    Ali, Zahir; Mahfouz, Magdy M. (Plant Physiology, Oxford University Press (OUP), 2021-05-12) [Article]
    Abstract Molecular engineering of plant immunity to confer resistance against plant viruses holds great promise for mitigating crop losses and improving plant productivity and yields, thereby enhancing food security. Several approaches have been employed to boost immunity in plants by interfering with the transmission or lifecycles of viruses. In this review, we discuss the successful application of CRISPR/Cas (clustered regularly interspaced short palindromic repeats [CRISPR]/CRISPR-associated protein [Cas]) systems to engineer plant immunity, increase plant resistance to viruses, and develop viral diagnostic tools. Furthermore, we examine the use of plant viruses as delivery systems to engineer virus resistance in plants and provide insight into the limitations of current CRISPR/Cas approaches and the potential of newly discovered CRISPR/Cas systems to engineer better immunity and develop better diagnostics tools for plant viruses. Finally, we outline potential solutions to key challenges in the field to enable the practical use of these systems for crop protection and viral diagnostics.
  • Rooting in the Desert: A Developmental Overview on Desert Plants

    Kirschner, Gwendolyn Kristin; Xiao, Ting Ting; Blilou, Ikram (Genes, MDPI AG, 2021-05-10) [Article]
    Plants, as sessile organisms, have evolved a remarkable developmental plasticity to cope with their changing environment. When growing in hostile desert conditions, plants have to grow and thrive in heat and drought. This review discusses how desert plants have adapted their root system architecture (RSA) to cope with scarce water availability and poor nutrient availability in the desert soil. First, we describe how some species can survive by developing deep tap roots to access the groundwater while others produce shallow roots to exploit the short rain seasons and unpredictable rainfalls. Then, we discuss how desert plants have evolved unique developmental programs like having determinate meristems in the case of cacti while forming a branched and compact root system that allows efficient water uptake during wet periods. The remote germination mechanism in date palms is another example of developmental adaptation to survive in the dry and hot desert surface. Date palms have also designed non-gravitropic secondary roots, termed pneumatophores, to maximize water and nutrient uptake. Next, we highlight the distinct anatomical features developed by desert species in response to drought like narrow vessels, high tissue suberization, and air spaces within the root cortex tissue. Finally, we discuss the beneficial impact of the microbiome in promoting root growth in desert conditions and how these characteristics can be exploited to engineer resilient crops with a greater ability to deal with salinity induced by irrigation and with the increasing drought caused by global warming.
  • Genetic mapping of the early responses to salt stress in Arabidopsis thaliana

    Awlia, Mariam Sahal Abdulaziz; Alshareef, Nouf Owdah Hameed; Saber, Noha; Korte, Arthur; Oakey, Helena; Panzarová, Klára; Trtílek, Martin; Negrão, Sónia; Tester, Mark A.; Julkowska, Magdalena M. (The Plant Journal, Wiley, 2021-05-08) [Article]
    Salt stress decreases plant growth prior to significant ion accumulation in the shoot. However, the processes underlying this rapid reduction in growth are still unknown. To understand the changes in salt stress responses through time and at multiple physiological levels, examining different plant processes within a single setup is required. Recent advances in phenotyping has allowed the image-based estimation of plant growth, morphology, colour and photosynthetic activity. In this study, we examined the salt stress-induced responses of 191 Arabidopsis accessions from one hour to seven days after treatment using high-throughput phenotyping. Multivariate analyses and machine learning algorithms identified that quantum yield measured in the light-adapted state (Fv´/Fm´) greatly affected growth maintenance in the early phase of salt stress, while maximum quantum yield (QY max) was crucial at a later stage. In addition, our genome-wide association study (GWAS) identified 770 loci that were specific to salt stress, in which two loci associated with QY max and Fv´/Fm´ were selected for validation using T-DNA insertion lines. We characterised an unknown protein kinase found in the QY max locus, which reduced photosynthetic efficiency and growth maintenance under salt stress. Understanding the molecular context of the identified candidate genes will provide valuable insights into the early plant responses to salt stress. Furthermore, our work incorporates high-throughput phenotyping, multivariate analyses and GWAS, uncovering details of temporal stress responses, while identifying associations across different traits and time points, which likely constitute the genetic components of salinity tolerance.
  • Manipulation of carotenoid metabolism stimulates biomass and stress tolerance in tomato

    Vallarino, José G; Mi, Jianing; Petřík, Ivan; Novak, Ondrej; Correa, Sandra Marcela; Kosmacz, Monika; Havaux, Michel; Rodriguez-Concepcion, Manuel; Al-Babili, Salim; Fernie, Alisdair R.; Skirycz, Aleksandra; Moreno, Juan C (Cold Spring Harbor Laboratory, 2021-05-07) [Preprint]
    Improving yield, nutritional value and tolerance to abiotic stress are major targets of current breeding and biotechnological approaches that aim at increasing crop production and ensuring food security. Metabolic engineering of carotenoids, the precursor of Vitamin-A and plant hormones that regulate plant growth and response to adverse growth conditions, has been mainly focusing on provitamin A biofortification or the production of high-value carotenoids. Here, we show that the introduction of a single gene of the carotenoid biosynthetic pathway in different tomato cultivars simultaneously improved photosynthetic capacity and tolerance to various abiotic stresses (e.g., high light, salt, and drought), caused an up to 77% fruit yield increase and enhanced fruit's provitamin A content and shelf life. Our findings pave the way for developing a new generation of crops that combine high productivity and increased nutritional value with the capability to cope with climate change-related environmental challenges.
  • Overlapping roles of spliceosomal components SF3B1 and PHF5A in rice splicing regulation

    Butt, Haroon; Bazin, Jeremie; Alshareef, Sahar; Eid, Ayman; Benhamed, Moussa; Reddy, Anireddy S. N.; Crespi, Martin; Mahfouz, Magdy M. (Communications Biology, Springer Science and Business Media LLC, 2021-05-05) [Article]
    AbstractThe SF3B complex, a multiprotein component of the U2 snRNP of the spliceosome, plays a crucial role in recognizing branch point sequence and facilitates spliceosome assembly and activation. Several chemicals that bind SF3B1 and PHF5A subunits of the SF3B complex inhibit splicing. We recently generated a splicing inhibitor-resistant SF3B1 mutant named SF3B1GEX1ARESISTANT 4 (SGR4) using CRISPR-mediated directed evolution, whereas splicing inhibitor-resistant mutant of PHF5A (Overexpression-PHF5A GEX1A Resistance, OGR) was generated by expressing an engineered version PHF5A-Y36C. Global analysis of splicing in wild type and these two mutants revealed the role of SF3B1 and PHF5A in splicing regulation. This analysis uncovered a set of genes whose intron retention is regulated by both proteins. Further analysis of these retained introns revealed that they are shorter, have a higher GC content, and contain shorter and weaker polypyrimidine tracts. Furthermore, splicing inhibition increased seedlings sensitivity to salt stress, consistent with emerging roles of splicing regulation in stress responses. In summary, we uncovered the functions of two members of the plant branch point recognition complex. The novel strategies described here should be broadly applicable in elucidating functions of splicing regulators, especially in studying the functions of redundant paralogs in plants.
  • Haplotype variations of major flowering time genes in quinoa unveil their role in the adaptation to different environmental conditions

    Patiranage, Dilan S.R.; Asare, Edward; Maldonado-Taipe, Nathaly; Rey, Elodie; Emrani, Nazgol; Tester, Mark A.; Jung, Christian (Plant, Cell & Environment, Wiley, 2021-04-20) [Article]
    Response to photoperiod is of major importance in crop production. It defines the adaptation of plants to local environments. Quinoa is a short day plant which had been domesticated in the Andeans regions. We wanted to understand the adaptation to long-day conditions by studying orthologs of two major flowering time regulators of Arabidopsis, FLOWERING LOCUS T (FT) and CONSTANS (CO) in quinoa accessions with contrasting photoperiod response. By searching the quinoa reference genome sequence, we identified 24 FT and six CO homologs. CqFT genes displayed remarkably different expression patterns between long-day and short-day conditions, whereas the influence of the photoperiod on CqCOL expressions was moderate. Cultivation of 276 quinoa accessions under short-day and long-day conditions revealed great differences in photoperiod sensitivity. After sequencing their genomes, we identified large sequence variations in 12 flowering time genes. We found non-random distribution of haplotypes across accessions from different geographical origins, highlighting the role of CqFT and CqCOL genes in the adaptation to different day-length conditions. We identified five haplotypes causing early flowering under long days. This study provides assets for quinoa breeding because superior haplotypes can be assembled in a predictive breeding approach to produce well-adapted early flowering lines under long-day photoperiods. This article is protected by copyright. All rights reserved.
  • SeedQuant: A deep learning-based tool for assessing stimulant and inhibitor activity on root parasitic seeds.

    Braguy, Justine; Ramazanova, Merey; Giancola, Silvio; Jamil, Muhammad; Kountche, Boubacar Amadou; Zarban, Randa Alhassan Yahya; Felemban, Abrar; Wang, Jian You; Lin, Pei-Yu; Haider, Imran; Zurbriggen, Matias; Ghanem, Bernard; Al-Babili, Salim (Plant physiology, Oxford University Press (OUP), 2021-04-15) [Article]
    Witchweeds (Striga spp.) and broomrapes (Orobanchaceae and Phelipanche spp.) are root parasitic plants that infest many crops in warm and temperate zones, causing enormous yield losses and endangering global food security. Seeds of these obligate parasites require rhizospheric, host-released stimulants to germinate, which opens up possibilities for controlling them by applying specific germination inhibitors or synthetic stimulants that induce lethal germination in host's absence. To determine their effect on germination, root exudates or synthetic stimulants/inhibitors are usually applied to parasitic seeds in in vitro bioassays, followed by assessment of germination ratios. Although these protocols are very sensitive, the germination recording process is laborious, representing a challenge for researchers and impeding high-throughput screens. Here, we developed an automatic seed census tool to count and discriminate germinated from non-germinated seeds. We combined deep learning, a powerful data-driven framework that can accelerate the procedure and increase its accuracy, for object detection with computer vision latest development based on the Faster R-CNN algorithm. Our method showed an accuracy of 94% in counting seeds of Striga hermonthica and reduced the required time from ˜5 minutes to 5 seconds per image. Our proposed software, SeedQuant, will be of great help for seed germination bioassays and enable high-throughput screening for germination stimulants/inhibitors. ​SeedQuant is an open-source software that can be further trained to count different types of seeds for research purposes.
  • Vigilant: An Engineered VirD2-Cas9 Complex for Lateral Flow Assay-Based Detection of SARS-CoV2

    Marsic, Tin; Ali, Zahir; Tehseen, Muhammad; Mahas, Ahmed; Hamdan, Samir; Mahfouz, Magdy M. (Nano Letters, American Chemical Society (ACS), 2021-04-12) [Article]
    Rapid, sensitive, and specific point-of-care testing for pathogens is crucial for disease control. Lateral flow assays (LFAs) have been employed for nucleic acid detection, but they have limited sensitivity and specificity. Here, we used a fusion of catalytically inactive SpCas9 endonuclease and VirD2 relaxase for sensitive, specific nucleic acid detection by LFA. In this assay, the target nucleic acid is amplified with biotinylated oligos. VirD2-dCas9 specifically binds the target sequence via dCas9 and covalently binds to a FAM-tagged oligonucleotide via VirD2. The biotin label and FAM tag are detected by a commercially available LFA. We coupled this system, named Vigilant (<u>Vi</u>rD2-dCas9 <u>g</u>u<u>i</u>ded and <u>L</u>FA-coupled <u>n</u>ucleic acid <u>t</u>est), to reverse transcription-recombinase polymerase amplification to detect SARS-CoV2 in clinical samples. Vigilant exhibited a limit of detection of 2.5 copies/μL, comparable to CRISPR-based systems, and showed no cross-reactivity with SARS-CoV1 or MERS. Vigilant offers an easy-to-use, rapid, cost-effective, and robust detection platform for SARS-CoV2.

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