Formerly the "Center for Desert Agriculture"

Recent Submissions

  • 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.
  • Characterization of Epidermal Bladder Cells in Chenopodium quinoa

    Otterbach, Sophie; Khoury, Holly; Rupasinghe, Thusitha; Mendis, Himasha; Kwan, Kim; Lui, Veronica; Natera, Siria; Klaiber, Iris; Allen, Nathaniel; Jarvis, David; Tester, Mark A.; Roessner, Ute; Schmöckel, Sandra (Authorea, Inc., 2021-05-10) [Preprint]
    Chenopodium quinoa (quinoa) is considered a superfood, as it has favourable nutrient composition and is gluten free. Quinoa has high tolerance to several abiotic stresses, i.e. salinity, water deficit (drought) and cold. The tolerance mechanisms are yet to be elucidated. Quinoa has Epidermal Bladder Cells (EBCs) that densely cover the shoot surface, particularly the younger parts of the plant. Here, we report on the EBC’s primary and secondary metabolomes, as well as the lipidome in response to abiotic stresses. EBCs were isolated from plants after cold, heat, high-light, water deficit and salt treatments. We used untargeted Gas Chromatography-Mass Spectrometry (GC-MS) to analyse metabolites and untargeted and targeted Liquid Chromatography-MS (LC-MS) for lipids and secondary metabolite analyses. We identified 64 primary metabolites, including sugars, organic acids and amino acids, 19 secondary metabolites, including phenolic compounds, betanin and saponins and 240 lipids categorized in five groups including glycerolipids and phospholipids. Although we found only few changes in the metabolic composition of bladders in response to abiotic stresses, metabolites related with heat, cold and high-light treatments, but not salt stress, were changed significantly. Na+ concentrations were low in EBCs with all treatments, and approximately two orders of magnitude lower than K+ concentrations.
  • 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.
  • Iso-anchorene is an endogenous metabolite that inhibits primary root growth in Arabidopsis.

    Jia, Kunpeng; Mi, Jianing; Ablazov, Abdugaffor; Ali, Shawkat; Yang, Yu; Balakrishna, Aparna; Berqdar, Lamis; Feng, Qitong; Blilou, Ikram; Al-Babili, Salim (The Plant journal : for cell and molecular biology, Wiley, 2021-04-10) [Article]
    Carotenoid-derived regulatory metabolites and hormones are generally known to arise through the oxidative cleavage of a single double bond in the carotenoid backbone, which yields mono-carbonyl products called apocarotenoids. However, the extended conjugated double bond system of these pigments predestines them also to repeated cleavage forming di-aldehyde products, diapocarotenoids, which have been less investigated due to their instability and low abundance. Recently, we reported on the short diapocarotenoid anchorene as an endogenous Arabidopsis metabolite and specific signaling molecule that promotes anchor root formation. In this work, we investigated the biological activity of a synthetic isomer of anchorene, iso-anchorene, which can derive from repeated carotenoid cleavage. We show that iso-anchorene is a growth inhibitor that specifically inhibits primary root growth by reducing cell division rates in the root apical meristem. Using auxin efflux transporter marker lines, we also show that the effect of iso-anchorene on primary root growth involves the modulation of auxin homeostasis. Moreover, by using liquid chromatography mass spectrometry (LC-MS) analysis, we demonstrate that iso-anchorene is a natural Arabidopsis metabolite. Chemical inhibition of carotenoid biosynthesis led to a significant decrease in the iso-anchorene level, indicating that it originates from this metabolic pathway. Taken together, our results reveal a further carotenoid-derived regulatory metabolite with a specific biological function that affects root growth, manifesting the biological importance of diapocarotenoids.
  • Early growth stage characterization and the biochemical responses for salinity stress in tomato

    Alam, Md Sarowar; Tester, Mark A.; Fiene, Gabriele; Mousa, Magdi Ali Ahmed (Plants, MDPI AG, 2021-04-07) [Article]
    Salinity is one of the most significant environmental stresses for sustainable crop production in major arable lands of the globe. Thus, we conducted experiments with 27 tomato genotypes to screen for salinity tolerance at seedling stage, which were treated with non-salinized (S1) control (18.2 mM NaCl) and salinized (S2) (200 mM NaCl) irrigation water. In all genotypes, the elevated salinity treatment contributed to a major depression in morphological and physiological character-istics; however, a smaller decrease was found in certain tolerant genotypes. Principal component analyses (PCA) and clustering with percentage reduction in growth parameters and different salt tolerance indices classified the tomato accessions into five key clusters. In particular, the tolerant genotypes were assembled into one cluster. The growth and tolerance indices PCA also showed the order of salt-tolerance of the studied genotypes, where Saniora was the most tolerant genotype and P.Guyu was the most susceptible genotype. To investigate the possible biochemical basis for salt stress tolerance, we further characterized six tomato genotypes with varying levels of salinity tolerance. A higher increase in proline content, and antioxidants activities were observed for the salt-tolerant genotypes in comparison to the susceptible genotypes. Salt-tolerant genotypes identified in this work herald a promising source in the tomato improvement program or for grafting as scions with improved salinity tolerance in tomato.
  • Digital insights: bridging the phenotype-to-genotype divide

    McCabe, Matthew; Tester, Mark A. (Journal of Experimental Botany, Oxford University Press (OUP), 2021-04-02) [Article]
    The convergence of autonomous platforms for field-based phenotyping with advances in machine learning for big data analytics and rapid sequencing for genome description herald the promise of new insights and discoveries in the plant sciences. Han et al. (2021) leverage these emerging tools to navigate the challenging path from field-based mapping of phenotypic features to identifying specific genetic loci in the laboratory: in this case, loci responsible for regulating daily flowering time in lettuce. While their contribution neatly illustrates these exciting technological developments, it also highlights the work that remains to bridge these multidisciplinary fields to more fully deliver upon the promise of digital agriculture.
  • Current progress in Striga management.

    Jamil, Muhammad; Kountche, Boubacar Amadou; Al-Babili, Salim (Plant physiology, Oxford University Press (OUP), 2021-04-01) [Article]
    The Striga, particularly S. he rmonthica, problem has become a major threat to food security, exacerbating hunger and poverty in many African countries. A number of Striga control strategies have been proposed and tested during the past decade, however, further research efforts are still needed to provide sustainable and effective solutions to the Striga problem. In this paper, we provide an update on the recent progress and the approaches used in Striga management, and highlight emerging opportunities for developing new technologies to control this enigmatic parasite.
  • Chromatin phosphoproteomics unravels a function for AT-hook motif nuclear localized protein AHL13 in PAMP-triggered immunity

    Rayapuram, Naganand; Jarad, Mai; Alhoraibi, Hanna; Bigeard, Jean; Abulfaraj, Aala A.; Volz, Ronny; Mariappan, Kiruthiga; Almeida-Trapp, Marilia; Schlöffel, Maria; Lastrucci, Emmanuelle; Bonhomme, Ludovic; Gust, Andrea A.; Mithöfer, Axel; Arold, Stefan T.; Pflieger, Delphine; Hirt, Heribert (NCBI, 2021-03-22) [Bioproject, Dataset]
    We report the transcriptome composition of ahl13-1 compared to WT (col-0) plant without treatment and after Pst hrcC-application Overall design: Illumina high-sequencing plateform was used to analyse the transcriptome composition of col0 and ahl13-1 under treated and untreated conditions. col0 samples are in GEO Series GSE118854.
  • Population genomics and haplotype analysis in spelt and bread wheat identifies a gene regulating glume color

    Abrouk, Michael; Athiyannan, Naveenkumar; Müller, Thomas; Pailles, Yveline; Stritt, Christoph; Roulin, Anne C.; Chu, Chenggen; Liu, Shuyu; Morita, Takumi; Handa, Hirokazu; Poland, Jesse; Keller, Beat; Krattinger, Simon G. (Communications Biology, Springer Nature, 2021-03-19) [Article]
    The cloning of agriculturally important genes is often complicated by haplotype variation across crop cultivars. Access to pan-genome information greatly facilitates the assessment of structural variations and rapid candidate gene identification. Here, we identified the red glume 1 (Rg-B1) gene using association genetics and haplotype analyses in ten reference grade wheat genomes. Glume color is an important trait to characterize wheat cultivars. Red glumes are frequent among Central European spelt, a dominant wheat subspecies in Europe before the 20th century. We used genotyping-by-sequencing to characterize a global diversity panel of 267 spelt accessions, which provided evidence for two independent introductions of spelt into Europe. A single region at the Rg-B1 locus on chromosome 1BS was associated with glume color in the diversity panel. Haplotype comparisons across ten high-quality wheat genomes revealed a MYB transcription factor as candidate gene. We found extensive haplotype variation across the ten cultivars, with a particular group of MYB alleles that was conserved in red glume wheat cultivars. Genetic mapping and transient infiltration experiments allowed us to validate this particular MYB transcription factor variants. Our study demonstrates the value of multiple high-quality genomes to rapidly resolve copy number and haplotype variations in regions controlling agriculturally important traits.

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