Formerly the "Center for Desert Agriculture"

Recent Submissions

  • Root endophyte induced plant thermotolerance by constitutive chromatin modification at heat stress memory gene loci

    Shekhawat, Kirti; Saad, Maged; Sheikh, Arsheed Hussain; Mariappan, Kiruthiga; Al-Mahmoudi, Henda; abdulhakim, fatimah; Eida, Abdul Aziz; Jalal, Rewaa S.; Masmoudi, Khaled; Hirt, Heribert (EMBO reports, EMBO, 2021-01-10) [Article]
    Global warming has become a critical challenge to food security, causing severe yield losses of major crops worldwide. Conventional and transgenic breeding strategies to enhance plant thermotolerance are laborious and expensive. Therefore, the use of beneficial microbes could be an alternative approach. Here, we report that the root endophyte Enterobacter sp. SA187 induces thermotolerance in wheat in the laboratory as well as in open-field agriculture. To unravel the molecular mechanisms, we used Arabidopsis thaliana as model plant. SA187 reprogramed the Arabidopsis transcriptome via HSFA2-dependent enhancement of H3K4me3 levels at heat stress memory gene loci. Unlike thermopriming, SA187-induced thermotolerance is mediated by ethylene signaling via the transcription factor EIN3. In contrast to the transient chromatin modification by thermopriming, SA187 induces constitutive H3K4me3 modification of heat stress memory genes, generating robust thermotolerance in plants. Importantly, microbial community composition of wheat plants in open-field agriculture is not influenced by SA187, indicating that beneficial microbes can be a powerful tool to enhance thermotolerance of crops in a sustainable manner.
  • 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 (Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, 2021-01-08) [Article]
    In many eukaryotic systems during immune responses, mitogen-activated protein kinases (MAPKs) link cytoplasmic signaling to chromatin events by targeting transcription factors, chromatin remodeling complexes, and the RNA polymerase machinery. So far, knowledge on these events is scarce in plants and no attempts have been made to focus on phosphorylation events of chromatin-associated proteins. Here we carried out chromatin phosphoproteomics upon elicitor-induced activation of Arabidopsis. The events in WT were compared with those in mpk3, mpk4, and mpk6 mutant plants to decipher specific MAPK targets. Our study highlights distinct signaling networks involving MPK3, MPK4, and MPK6 in chromatin organization and modification, as well as in RNA transcription and processing. Among the chromatin targets, we characterized the AT-hook motif containing nuclear localized (AHL) DNA-binding protein AHL13 as a substrate of immune MAPKs. AHL13 knockout mutant plants are compromised in pathogen-associated molecular pattern (PAMP)-induced reactive oxygen species production, expression of defense genes, and PAMP-triggered immunity. Transcriptome analysis revealed that AHL13 regulates key factors of jasmonic acid biosynthesis and signaling and affects immunity toward Pseudomonas syringae and Botrytis cinerea pathogens. Mutational analysis of the phosphorylation sites of AHL13 demonstrated that phosphorylation regulates AHL13 protein stability and thereby its immune functions.
  • Carotenoid Biofortification of Crops in the CRISPR Era

    Zheng, Xiongjie; Kuijer, Hendrik N.J.; Al-Babili, Salim (Trends in Biotechnology, Elsevier BV, 2020-12-29) [Article]
    Carotenoids are micronutrients important for human health. The continuous improvements in clustered regularly interspaced short palindromic repeats (CRISPR)-based genome-editing techniques make rapid, DNA/transgene-free and targeted multiplex genetic modification a reality, thus promising to accelerate the breeding and generation of ‘golden’ staple crops. We discuss here the progress and future prospects of CRISPR/Cas9 applications for carotenoid biofortification.
  • Development and Cell Cycle Activity of the Root Apical Meristem in the Fern Ceratopteris richardii

    Aragon-Raygoza, Alejandro; Vasco, Alejandra; Blilou, Ikram; Herrera-Estrella, Luis Rafael; Cruz-Ramírez, Alfredo (Genes, MDPI AG, 2020-12-09) [Article]
    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 h 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.
  • Plant Apocarotenoids: From Retrograde Signaling to Interspecific Communication.

    Moreno, Juan C; Mi, Jianing; Alagoz, Yagiz; Al-Babili, Salim (The Plant journal : for cell and molecular biology, Wiley, 2020-12-01) [Article]
    Carotenoids are isoprenoid compounds synthesized by all photosynthetic and some non-photosynthetic organisms. They are essential for photosynthesis and contribute to many other aspects of a plant's life. The oxidative breakdown of carotenoids gives rise to the formation of a diverse family of essential metabolites called apocarotenoids. This metabolic process either takes place spontaneously through reactive oxygen species (ROS) or is catalyzed by enzymes generally belonging to the carotenoid cleavage dioxygenase (CCD) family. Apocarotenoids include the phytohormones abscisic acid (ABA) and strigolactones (SLs), signaling molecules, and growth regulators. ABA and SLs are vital in regulating plant growth, development, and stress response. SLs are also an essential component in plants'rhizospheric communication with symbionts and parasites. Other apocarotenoid small molecules, such as blumenols, mycorradicins, zaxinone, anchorene, β-cyclocitral, β-cyclogeranic acid, β-ionone, and loliolide, are involved in plant growth and development, and/or contribute to different processes, including arbuscular mycorrhiza (AM) symbiosis, abiotic stress response, plant-plant and plant-herbivore interactions, and plastid retrograde signaling. There are also indications for the presence of structurally unidentifiedlinearcis-carotene-derived apocarotenoids (LCDAs), which are presumed to modulateplastid biogenesis and leaf morphology, among other developmental processes. Here, we provide an overview on the biology of old, recently discovered, and supposed plant apocarotenoid signaling molecules, describing their biosynthesis, developmental and physiological functions, and role as a messenger in plants' communication.
  • Engineering crops of the future: CRISPR approaches to develop climate-resilient and disease-resistant plants

    Zaidi, Syed Shan-e-Ali; Mahas, Ahmed; Vanderschuren, Hervé; Mahfouz, Magdy M. (Genome Biology, Springer Science and Business Media LLC, 2020-11-30) [Article]
    AbstractTo meet increasing global food demand, breeders and scientists aim to improve the yield and quality of major food crops. Plant diseases threaten food security and are expected to increase because of climate change. CRISPR genome-editing technology opens new opportunities to engineer disease resistance traits. With precise genome engineering and transgene-free applications, CRISPR is expected to resolve the major challenges to crop improvement. Here, we discuss the latest developments in CRISPR technologies for engineering resistance to viruses, bacteria, fungi, and pests. We conclude by highlighting current concerns and gaps in technology, as well as outstanding questions for future research.
  • 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.
  • Potential of Platinum Standard Reference Genomes to Exploit Natural Variation in the Wild Relatives of Rice

    Mussurova, Saule; Al-Bader, Noor; Zuccolo, Andrea; Wing, Rod Anthony (Frontiers in Plant Science, Frontiers Media SA, 2020-09-23) [Article]
    As the world’s population expands from 7.6 billion to 10 billion over the next 30 years, scientists and farmers across the globe must explore every angle necessary to provide a safe, stable and sustainable food supply for generations to come. Rice, and its wild relatives in the genus Oryza, will play a significant role in helping to solve this 10 billion people question due to its place as a staple food for billions. The genus Oryza is composed of 27 species that span 15 million years of evolutionary diversification and have been shown to contain a plethora of untapped adaptive traits, e.g., biotic and abiotic resistances, which can be used to improve cultivated rice. Such traits can be introduced into cultivated rice, in some cases by conventional crossing, and others via genetic transformation and gene editing methods. In cases where traits are too complex to easily transfer to cultivated rice [e.g., quantitative trait loci (QTL)], an alternative strategy is to domesticate the wild relative that already contains the desired adaptive traits – i.e., “neodomestication”. To utilize the Oryza genus for crop improvement and neodomestication, we first need a set of genomic resources that can be used to efficiently identify, capture, and guide molecular crop improvement. Here, we introduce the concept of platinum standard reference genome sequences (PSRefSeq) – a new standard by which contiguous near-gap free reference genomes can now be produced. By having a set of PSRefSeqs for every Oryza species we set a new bar for how crop wild relatives can be integrated into crop improvement programs.
  • Fonio millet genome unlocks African orphan crop diversity for agriculture in a changing climate

    Abrouk, Michael; Ahmed, Hanin Ibrahim; Cubry, Philippe; Šimoníková, Denisa; Cauet, Stéphane; Pailles, Yveline; Bettgenhaeuser, Jan; Gapa, Liubov; Scarcelli, Nora; Couderc, Marie; Zekraoui, Leila; Kathiresan, Nagarajan; Čížková, Jana; Hřibová, Eva; Doležel, Jaroslav; Arribat, Sandrine; Bergès, Hélène; Wieringa, Jan J.; Gueye, Mathieu; Kane, Ndjido A.; Leclerc, Christian; Causse, Sandrine; Vancoppenolle, Sylvie; Billot, Claire; Wicker, Thomas; Vigouroux, Yves; Barnaud, Adeline; Krattinger, Simon G. (Nature Communications, Springer Science and Business Media LLC, 2020-09-08) [Article]
    Abstract Sustainable food production in the context of climate change necessitates diversification of agriculture and a more efficient utilization of plant genetic resources. Fonio millet (Digitaria exilis) is an orphan African cereal crop with a great potential for dryland agriculture. Here, we establish high-quality genomic resources to facilitate fonio improvement through molecular breeding. These include a chromosome-scale reference assembly and deep re-sequencing of 183 cultivated and wild Digitaria accessions, enabling insights into genetic diversity, population structure, and domestication. Fonio diversity is shaped by climatic, geographic, and ethnolinguistic factors. Two genes associated with seed size and shattering showed signatures of selection. Most known domestication genes from other cereal models however have not experienced strong selection in fonio, providing direct targets to rapidly improve this crop for agriculture in hot and dry environments.
  • 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), 2020-08-28) [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.
  • 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.
  • 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, 2020-08-21) [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
  • 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, 2020-08) [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.
  • 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.
  • 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, 2020-07-27) [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.
  • 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.
  • CRISPR/Cas9 Mutagenesis by Translocation of Cas9 Protein Into Plant Cells via the Agrobacterium Type IV Secretion System

    Schmitz, Daan J.; Ali, Zahir; Wang, Chenglong; Aljedaani, Fatimah R.; Hooykaas, Paul J. J.; Mahfouz, Magdy M.; de Pater, Sylvia (Frontiers in Genome Editing, Frontiers Media SA, 2020-07-17) [Article]
    Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) is a powerful tool for genome engineering in plants. The RNA-guided Cas9 endonuclease is usually delivered into plant cells as a DNA construct encoding Cas9 and the single guide RNA (sgRNA). However, constitutive expression of nucleases may cause off target mutations. In addition, DNA constructs can integrate into the host genome, causing mutations and complicating regulatory approval. Instead of DNA, here we deliver Cas9 through the Agrobacterium T4SS, accomplished by fusion of the VirF T4SS translocation peptide to Cas9 (NCas9F). Co-cultivation of Agrobacteria expressing NCas9F with yeast (Saccharomyces cerevisiae) harboring a sgRNA targeting CAN1 showed that NCas9F was translocated via T4SS and induced targeted mutations in the yeast genome. Infiltration of Nicotiana benthamiana leaves with Agrobacteria expressing NCas9F and sgRNA-PHYTOENE DESATURASE (PDS) resulted in targeted modifications at the PDS locus, albeit at a very low rate. In order to increase the mutation frequency NCas9F protein was co-transported with a T-DNA encoding sgRNA-PDS1. Next generation sequencing confirmed that this resulted in targeted mutations at the PDS locus with a similar distribution but at a 5-fold lower frequency as the mutations obtained with a T-DNA encoding both Cas9 and sgRNA-PDS1. Similarly, infection with Tobacco rattle virus (TRV) encoding sgRNA-PDS2 combined with NCas9F protein translocation resulted in an equally high frequency of PDS mutations in N. benthamiana compared to T-DNA encoded sgRNA-PDS1 combined with NCas9F protein translocation. Our results revealed that translocation of NCas9F protein via the Agrobacterium T4SS can be used for targeted mutagenesis in host cells instead of the permanent and constitutive expression of Cas9 from a T-DNA.

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