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Recent Submissions

  • Engineering carbon sequestration on arid lands

    Hirt, Heribert; Boukcim, Hassan; Ducousso, Marc; Saad, Maged (Trends in Plant Science, Elsevier BV, 2023-09-21) [Article]
    To limit the effects of global warming, arid lands, which constitute approximately one-third of terrestrial surfaces and are not utilized for agriculture, could serve as an effective method for long-term carbon (C) storage. We propose that soil–plant–microbiome engineering with oxalogenic plants and oxalotrophic microbes could facilitate C sequestration on a global scale.
  • Septoria tritici blotch resistance gene Stb15 encodes a lectin receptor-like kinase

    Hafeez, Amber; Chartrain, Laetitia; Feng, Cong; Cambon, Florence; Clarke, Martha; Griffiths, Simon; Hayta, Sadiye; Jiang, Mei; Keller, Beat; Kirby, Rachel; Kolodziej, Markus C.; Powell, Oliver R.; Smedley, Mark A.; Steuernagel, Burkhard; Xian, Wenfei; Wingen, Luzie; Cheng, Shifeng; Saintenac, Cyrille; Wulff, Brande B. H.; Brown, James K. M. (Cold Spring Harbor Laboratory, 2023-09-12) [Preprint]
    Septoria tritici blotch (STB), caused by the Dothideomycete fungus Zymoseptoria tritici, is of one of the most damaging diseases of bread wheat (Triticum aestivum)1 and the target of costly fungicide applications2. In line with the fungus’ apoplastic lifestyle, STB resistance genes isolated to date encode receptor-like kinases (RLKs) including a wall-associated kinase (Stb6) and a cysteine-rich kinase (Stb16q)3,4. Here, we used genome-wide association studies (GWAS) on a panel of 300 whole-genome shotgun-sequenced diverse wheat landraces (WatSeq consortium) to identify a 99 kb region containing six candidates for the Stb15 resistance gene. Mutagenesis and transgenesis confirmed a gene encoding an intronless G-type lectin RLK (LecRK) as Stb15. The characterisation of Stb15 exemplifies the unexpected diversity of RLKs conferring Z. tritici resistance in wheat.
  • A study of the Root meristem control by the Retinoblastoma-related protein and the effect of beneficial and pathogenic bacteria on root growth

    Castillo Hernandez, Tatiana (2023-08-24) [Thesis]
    Advisor: Blilou, Ikram
    Committee members: Wulff, Brande B. H.; Frøkjær-Jensen, Christian
    Roots are considered an important organ as they transport nutrients and water and provide anchor and support in the plants. The development of roots involves the participation of specific proteins such as RETINOBLASTOMA-RELATED (RBR) which has been found to play a role in cell cycle regulation and stem cell niche maintenance. Additionally, roots can interact with the environment and soil microorganisms that can influence processes in plant growth and development. For instance, plant growth-promoting rhizobacteria (PGPR) have been found to have the ability to alter the root system by their influence on signaling pathways or phytohormones. In this study, we generated RBR mutant lines using CRISPR-Cas9 to determine the role of this protein in early plant growth. We found that the mutant lines contained partial abortion in ovules and mild reduction in siliques suggesting the participation of this protein in the early stages of plant development. Furthermore, we also use beneficial and pathogenic bacteria strains to study their effect on root patterning. We showed that WSC417 beneficial bacteria can influence root structure by promoting the growth of root hairs which might suggest a plant improvement in nutrient uptake. Also, we could observe that WSC417 can exert some protection against DC 3000 pathogenic bacteria when plant seedlings were inoculated with both strains. Overall, we could determine that RBR plays a role in early developmental stages and root development can also be influenced by biotic factors such as microorganisms.
  • Deciphering Salt Stress Responses in Solanum pimpinellifolium through High-Throughput Phenotyping.

    Morton, Mitchell; Fiene, Gabriele; Ahmed, Hanin; Rey, Elodie; Abrouk, Michael; Angel, Yoseline; Johansen, Kasper; Saber, Noha; Malbeteau, Yoann; Almashharawi, Samir; Ziliani, Matteo Giuseppe; Aragon Solorio, Bruno Jose Luis; Oakey, Helena; Berger, Bettina; Brien, Chris; Krattinger, Simon G.; Mousa, Magdi Ali Ahmed; McCabe, Matthew; Negrão, Sónia; Tester, Mark A.; Julkowska, Magdalena M. (Cold Spring Harbor Laboratory, 2023-08-17) [Preprint]
    Soil salinity is a major environmental stressor affecting agricultural productivity worldwide. Understanding plant responses to salt stress is crucial for developing resilient crop varieties. Wild relatives of cultivated crops, such as wild tomato, Solanum pimpinellifolium, can serve as a useful resource to further expand the resilience potential of the cultivated germplasm, S. lycopersicum. In this study, we employed high-throughput phenotyping in the greenhouse and field conditions to explore salt stress responses of a S. pimpinellifolium diversity panel. Our study revealed extensive phenotypic variations in response to salt stress, with traits such as transpiration rate, shoot mass, and ion accumulation showing significant correlations with plant performance. We found that while transpiration was a key determinant of plant performance in the greenhouse, shoot mass strongly correlated with yield under field conditions. Conversely, ion accumulation was the least influential factor under greenhouse conditions. Through a Genome Wide Association Study, we identified candidate genes not previously associated with salt stress, highlighting the power of high-throughput phenotyping in uncovering novel aspects of plant stress responses. This study contributes to our understanding of salt stress tolerance in S. pimpinellifolium and lays the groundwork for further investigations into the genetic basis of these traits, ultimately informing breeding efforts for salinity tolerance in tomato and other crops.
  • Integration of genetic and genomics resources in einkorn wheat enables precision mapping of important traits

    Saripalli, Gautam; Adhikari, Laxman; Amos, Cameron; Kibriya, Ashraf Masood; Ahmed, Hanin; Heuberger, Matthias; Raupp, John; Athiyannan, Naveenkumar; Wicker, Thomas; Abrouk, Michael; Wallace, Sydney; Hosseinirad, Seyedali; Chhuneja, Parveen; Livesay, Janelle; Rawat, Nidhi; Krattinger, Simon G.; Poland, Jesse; Tiwari, Vijay (Communications Biology, Springer Science and Business Media LLC, 2023-08-12) [Article]
    Einkorn wheat (Triticum monococcum) is an ancient grain crop and a close relative of the diploid progenitor (T. urartu) of polyploid wheat. It is the only diploid wheat species having both domesticated and wild forms and therefore provides an excellent system to identify domestication genes and genes for traits of interest to utilize in wheat improvement. Here, we leverage genomic advancements for einkorn wheat using an einkorn reference genome assembly combined with skim-sequencing of a large genetic population of 812 recombinant inbred lines (RILs) developed from a cross between a wild and a domesticated T. monococcum accession. We identify 15,919 crossover breakpoints delimited to a median and average interval of 114 Kbp and 219 Kbp, respectively. This high-resolution mapping resource enables us to perform fine-scale mapping of one qualitative (red coleoptile) and one quantitative (spikelet number per spike) trait, resulting in the identification of small physical intervals (400 Kb to 700 Kb) with a limited number of candidate genes. Furthermore, an important domestication locus for brittle rachis is also identified on chromosome 7A. This resource presents an exciting route to perform trait discovery in diploid wheat for agronomically important traits and their further deployment in einkorn as well as tetraploid pasta wheat and hexaploid bread wheat cultivars.
  • Einkorn genomics sheds light on history of the oldest domesticated wheat

    Ahmed, Hanin; Heuberger, Matthias; Schoen, Adam; Koo, Dal-Hoe; Quiroz-Chávez, Jesús; Adhikari, Laxman; Raupp, John; Cauet, Stéphane; Rodde, Nathalie; Cravero, Charlotte; Callot, Caroline; Lazo, Gerard R.; Kathiresan, Nagarajan; Sharma, Parva K.; Moot, Ian; Yadav, Inderjit Singh; Singh, Lovepreet; Saripalli, Gautam; Rawat, Nidhi; Datla, Raju; Athiyannan, Naveenkumar; Ramirez-Gonzalez, Ricardo H.; Uauy, Cristobal; Wicker, Thomas; Tiwari, Vijay; Abrouk, Michael; Poland, Jesse; Krattinger, Simon G. (Springer Science and Business Media LLC, 2023-08-02) [Article]
    Einkorn (Triticum monococcum) was the first domesticated wheat species, and was central to the birth of agriculture and the Neolithic Revolution in the Fertile Crescent around 10,000 years ago1,2. Here we generate and analyse 5.2-Gb genome assemblies for wild and domesticated einkorn, including completely assembled centromeres. Einkorn centromeres are highly dynamic, showing evidence of ancient and recent centromere shifts caused by structural rearrangements. Whole-genome sequencing analysis of a diversity panel uncovered the population structure and evolutionary history of einkorn, revealing complex patterns of hybridizations and introgressions after the dispersal of domesticated einkorn from the Fertile Crescent. We also show that around 1% of the modern bread wheat (Triticum aestivum) A subgenome originates from einkorn. These resources and findings highlight the history of einkorn evolution and provide a basis to accelerate the genomics-assisted improvement of einkorn and bread wheat.
  • New Series of Zaxinone Mimics (MiZax) for Fundamental and Applied Research

    Jamil, Muhammad; Pei-Yu, Lin; Berqdar, Lamis; Wang, Jian You; Takahashi, Ikuo; Ota, Tsuyoshi; Alhammad, Noor; Chen, Guan-Ting Erica; Asami, Tadao; Al-Babili, Salim (Biomolecules, MDPI AG, 2023-08-01) [Article]
    The apocarotenoid zaxinone is a recently discovered regulatory metabolite required for proper rice growth and development. In addition, zaxinone and its two mimics (MiZax3 and MiZax5) were shown to have a remarkable growth-promoting activity on crops and a capability to reduce infestation by the root parasitic plant Striga through decreasing strigolactone (SL) production, suggesting their potential for application in agriculture and horticulture. In the present study, we developed a new series of MiZax via structural modification of the two potent zaxinone mimics (MiZax3 and MiZax5) and evaluated their effect on plant growth and Striga infestation. In general, the structural modifications to MiZax3 and MiZax5 did not additionally improve their overall performance but caused an increase in certain activities. In conclusion, MiZax5 and especially MiZax3 remain the likely most efficient zaxinone mimics for controlling Striga infestation.
  • Disruption of the cytochrome CYP711A5 gene reveals MAX1 redundancy in rice strigolactone biosynthesis.

    Wang, Jian You; Chen, Guan-Ting Erica; Braguy, Justine; Jamil, Muhammad; Berqdar, Lamis; Al-Babili, Salim (Journal of plant physiology, Elsevier BV, 2023-07-31) [Article]
    Strigolactones (SLs) inhibit shoot branching/tillering and are secreted by plant roots as a signal to attract symbiotic mycorrhizal fungi in the rhizosphere, particularly under phosphate starvation. However, SLs are also hijacked by root parasitic weeds as inducer for the germination of their seeds. There are around 35 natural SLs divided, based on their structures, into canonical and non-canonical SLs. Cytochrome P450 enzymes of the 711 clade, such as MORE AXILLARY GROWTH1 (MAX1) in Arabidopsis, are a major driver of SL structural diversity. Monocots, such as rice, contain several MAX1 homologs that participate in SL biosynthesis. To investigate the function of OsMAX1-1900 in planta, we generated CRISPR/Cas9 mutants disrupted in the corresponding gene. Characterizing of the generated mutants at metabolite and phenotype level suggests that OsMAX1-1900 loss-of-function does neither affect the SL pattern nor rice architecture, indicating functional redundancy among rice MAX1 homologs.
  • A single NLR gene confers resistance to leaf and stripe rust in wheat

    Sharon, Amir; Sharma, Davinder; Avni, Raz; Gutierrez-Gonzalez, Juan; Kumar, Rakesh; Sela, Hanan; Prusty, Manas; Cohen, Arava; Molnár, István; Holušová, Kateřina; Said, Mahmoud; Doležel, Jaroslav; Millet, Eitan; Khazan, Sofia; Landau, Udi; Bethke, Gerit; Ezrati, Smadar; Ronen, Moshe; Maatuk, Oxana; Eilam, Tamar; Manisterski, Jacob; Ben-Yehuda, Pnina; Anikster, Yehoshua; Matny, Oadi; Steffenson, Brian J.; Mascher, Martin; Brabham, Helen; Moscou, Matthew J.; Liang, Yong; Yu, Guotai; Wulff, Brande B. H.; Muehlbauer, Gary; Minz-Dub, Anna (Research Square Platform LLC, 2023-07-28) [Preprint]
    Nucleotide-binding site leucine-rich repeat (NLR) disease-resistance genes typically confer resistance against races of a single pathogen. We report that Lr/Yr548, an NLR gene from Aegilops sharonensis and Aegilops longissima, confers specific resistance against Puccinia triticina (Pt) and P. striiformis tritici (Pst) that cause leaf and stripe rust, respectively. Lr/Yr548 prevented disease development in wheat introgression as well as transgenic wheat lines. Comparative analysis of Lr/Yr548 and all cloned Triticeae NLR disease-resistance genes showed that Lr/Yr548 contains a distinctive coiled-coil domain and that it is unique to Ae. sharonensis and Ae. longissima. A phylogenetic analysis indicated multiple events of gene flow of Lr/Yr548 between the two species, and suggested loss of resistance in susceptible isolates. The confinement of Lr/Yr548 to Ae. longissima and Ae. sharonensis and the cross resistance that it confers against Pt and Pst in wheat highlight the potential of these species as sources of novel disease-resistance genes for wheat improvement.
  • Genome-wide association mapping of rust resistance in Aegilops longissima

    Page, Rae; Huang, Shuyi; Ronen, Moshe; Sela, Hanan; Sharon, Amir; Shrestha, Sandesh; Poland, Jesse; Steffenson, Brian J. (Frontiers in Plant Science, Frontiers Media SA, 2023-07-27) [Article]
    The rust diseases, including leaf rust caused by Puccinia triticina (Pt), stem rust caused by P. graminis f. sp. tritici (Pgt), and stripe rust caused by P. striiformis f. sp. tritici (Pst), are major limiting factors in wheat production worldwide. Identification of novel sources of rust resistance genes is key to developing cultivars resistant to rapidly evolving pathogen populations. Aegilops longissima is a diploid wild grass native to the Levant and closely related to the modern bread wheat D subgenome. To explore resistance genes in the species, we evaluated a large panel of Ae. longissima for resistance to several races of Pt, Pgt, and Pst, and conducted a genome-wide association study (GWAS) to map rust resistance loci in the species. A panel of 404 Ae. longissima accessions, mostly collected from Israel, were screened for seedling-stage resistance to four races of Pt, four races of Pgt, and three races of Pst. Out of the 404 accessions screened, two were found that were resistant to all 11 races of the three rust pathogens screened. The percentage of all accessions screened that were resistant to a given rust pathogen race ranged from 18.5% to 99.7%. Genotyping-by-sequencing (GBS) was performed on 381 accessions of the Ae. longissima panel, wherein 125,343 single nucleotide polymorphisms (SNPs) were obtained after alignment to the Ae. longissima reference genome assembly and quality control filtering. Genetic diversity analysis revealed the presence of two distinct subpopulations, which followed a geographic pattern of a northern and a southern subpopulation. Association mapping was performed in the genotyped portion of the collection (n = 381) and in each subpopulation (n = 204 and 174) independently via a single-locus mixed-linear model, and two multi-locus models, FarmCPU, and BLINK. A large number (195) of markers were significantly associated with resistance to at least one of 10 rust pathogen races evaluated, nine of which are key candidate markers for further investigation due to their detection via multiple models and/or their association with resistance to more than one pathogen race. The novel resistance loci identified will provide additional diversity available for use in wheat breeding.
  • Resistance that stacks up: engineering rust and mildew disease control in the cereal crops wheat and barley.

    Dracatos, Peter M; Lu, Jing; Sánchez-Martín, Javier; Wulff, Brande B. H. (Plant biotechnology journal, 2023-07-26) [Article]
    Staying ahead of the arms race against rust and mildew diseases in cereal crops is essential to maintain and preserve food security. The methodological challenges associated with conventional resistance breeding are major bottlenecks for deploying resistance (R) genes in high-yielding crop varieties. Advancements in our knowledge of plant genomes, structural mechanisms, innovations in bioinformatics, and improved plant transformation techniques have alleviated this bottleneck by permitting rapid gene isolation, functional studies, directed engineering of synthetic resistance and precise genome manipulation in elite crop cultivars. Most cloned cereal R genes encode canonical immune receptors which, on their own, are prone to being overcome through selection for resistance-evading pathogenic strains. However, the increasingly large repertoire of cloned R genes permits multi-gene stacking that, in principle, should provide longer-lasting resistance. This review discusses how these genomics-enabled developments are leading to new breeding and biotechnological opportunities to achieve durable rust and powdery mildew control in cereals.
  • Genomic Characterization and Gene Bank Curation of Aegilops: The Wild Relatives of Wheat

    Adhikari, Laxman; Raupp, John; Wu, Shuangye; Koo, Dal-Hoe; Friebe, Bernd; Poland, Jesse (Cold Spring Harbor Laboratory, 2023-07-25) [Preprint]
    Genetic diversity found in crop wild relatives is critical to preserve and utilize for crop improvement to achieve sustainable food production amid climate change and increased demand. We genetically characterized a large collection of 1,041 Aegilops accessions distributed among 23 different species using more than 45K single nucleotide polymorphisms identified by genotyping-by-sequencing (GBS). The Wheat Genetics Resource Center (WGRC) Aegilops germplasm collection was curated through the identification of misclassified and redundant accessions. There were 49 misclassified and 28 sets of redundant accessions within the four diploid species. The curated germplasm sets now have improved utility for genetic studies and wheat improvement. We constructed a phylogenetic tree and PCA cluster for all Aegilops species together, giving one of the most comprehensive views of Aegilops. The Sitopsis section and the U genome Aegilops clade were further scrutinized with in-depth population analysis. The genetic relatedness among the pair of Aegilops species provided strong evidence for the species evolution, speciation and diversification. We inferred genome symbols for two species Ae. neglecta and Ae. columnaris based on the sequence read mapping and the presence of segregating loci on the pertinent genomes as well as genetic clustering. The high genetic diversity observed among Aegilops species indicated that the genus could play an even greater role in providing the critical need for untapped genetic diversity for future wheat breeding and improvement. To fully characterize these Aegilops species, there is an urgent need to generate reference assemblies for these wild wheats, especially for the polyploid Aegilops.
  • Abscisic acid inhibits germination of Striga seeds and is released by them as a rhizospheric signal providing competitive advantage and supporting host infestation

    Jamil, Muhammad; Alagoz, Yagiz; Wang, Jian You; Chen, Guan-Ting Erica; Berqdar, Lamis; Kharbatia, Najeh M.; Moreno, Juan C; Kuijer, Hendrik N. J.; Al-Babili, Salim (Cold Spring Harbor Laboratory, 2023-07-07) [Preprint]
    Seeds of the root parasitic plant Striga hermonthica undergo a conditioning process under humid and warm environments before germinating in response to host-released stimulants, particularly strigolactones (SLs). The plant hormone abscisic acid (ABA) regulates different growth and developmental processes, and stress response; however, its role during Striga seed germination and early interactions with host plants is under-investigated. Here, we show that ABA inhibited Striga seed germination and that hindering its biosynthesis induced conditioning and germination in unconditioned seeds, which was significantly enhanced by treatment with the SL analog rac-GR24. However, the inhibitory effect of ABA remarkably decreased during conditioning, confirming the loss of sensitivity towards ABA in later developmental stages. ABA measurement showed a significant reduction of its content during the early conditioning stage and a significant increase upon rac-GR24-triggered germination. We observed this increase also in released seed exudates, which was further confirmed by using the Arabidopsis ABA-reporter GUS marker line. Seed exudates of germinated seeds, containing elevated levels of ABA, impaired the germination of surrounding Striga seeds in vitro and promoted root growth of a rice host towards germinated Striga seeds. Application of ABA as a positive control caused similar effects, indicating its function in Striga/Striga and Striga/host communications. In summary, we show that ABA is an essential player during seed dormancy and germination processes in Striga and acts as a rhizospheric signal released by germinated parasitic seeds to provide a competitive advantage and support host infestation.
  • Genomic characterization and gene bank curation of Aegilops using genotyping-by-sequencing

    Adhikari, Laxman; Raupp, John; Wu, Shuangye; Koo, Dal-Hoe; Friebe, Bernd; Poland, Jesse (Dryad, 2023-07-05) [Dataset]
    In this study, genotyping-by-sequencing (GBS) was performed on 1041 Aegilops accessions, representing 23 different species. These accessions have been maintained by the Wheat Genetics and Resource Center (WGRC) at Kansas State University. The GBS FASTQ files have been uploaded to the NCBI SRA public repository under the BioProject accession number # PRJNA985892. We have provided other files related to data analysis, such as the barcode key file, SNP matrices, and taxonomic information of the accessions in this Dryad repository, which can be accessed through the provided link. The aim of the study was to explore the genetic and genomic characteristics of wild wheat relatives, Aegilops, using a larger number of SNP markers. Here, we also curated the WGRC gene bank Aegilops collection via the identification of misclassified accessions and genetically identical redundant accessions. Further, we explored the genomic relationship between wheat and the different Aegilops species.
  • Identification of bird cherry-oat aphid and greenbug resistance sources from Aegilops tauschii for wheat improvement

    Xu, Xiangyang; Li, Genqiao; Lhamo, Dhondup; Carver, Brett F.; Wulff, Brande B. H.; Gu, Yongqiang; Xu, Steven S.; Armstrong, Scott (Crop Science, Wiley, 2023-06-22) [Article]
    Bird cherry-oat aphid (BCOA) and greenbug pose a persistent threat to wheat production in many wheat-growing regions. Currently, greenbug resistance genes are limited for wheat improvement, and BCOA resistance sources are even more scarce. Thus, it is urgent to identify BCOA and greenbug resistance sources in wheat gene pools. An Aegilops tauschii (Ae. tauschii) panel of 260 accessions, which accounted for 48% of the total Ae. tauschii accessions available in global germplasm banks, was evaluated for BCOA resistance, and a set of BCOA-resistant lines were identified. The same panel was evaluated for response to greenbug biotypes C, E, F, G, I, and TX1. A total of 102 lines exhibited 14 unique resistance profiles or phenotypes featuring resistance to at least one biotype. The frequency of resistant lines varied among lineages or subspecies, from 62% in Lineage 1 (subspecies tauschii) to 18% in Lineage 2 (subspecies stangulata), indicating conservation of genetic variance for greenbug resistance was nonrandom. Ae. tauschii accessions resistant to both BCOA and greenbug were identified for enhancing aphid resistance.
  • Cytokinins as an alternative suicidal Striga germination compound

    Jamil, Muhammad; Wang, Jian You; Berqdar, Lamis; Alagoz, Yagiz; Behisi, Ahmed; Al-Babili, Salim (Weed Research, Wiley, 2023-06-15) [Article]
    The witchweed Striga hermonthica, an obligate and noxious root–parasitic plant, remains a persistent threat to cereal production and poses a great challenge to smallholder farmers in Sub-Saharan Africa. Inducing suicidal germination of Striga seeds by applying strigolactone analogs is a promising strategy to deplete the Striga seed bank of infested soils. Nevertheless, there is a need to increase the efficiency and improve the applicability of this strategy, which may be achieved by testing further Striga germination stimulants. Herein, we explored the potential of cytokinins in inducing Striga seed germination. We investigated their activity as a suicidal germination agent along with fluridone that inhibits carotenoid biosynthesis and hence reduces abscisic acid formation and facilitates breaking of seed dormancy. Under lab conditions, application of fluridone (at 100 μM) or cytokinins (at 100 μM) showed 19% and 63% Striga germination, respectively, while combining different cytokinins with fluridone led to above 93% germination of treated seeds, with thidiazuron as the most active cytokinin. Using rice (cv IAC-165), we also show that co-application of fluoridone and thidiazuron to Striga infested pots before planting the host led to up to 86%–100% reduction in Striga emergence. In summary, cytokinins, particularly thidiazuron, could be useful suicidal agents to induce Striga seed germination and ultimately deplete the seedbank in Striga-infested regions.
  • Biomimetic Mineralization for Smart Biostimulant Delivery and Crop Micronutrients Fortification

    Aguliar Perez, Katya M.; Alagoz, Yagiz; Maatouk, Batoul; Wang, Jiangyou; Berqdar, Lamis; Qutub, Somayah S.; Jamil, Muhammad; AlNasser, Sara; BinSaleh, Nouf; Lin, Peiyu; Almarwaey, Lamyaa O.; Asami, Tadao; Al-Babili, Salim; Khashab, Niveen M. (Nano Letters, American Chemical Society (ACS), 2023-06-05) [Article]
    Sustainable and precise fortification practices are necessary to ensure food security for the increasing human population. Precision agriculture aims to minimize the use of fertilizers and pesticides by developing smart materials for real-life agricultural practices. Here, we show that biomimetic mineralization can be efficiently employed to encapsulate and controllably release plant biostimulants (MiZax-3) to improve the quality and yield of capsicum (<i>Capsicum annum</i>) crops in field experiments. ZIF-8 encapsulation of MiZax-3 (MiZIFs) could significantly enhance its stability up to around 679 times (6p value = 0.0072) at field conditions. Our results demonstrate that the coordinating Zn ions and the MiZax-3 play a vital role in improving Zn content in the produced fruits by 2-fold, which is the first report of this nature on Zn content in fruits. We envision this platform as a starting point to investigate other biocompatible coordination-based platforms for micronutrient delivery in precision agriculture.
  • A Fast and Cost-Effective Genotyping Method for CRISPR-Cas9-Generated Mutant Rice Lines

    Ablazov, Abdugaffor; Felemban, Abrar; Braguy, Justine; Kuijer, Hendrik N.J.; Al-Babili, Salim (Plants, MDPI AG, 2023-05-31) [Article]
    With increasing throughput in both the generation and phenotyping of mutant lines in plants, it is important to have an efficient and reliable genotyping method. Traditional workflows, still commonly used in many labs, have time-consuming and expensive steps, such as DNA purification, cloning and growing E. coli cultures. We propose an alternative workflow where these steps are bypassed, using Phire polymerase on fresh plant tissue, and ExoProStar treatment as preparation for sequencing. We generated CRISPR-Cas9 mutants for ZAS (ZAXINONE SYNTHASE) in rice with two guide RNAs. Using both a traditional workflow and our proposed workflow, we genotyped nine T1 plants. To interpret the sequencing output, which is often complex in CRISPR-generated mutants, we used free online automatic analysis systems and compared the results. Our proposed workflow produces results of the same quality as the old workflow, but in 1 day instead of 3 days and about 35 times cheaper. This workflow also consists of fewer steps and reduces the risk of cross contamination and mistakes. Furthermore, the automated sequence analysis packages are mostly accurate and could easily be used for bulk analysis. Based on these advantages, we encourage academic and commercial labs conducting genotyping to consider switching over to our proposed workflow.
  • Essential role of the CD docking motif of MPK4 in plant immunity, growth, and development

    Siodmak, Anna E.; Hameed, Umar Farook Shahul; Rayapuram, Naganand; Volz, Ronny; Boudsocq, Marie; Alharbi, Siba; Alhoraibi, Hannah; Lee, Yong-Hwan; Blilou, Ikram; Arold, Stefan T.; Hirt, Heribert (New Phytologist, Wiley, 2023-05-27) [Article]
    MAPKs are universal eukaryotic signaling factors whose functioning is assumed to depend on the recognition of a common docking motif (CD) by its activators, substrates, and inactivators. We studied the role of the CD domain of Arabidopsis MPK4 by performing interaction studies and determining the ligand-bound MPK4 crystal structure. We revealed that the CD domain of MPK4 is essential for interaction and activation by its upstream MAPKKs MKK1, MKK2, and MKK6. Cys181 in the CD site of MPK4 was shown to become sulfenylated in response to reactive oxygen species in vitro. To test the function of C181 in vivo, we generated wild-type (WT) MPK4-C181, nonsulfenylatable MPK4-C181S, and potentially sulfenylation mimicking MPK4-C181D lines in the mpk4 knockout background. We analyzed the phenotypes in growth, development, and stress responses, revealing that MPK4-C181S has WT activity and complements the mpk4 phenotype. By contrast, MPK4-C181D cannot be activated by upstream MAPKK and cannot complement the phenotypes of mpk4. Our findings show that the CD motif is essential and is required for activation by upstream MAPKK for MPK4 function. Furthermore, growth, development, or immunity functions require upstream activation of the MPK4 protein kinase.
  • An unusual tandem kinase fusion protein confers leaf rust resistance in wheat

    Wang, Yajun; Abrouk, Michael; Gourdoupis, Spyridon; Koo, Dal-Hoe; Karafiátová, Miroslava; Molnár, István; Holušová, Kateřina; Doležel, Jaroslav; Athiyannan, Naveenkumar; Cavalet-Giorsa, Emile; Jaremko, Lukasz; Poland, Jesse; Krattinger, Simon G. (Nature Genetics, Springer Science and Business Media LLC, 2023-05-22) [Article]
    The introgression of chromosome segments from wild relatives is an established strategy to enrich crop germplasm with disease-resistance genes1. Here we use mutagenesis and transcriptome sequencing to clone the leaf rust resistance gene Lr9, which was introduced into bread wheat from the wild grass species Aegilops umbellulata2. We established that Lr9 encodes an unusual tandem kinase fusion protein. Long-read sequencing of a wheat Lr9 introgression line and the putative Ae. umbellulata Lr9 donor enabled us to assemble the ~28.4-Mb Lr9 translocation and to identify the translocation breakpoint. We likewise cloned Lr58, which was reportedly introgressed from Aegilops triuncialis3, but has an identical coding sequence compared to Lr9. Cytogenetic and haplotype analyses corroborate that the two genes originate from the same translocation event. Our work sheds light on the emerging role of kinase fusion proteins in wheat disease resistance, expanding the repertoire of disease-resistance genes for breeding.

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