Formerly the "Center for Desert Agriculture"

Recent Submissions

  • Genetic mapping of the early responses to salt stress in Arabidopsis thaliana

    Awlia, Mariam; Alshareef, Nouf Owdah Hameed; Saber, Noha; Korte, Arthur; Oakey, Helena; Panzarova, Klara; Trtilek, Martin; Negrão, Sónia; Tester, Mark A.; Julkowska, Magdalena M. (Cold Spring Harbor Laboratory, 2020-10-04) [Preprint]
    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.
  • Moving with purpose and direction: transcription factor movement and cell fate determination revisited

    Gundu, Shyam; Tabassum, Naheed; Blilou, Ikram (Current Opinion in Plant Biology, Elsevier BV, 2020-09-28) [Article]
    Cell diversity in a multicellular organism relies on cell–cell communication where cells must receive positional information as input signals to adopt their proper cell fate in the right place and at the right time. This process is achieved through triggering signaling cascades that drive cellular changes during development. In plants, signaling through mobile transcription factors (TF) plays a central role in development. Rather than acting cell-autonomously and exclusive to their expression domains, many TFs move between cells and deploy regulatory networks and cell type-specific effectors to achieve their biological functions. Here, we highlight a few examples of mobile TFs central to cell fate specification in Arabidopsis.
  • The genome of the cauliflower coral Pocillopora verrucosa.

    Buitrago Lopez, Carol; Mariappan, Kiruthiga; Cardenas, Anny; Gegner, Hagen M; Voolstra, Christian R. (Genome biology and evolution, Oxford University Press (OUP), 2020-08-29) [Article]
    Climate change and ocean warming threaten the persistence of corals worldwide. Genomic resources are critical to study the evolutionary trajectory, adaptive potential, and genetic distinctiveness of coral species. Here we provide a reference genome of the cauliflower coral Pocillopora verrucosa, a broadly prevalent reef-building coral with important ecological roles in the maintenance of reefs across the Red Sea, the Indian Ocean, and the Pacific Ocean. The genome has an assembly size of 380,505,698 bp with a scaffold N50 of 333,696 bp and a contig N50 of 75,704 bp. The annotation of the assembled genome returned 27,439 gene models of which 89.88% have evidence of transcription from RNA-Seq data and 97.87% show homology to known genes. A high proportion of the genome (41.22%) is comprised of repetitive elements in comparison to other cnidarian genomes, in particular in relation to the small genome size of P. verrucosa.
  • Development and cell cycle dynamics of the root apical meristem in the fern Ceratopteris richardii

    Aragon-Raygoza, Alejandro; Vasco, Alejandra; Blilou, Ikram; Herrera-Estrella, Luis Rafael; Cruz-Ramirez, Luis Alfredo (Cold Spring Harbor Laboratory, 2020-08-29) [Preprint]
    Ferns are a representative clade in plant evolution although underestimated in the genomic era. Ceratopteris richardii is an emergent model for developmental processes in ferns, yet a complete scheme of the different growth stages is necessary. Here, we present a developmental analysis, at the tissue and cellular levels, of the first shoot-borne root of Ceratopteris. We followed early stages and emergence of the root meristem in sporelings. While assessing root growth, the first shoot-borne root ceases its elongation between the emergence of the fifth and sixth roots, suggesting Ceratopteris roots follow a determinate developmental program. We report cell division frequencies in the stem cell niche after detecting labeled nuclei in the root apical cell (RAC) and derivatives after 8 hours of exposure. These results demonstrate the RAC has a continuous mitotic activity during root development. Detection of cell cycle activity in the RAC at early times suggests this cell acts as a non-quiescent organizing center. Overall, our results provide a framework to study root function and development in ferns and to better understand the evolutionary history of this organ.
  • Mobilizing Crop Biodiversity.

    McCouch, Susan; Navabi, Katy; Abberton, Michael; Anglin, Noelle L; Barbieri, Rosa Lia; Baum, Michael; Bett, Kirsten; Booker, Helen; Brown, Gerald L; Bryan, Glenn J; Cattivelli, Luigi; Charest, David; Eversole, Kellye; Freitas, Marcelo; Ghamkhar, Kioumars; Grattapaglia, Dario; Henry, Robert; Valadares Inglis, Maria Cleria; Islam, Tofazzal; Kehel, Zakaria; Kersey, Paul J; Kresovich, Stephen; Marden, Emily; Mayes, Sean; Ndjiondjop, Marie Noelle; Nguyen, Henry T; Paiva, Samuel; Papa, Roberto; Phillips, Peter W B; Rasheed, Awais; Richards, Christopher; Rouard, Mathieu; Amstalden Sampaio, Maria Jose; Scholz, Uwe; Shaw, Paul D; Sherman, Brad; Staton, S Evan; Stein, Nils; Svensson, Jan; Tester, Mark A.; Montenegro Valls, Jose Francisco; Varshney, Rajeev; Visscher, Stephen; von Wettberg, Eric; Waugh, Robbie; Wenzl, Peter W B; Rieseberg, Loren H (Molecular plant, Elsevier BV, 2020-08-25) [Article]
    Over the past 70 years, the world has witnessed extraordinary growth in crop productivity, enabled by a suite of technological advances, including higher yielding crop varieties, improved farm management, synthetic agrochemicals, and agricultural mechanization. While this “Green Revolution” intensified crop production, and is credited with reducing famine and malnutrition, its benefits were accompanied by several undesirable collateral effects (Pingali, 2012). These include a narrowing of agricultural biodiversity, stemming from increased monoculture and greater reliance on a smaller number of crops and crop varieties for the majority of our calories. This reduction in diversity has created vulnerabilities to pest and disease epidemics, climate variation, and ultimately to human health (Harlan, 1972). The value of crop diversity has long been recognized (Vavilov, 1992). A global system of genebanks (e.g. was established in the 1970s to preserve the abundant genetic variation found in traditional “landrace” varieties of crops and in crop wild relatives (Harlan, 1972). While preserving crop variation is a critical first step, the time has come to make use of this variation to breed more resilient crops. The DivSeek International Network ( is a scientific, not-for- profit organization that aims to accelerate such efforts. Crop diversity: value, barriers to use, and mitigation strategies There are >1750 national and international genebanks worldwide. They house ~7 million crop germplasm accessions (, including samples of diverse natural populations, with many more managed in situ. These accessions arguably represent one of humanity’s greatest treasures, as they contain genetic variation that can be harnessed to create better tasting, higher yielding, disease/pest resistant, and climate resilient cultivars that require fewer agricultural inputs (Figure 1). Unfortunately, most genebank accessions are poorly characterized, and few have been utilized in breeding. Yet when a serious effort has been made to search genebanks for traits of interest, the effort has been highly rewarded. Examples include the discovery of a submergence-tolerant landrace used to breed new, high-yielding, submergence-tolerant rice varieties currently grown on tens of millions of acres (Mackill et al., 2012) and durable resistance to late blight, a devastating pathogen of potato, derived from a wild relative (Bernal-Galeano, 2020). Given the high value of the genetic diversity found in crop wild relatives and traditional landraces, why are these genetic resources not more widely employed in breeding programs? One reason for the limited use of genebank holdings is the paucity of information about them, which increases the time, expense, and risk associated with mining genebank diversity. To address this Journal Pre-proof
  • iSCAN: An RT-LAMP-coupled CRISPR-Cas12 module for rapid, sensitive detection of SARS-CoV-2.

    Ali, Zahir; Aman, Rashid; Mahas, Ahmed; Rao, Gundra Sivakrishna; Tehseen, Muhammad; Marsic, Tin; Salunke, Rahul; Subudhi, Amit K; Hala, Sharif M; Hamdan, Samir; Pain, Arnab; Alofi, Fadwa S; Alsomali, Afrah; Hashem, Anwar M; Khogeer, Asim; Almontashiri, Naif A M; Abedalthagafi, Malak; Hassan, Norhan; Mahfouz, Magdy M. (Virus research, Elsevier BV, 2020-08-22) [Article]
    The COVID-19 pandemic caused by SARS-CoV-2 affects all aspects of human life. Detection platforms that are efficient, rapid, accurate, specific, sensitive, and user friendly are urgently needed to manage and control the spread of SARS-CoV-2. RT-qPCR based methods are the gold standard for SARS-CoV-2 detection. However, these methods require trained personnel, sophisticated infrastructure, and a long turnaround time, thereby limiting their usefulness. Reverse transcription-loop-mediated isothermal amplification (RT-LAMP), a one-step nucleic acid amplification method conducted at a single temperature, has been used for colorimetric virus detection. CRISPR-Cas12 and CRISPR-Cas13 systems, which possess collateral activity against ssDNA and RNA, respectively, have also been harnessed for virus detection. Here, we built an efficient, rapid, specific, sensitive, user-friendly SARS-CoV-2 detection module that combines the robust virus amplification of RT-LAMP with the specific detection ability of SARS-CoV-2 by CRISPR-Cas12. Furthermore, we combined the RT-LAMP-CRISPR-Cas12 module with lateral flow cells to enable highly efficient point-of-care SARS-CoV-2 detection. Our iSCAN SARS-CoV-2 detection module, which exhibits the critical features of a robust molecular diagnostic device, should facilitate the effective management and control of COVID-19.
  • Efficient Mimics for Elucidating Zaxinone Biology and Promoting Agricultural Applications

    Wang, Jian You; Jamil, Muhammad; Lin, Pei-Yu; Ota, Tsuyoshi; Fiorilli, Valentina; Novero, Mara; Zarban, Randa Alhassan Yahya; Kountche, Boubacar Amadou; Takahashi, Ikuo; Martínez, Claudio; Lanfranco, Luisa; Bonfante, Paola; de Lera, Angel R.; Asami, Tadao; Al-Babili, Salim (Molecular Plant, Elsevier BV, 2020-08-21) [Article]
    Zaxinone is an apocarotenoid regulatory metabolite required for normal rice growth and development. In addition, zaxinone has a large application potential in agriculture, due to its growth promoting activity and capability to alleviate infestation by the root parasitic plant Striga through decreasing strigolactone (SL) production. However, zaxinone is poorly accessible to the scientific community because of its laborious organic synthesis that impedes its further investigation and utilization. Here, we developed easy-to-synthesize and highly efficient mimics of zaxinone (MiZax). We performed a structure-activity-relationship study using a series of apocarotenoids distinguished from zaxinone by different structural features. Using the obtained results, we designed several phenyl-based compounds synthesized with a high-yield through a simple method. Activity tests showed that MiZax3 and MiZax5 exert zaxinone activity in rescuing root growth of a zaxinone-deficient rice mutant, promoting growth, and reducing SL content in roots and root exudates of wild-type plants. Moreover, these compounds were at least as efficient as zaxinone in suppressing transcript level of SL biosynthesis genes and in alleviating Striga infestation under greenhouse conditions, and did not negatively impact mycorrhization. Taken together, MiZax are a promising tool for elucidating zaxinone biology and investigating rice development, and suitable candidates for combating Striga and increasing crop growth.
  • On the biosynthesis and evolution of apocarotenoid plant growth regulators.

    Wang, Jian You; Lin, Pei-Yu; Al-Babili, Salim (Seminars in cell & developmental biology, Elsevier BV, 2020-08-01) [Article]
    Carotenoids are an important source of metabolites with regulatory function, which include the plant hormones abscisic acid (ABA) and strigolactones (SLs), and several recently identified growth regulators and signaling molecules. These carotenoid-derivatives originate from oxidative breakdown of double bonds in the carotenoid polyene, a common metabolic process that gives rise to diverse carbonyl cleavage-products known as apocarotenoids. Apocarotenoids exert biologically important functions in all taxa. In plants, they are a major regulator of plant growth, development and response to biotic and abiotic environmental stimuli, and mediate plant's communication with surrounding organisms. In this article, we provide a general overview on the biology of plant apocarotenoids, focusing on ABA, SLs, and recently identified apocarotenoid growth regulators. Following an introduction on carotenoids, we describe plant apocarotenoid biosynthesis, signal transduction, and evolution and summarize their biological functions. Moreover, we discuss the evolution of these intriguing metabolites, which has not been adequately addressed in the literature.
  • Healthy soils for healthy plants for healthy humans

    Hirt, Heribert (EMBO reports, EMBO, 2020-07-31) [Article]
    The microbiota of the human gut and the plant rhizome are similar in many ways and intricately connected with each other. A healthy plant therefore affects human microbiota and human health.
  • Dissecting new genetic components of salinity tolerance in two-row spring barley at the vegetative and reproductive stages

    saade, stephanie; Brien, Chris; Pailles, Yveline; Berger, Bettina; Shahid, Mohammad; Russell, Joanne; Waugh, Robbie; Negrão, Sónia; Tester, Mark A. (PLOS ONE, Public Library of Science (PLoS), 2020-07-23) [Article]
    Soil salinity imposes an agricultural and economic burden that may be alleviated by identifying the components of salinity tolerance in barley, a major crop and the most salt tolerant cereal. To improve our understanding of these components, we evaluated a diversity panel of 377 two-row spring barley cultivars during both the vegetative, in a controlled environment, and the reproductive stages, in the field. In the controlled environment, a high-throughput phenotyping platform was used to assess the growth-related traits under both control and saline conditions. In the field, the agronomic traits were measured from plots irrigated with either fresh or saline water. Association mapping for the different components of salinity tolerance enabled us to detect previously known associations, such as HvHKT1;5. Using an "interaction model", which took into account the interaction between treatment (control and salt) and genetic markers, we identified several loci associated with yield components related to salinity tolerance. We also observed that the two developmental stages did not share genetic regions associated with the components of salinity tolerance, suggesting that different mechanisms play distinct roles throughout the barley life cycle. Our association analysis revealed that genetically defined regions containing known flowering genes (Vrn-H3, Vrn-H1, and HvNAM-1) were responsive to salt stress. We identified a salt-responsive locus (7H, 128.35 cM) that was associated with grain number per ear, and suggest a gene encoding a vacuolar H+-translocating pyrophosphatase, HVP1, as a candidate. We also found a new QTL on chromosome 3H (139.22 cM), which was significant for ear number per plant, and a locus on chromosome 2H (141.87 cM), previously identified using a nested association mapping population, which associated with a yield component and interacted with salinity stress. Our study is the first to evaluate a barley diversity panel for salinity stress under both controlled and field conditions, allowing us to identify contributions from new components of salinity tolerance which could be used for marker-assisted selection when breeding for marginal and saline regions.
  • Desert Microbes for Boosting Sustainable Agriculture in Extreme Environments

    Alsharif, Wiam; Saad, Maged; Hirt, Heribert (Frontiers in Microbiology, Frontiers Media SA, 2020-07-22) [Article]
    A large portion of the earth’s surface consists of arid, semi-arid and hyper-arid lands. Life in these regions is profoundly challenged by harsh environmental conditions of water limitation, high levels of solar radiation and temperature fluctuations, along with soil salinity and nutrient deficiency, which have serious consequences on plant growth and survival. In recent years, plants that grow in such extreme environments and their naturally associated beneficial microbes have attracted increased interest. The rhizosphere, rhizosheath, endosphere, and phyllosphere of desert plants display a perfect niche for isolating novel microbes. They are well adapted to extreme environments and offer an unexploited reservoir for bio-fertilizers and bio-control agents against a wide range of abiotic and biotic stresses that endanger diverse agricultural ecosystems. Their properties can be used to improve soil fertility, increase plant tolerance to various environmental stresses and crop productivity as well as benefit human health and provide enough food for a growing human population in an environment-friendly manner. Several initiatives were launched to discover the possibility of using beneficial microbes. In this review, we will be describing the efforts to explore the bacterial diversity associated with desert plants in the arid, semi-arid, and hyper-arid regions, highlighting the latest discoveries and applications of plant growth promoting bacteria from the most studied deserts around the world.
  • The Use of High-Throughput Phenotyping for Assessment of Heat Stress-Induced Changes in Arabidopsis

    Gao, Ge; Tester, Mark A.; Julkowska, Magdalena M. (Plant Phenomics, American Association for the Advancement of Science (AAAS), 2020-07-17) [Article]
    The worldwide rise in heatwave frequency poses a threat to plant survival and productivity. Determining the new marker phenotypes that show reproducible response to heat stress and contribute to heat stress tolerance is becoming a priority. In this study, we describe a protocol focusing on the daily changes in plant morphology and photosynthetic performance after exposure to heat stress using an automated noninvasive phenotyping system. Heat stress exposure resulted in an acute reduction of the quantum yield of photosystem II and increased leaf angle. In longer term, the exposure to heat also affected plant growth and morphology. By tracking the recovery period of the WT and mutants impaired in thermotolerance (hsp101), we observed that the difference in maximum quantum yield, quenching, rosette size, and morphology. By examining the correlation across the traits throughout time, we observed that early changes in photochemical quenching corresponded with the rosette size at later stages, which suggests the contribution of quenching to overall heat tolerance. We also determined that 6 h of heat stress provides the most informative insight in plant’s responses to heat, as it shows a clear separation between treated and nontreated plants as well as the WT and hsp101. Our work streamlines future discoveries by providing an experimental protocol, data analysis pipeline, and new phenotypes that could be used as targets in thermotolerance screenings.
  • Karrikin Signaling Acts Parallel to and Additively with Strigolactone Signaling to Regulate Rice Mesocotyl Elongation in Darkness.

    Zheng, Jianshu; Hong, Kai; Zeng, Longjun; Wang, Lei; Kang, Shujing; Qu, Minghao; Dai, Jiarong; Zou, Linyuan; Zhu, Lixin; Tang, Zhanpeng; Meng, Xiangbing; Wang, Bing; Hu, Jiang; Zhao, Yonghui; Zeng, Dali; Cui, Peng; Wang, Quan; Qian, Qian; Wang, Yonghong; Li, Jiayang; Xiong, Guosheng (The Plant cell, American Society of Plant Biologists (ASPB), 2020-07-16) [Article]
    Seedling emergence in monocots depends mainly on mesocotyl elongation, requiring the coordination between developmental signals and environmental stimuli. Strigolactones (SLs) and karrikins are butenolide compounds that regulate various developmental processes; both are able to negatively regulate rice (Oryza sativa) mesocotyl elongation in the dark. Here, we report that a karrikin signaling complex, DWARF 14-LIKE (D14L)-DWARF 3 (D3)-Oryza sativa SUPPRESSOR OF MAX2 1 (OsSMAX1), regulates rice mesocotyl elongation in the dark. We demonstrate that D14L recognizes the karrikin signal and recruits the SCFD3 ubiquitin ligase for the ubiquitination and degradation of OsSMAX1, mirroring the SL-induced and D14- and D3-dependent ubiquitination and degradation of D53. Overexpression of OsSMAX1 promoted mesocotyl elongation in the dark, whereas knockout of OsSMAX1 suppressed the elongated-mesocotyl phenotypes of d14l and d3 but had little effect on their shoot branching phenotype. OsSMAX1 localizes in nucleus and interacts with TOPLESS-RELATED PROTEINs (TPRs), regulating downstream gene expression. Moreover, we showed that the GR24 enantiomers GR245DS and GR24ent-5DS specifically inhibit mesocotyl elongation and regulate downstream gene expression in a D14- and D14L-dependent manner, respectively. Our work revealed that karrikin and SL signaling play parallel and additive roles in modulating downstream genes expression and negatively regulating mesocotyl elongation in the dark.
  • Expression of a carotenogenic gene allows faster biomass production by redesigning plant architecture and improving photosynthetic efficiency in tobacco.

    Moreno, Juan C; Mi, Jianing; Agrawal, Shreya; Kössler, Stella; Turečková, Veronika; Tarkowská, Danuše; Thiele, Wolfram; Al-Babili, Salim; Bock, Ralph; Schöttler, Mark Aurel (The Plant journal : for cell and molecular biology, Wiley, 2020-07-06) [Article]
    Because carotenoids act as accessory pigments in photosynthesis, play a key photoprotective role, and are of major nutritional importance, carotenogenesis has been a target for crop improvement. Although carotenoids are important precursors of phytohormones, previous genetic manipulations reported little if any effects on biomass production and plant development, but resulted in specific modifications in carotenoid content. Unexpectedly, the expression of the carrot lycopene b-cyclase (DcLCYB1) in Nicotiana tabacum cv. Xanthi not only resulted in increased carotenoid accumulation, but also in altered plant architecture characterized by longer internodes, faster plant growth, early flowering and increased biomass. Here, we have challenged these transformants with a range of growth conditions to determine the robustness of their phenotype and analyze the underlying mechanisms. Transgenic DcLCYB1 lines showed increased transcript levels of key genes involved in carotenoid, chlorophyll, gibberellin (GA) and abscisic acid (ABA) biosynthesis, but also in photosynthesis-related genes. Accordingly, their carotenoid, chlorophyll, ABA and GA contents were increased. Hormone application and inhibitor experiments confirmed the key role of altered GA/ABA contents in the growth phenotype. Because the longer internodes reduce shading of mature leaves, induction of leaf senescence was delayed, and mature leaves maintained a high photosynthetic capacity. This increased total plant assimilation, as reflected in higher plant yields under both fully-controlled constant and fluctuating light, and in non-controlled conditions. Furthermore, our data is a warning that engineering of isoprenoid metabolism can cause complex changes in phytohormone homeostasis and therefore plant development, which have not been sufficiently considered in previous studies.
  • Emerging Technologies to Enable Sustainable Controlled Environment Agriculture in the Extreme Environments of Middle East-North Africa Coastal Regions

    Lefers, Ryan; Tester, Mark A.; Lauersen, Kyle J. (Frontiers in Plant Science, Frontiers Media SA, 2020-07-02) [Article]
    Despite global shifts in attitudes toward sustainability and increasing awareness of human impact on the environment, projected population growth and climate change require technological adaptations to ensure food and resource security at a global scale. Although desert areas have long been proposed as ideal sites for solar electricity generation, only recently have efforts shifted toward development of specialized and regionally focused agriculture in these extreme environments. In coastal regions of the Middle East and North Africa (MENA), the most abundant resources are consistent intense sunlight and saline sea water. MENA coastal regions hold incredible untapped potential for agriculture driven by the combination of key emerging technologies in future greenhouse concepts: transparent infrared collecting solar panels and low energy salt water cooling. These technologies can be combined to create greenhouses that drive regionally relevant agriculture in this extreme environment, especially when the target crops are salt-tolerant plants and algal biomass. Future controlled environment agriculture concepts will not compete for municipal fresh water and can be readily integrated into local human/livestock/fisheries food chains. With strategic technological implementation, marginal lands in these environments could participate in production of biomass, sustainable energy generation, and the circular carbon economy. The goal of this perspective is to reframe the idea of these environments as extreme, to having incredible untapped development potential.
  • iSCAN: An RT-LAMP-coupled CRISPR-Cas12 module for rapid, sensitive detection of SARS-CoV-2

    Ali, Zahir; Aman, Rashid; Mahas, Ahmed; gundra, sivakrishna; Tehseen, Muhammad; Marsic, Tin; Salunke, Rahule; Subudhi, Amit; Hala, Sharif; Hamdan, Samir; Pain, Arnab; Hassan, Norhan; Mahfouz, Magdy M. (Cold Spring Harbor Laboratory, 2020-06-05) [Preprint]
    The COVID-19 pandemic caused by SARS-CoV-2 affects all aspects of human life. Detection platforms that are efficient, rapid, accurate, specific, sensitive, and user friendly are urgently needed to manage and control the spread of SARS-CoV-2. RT-qPCR based methods are the gold standard for SARS-CoV-2 detection. However, these methods require trained personnel, sophisticated infrastructure, and a long turnaround time, thereby limiting their usefulness. Reverse transcription-loop-mediated isothermal amplification (RT-LAMP), a one-step nucleic acid amplification method conducted at a single temperature, has been used for colorimetric virus detection. CRISPR-Cas12 and CRISPR-Cas13 systems, which possess collateral activity against ssDNA and RNA, respectively, have also been harnessed for virus detection. Here, we built an efficient, rapid, specific, sensitive, user-friendly SARS-CoV-2 detection module that combines the robust virus amplification of RT-LAMP with the specific detection ability of SARS-CoV-2 by CRISPR-Cas12. Furthermore, we combined the RT-LAMP-CRISPR-Cas12 module with lateral flow cells to enable highly efficient point-of-care SARS-CoV-2 detection. Our iSCAN SARS-CoV-2 detection module, which exhibits the critical features of a robust molecular diagnostic device, should facilitate the effective management and control of COVID-19.
  • The Apocarotenoid Zaxinone Is a Positive Regulator of Strigolactone and Abscisic Acid Biosynthesis in Arabidopsis Roots.

    Ablazov, Abdugaffor; Mi, Jianing; Jamil, Muhammad; Jia, Kunpeng; Wang, Jian You; Feng, Qitong; Al-Babili, Salim (Frontiers in plant science, Frontiers Media SA, 2020-05-31) [Article]
    Carotenoids are ubiquitous precursors of important metabolites including hormones, such as strigolactones (SLs) and abscisic acid (ABA), and signaling and regulatory molecules, such as the recently discovered zaxinone. Strigolactones and ABA are key regulators of plant growth and development, adaptation to environmental changes and response to biotic and abiotic stress. Previously, we have shown that zaxinone, an apocarotenoid produced in rice by the enzyme zaxinone synthase (ZAS) that is common in mycorrhizal plants, is required for normal rice growth and development, and a negative regulator of SL biosynthesis. Zaxinone is also formed in Arabidopsis, which lacks ZAS, via an unknown route. In the present study, we investigated the biological activity of zaxinone in Arabidopsis, focusing on its effect on SL and ABA biosynthesis. For this purpose, we quantified the content of both hormones and determined the levels of related transcripts in Arabidopsis (Arabidopsis thaliana), roots upon zaxinone treatment. For SL quantification, we also employed Striga seed germination bioassay. Results obtained show that zaxinone application to hydroponically grown Arabidopsis seedlings enhanced transcript levels of key biosynthetic genes of both hormones, led to higher root ABA and SL (methyl carlactonoate, MeCLA) content, and increased SL release, even under sufficient phosphate supply. Using the SL insensitive (max2-1) and the ABA deficient (aba1-6, aba2-1, and nced3) mutants, we also show that zaxinone application reduced hypocotyl growth and that this effect is caused by increasing ABA content. Our results suggest that zaxinone is a regulatory metabolite also in Arabidopsis, which triggers the biosynthesis of both carotenoid-derived hormones, SLs and ABA, in roots. In the non-mycotrophic plant Arabidopsis, zaxinone does not increase growth and may be perceived as a stress signal, while it acts as a growth-promoting metabolite and suppressor of SL biosynthesis in rice.
  • Engineering herbicide resistance via prime editing in rice

    Butt, Haroon; Rao, Gundra Sivakrishna; Sedeek, Khalid Elwy Mohamed; Aman, Rashid; Kamel, Radwa; Mahfouz, Magdy M. (Plant Biotechnology Journal, Wiley, 2020-05-16) [Article]
    Although CRISPR-Cas9 has revolutionized our ability to generate site-specific double-strand breaks, precise editing of the genome remains challenging in most eukaryotes, including plants (Shan et al., 2013). In plants homology-directed repair is inefficient, limiting our ability to make precise edits of the DNA sequence (Ali et al., 2020; Butt et al., 2017). Moreover, cytosine and adenine base editors have serious drawbacks including lower efficiency, unclean edited sequence, and the possibility of off-target mutations at other loci (Rees and Liu, 2018). Chimeric single guide RNAs (sgRNAs) can provide editing information, in RNA form, but this modality suffers from several limitations including lower efficiency, less versatility, and the need for long homology arms (Butt et al., 2017).
  • Wheat chromatin architecture is organized in genome territories and transcription factories

    Concia, Lorenzo; Veluchamy, Alaguraj; Ramirez-Prado, Juan S.; Martin-Ramirez, Azahara; Huang, Ying; Perez, Magali; Domenichini, Severine; Rodriguez Granados, Natalia Y.; Kim, SoonKap; Blein, Thomas; Duncan, Susan; Pichot, Clement; Manza-Mianza, Deborah; Juery, Caroline; Paux, Etienne; Moore, Graham; Hirt, Heribert; Bergounioux, Catherine; Crespi, Martin; Mahfouz, Magdy M.; Bendahmane, Abdelhafid; Liu, Chang; Hall, Anthony; Raynaud, Cécile; Latrasse, David; Benhamed, Moussa (Genome Biology, Springer Science and Business Media LLC, 2020-04-29) [Article]
    Polyploidy is ubiquitous in eukaryotic plant and fungal lineages, and it leads to the co-existence of several copies of similar or related genomes in one nucleus. In plants, polyploidy is considered a major factor in successful domestication. However, polyploidy challenges chromosome folding architecture in the nucleus to establish functional structures.
  • Role of MPK4 in pathogen-associated molecular pattern-triggered alternative splicing in Arabidopsis

    Bazin, Jeremie; Mariappan, Kiruthiga; Jiang, Yunhe; Blein, Thomas; Volz, Ronny; Crespi, Martin; Hirt, Heribert (PLOS Pathogens, Public Library of Science (PLoS), 2020-04-17) [Article]
    Alternative splicing (AS) of pre-mRNAs in plants is an important mechanism of gene regulation in environmental stress tolerance but plant signals involved are essentially unknown. Pathogen-associated molecular pattern (PAMP)-triggered immunity (PTI) is mediated by mitogen-activated protein kinases and the majority of PTI defense genes are regulated by MPK3, MPK4 and MPK6. These responses have been mainly analyzed at the transcriptional level, however many splicing factors are direct targets of MAPKs. Here, we studied alternative splicing induced by the PAMP flagellin in Arabidopsis. We identified 506 PAMP-induced differentially alternatively spliced (DAS) genes. Importantly, of the 506 PAMP-induced DAS genes, only 89 overlap with the set of 1950 PAMP-induced differentially expressed genes (DEG), indicating that transcriptome analysis does not identify most DAS events. Global DAS analysis of mpk3, mpk4, and mpk6 mutants in the absence of PAMP treatment showed no major splicing changes. However, in contrast to MPK3 and MPK6, MPK4 was found to be a key regulator of PAMP-induced DAS events as the AS of a number of splicing factors and immunity-related protein kinases is affected, such as the calcium-dependent protein kinase CPK28, the cysteine-rich receptor like kinases CRK13 and CRK29 or the FLS2 co-receptor SERK4/BKK1. Although MPK4 is guarded by SUMM2 and consequently, the mpk4 dwarf and DEG phenotypes are suppressed in mpk4 summ2 mutants, MPK4-dependent DAS is not suppressed by SUMM2, supporting the notion that PAMP-triggered MPK4 activation mediates regulation of alternative splicing.

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