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The Potyviridae are the largest family of plant-pathogenic viruses. Members of this family are the soil-borne bymoviruses barley yellow mosaic virus (BaYMV) and barley mild mosaic virus (BaMMV), which, upon infection of young winter barley seedlings in autumn, can cause yield losses as high as 50%. Resistance breeding plays a major role in coping with these pathogens. However, some viral strains have overcome the most widely used resistance. Thus, there is a need for novel sources of resistance. In ancient landraces and wild relatives of cultivated barley, alleles of the susceptibility factor PROTEIN DISULFIDE ISOMERASE LIKE 5-1 (PDIL5-1) were identified to confer resistance to all known strains of BaYMV and BaMMV. Although the gene is highly conserved throughout all eukaryotes, barley is thus far the only species for which PDIL5-1-based virus resistance has been reported. Whereas introgression by crossing to the European winter barley breeding pool is tedious, time-consuming and additionally associated with unwanted linkage drag, the present study exemplifies an approach to targeted mutagenesis of two barley cultivars employing CRISPR-associated endonuclease technology to induce site-directed mutations similar to those described for PDIL5-1 alleles that render certain landraces resistant. Homozygous primary mutants were produced in winter barley, and transgene-free homozygous M 2 mutants were produced in spring barley. A variety of mutants carrying novel PDIL5-1 alleles were mechanically inoculated with BaMMV, by which all frameshift mutations and certain in-frame mutations were demonstrated to confer resistance to this virus. Under greenhouse conditions, virus-resistant mutants showed no adverse effects in terms of growth and yield., (© 2022 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.)

Wheat stripe rust (caused by Puccinia striiformis f. tritici Erikss.) causes severe yield losses worldwide. Due to the continuous appearance of new stripe rust races, resistance has been broken in most of the highly resistant genotypes in Egypt and worldwide. Therefore, looking for new ways to resist such a severe disease is urgently needed. Trichoderma asperellum strain T34 has been known as an effective bioagent against many crop diseases. It exists naturally in Egyptian fields. Therefore, in our study, the effectiveness of strain T34 was tested as a bioagent against wheat stripe rust. For this purpose, 198 spring wheat genotypes were tested for their resistance against two different P. striiformis f. tritici populations collected from the Egyptian fields. The most highly aggressive P. striiformis f. tritici population was used to test the effectiveness of strain T34. Highly significant differences were found between strain T34 and stripe rust, suggesting the effectiveness of strain T34 in stripe rust resistance. A genome-wide association study identified 48 gene models controlling resistance under normal conditions and 46 gene models controlling strain T34-induced resistance. Of these gene models, only one common gene model was found, suggesting the presence of two different genetic systems controlling resistance under each condition. The pathways of the biological processes were investigated under both conditions. This study provided in-depth understanding of genetic control and, hence, will accelerate the future of wheat breeding programs for stripe rust resistance.

Drought stress is a major yield-limiting factor throughout the world in wheat ( Triticum aestivum L.), causing losses of up to 80% of the total yield. The identification of factors affecting drought stress tolerance in the seedling stage is especially important to increase adaptation and accelerate the grain yield potential. In the current study, 41 spring wheat genotypes were tested for their tolerance to drought at the germination stage under two different polyethylene glycol concentrations (PEG) of 25% and 30%. For this purpose, twenty seedlings from each genotype were evaluated in triplicate with a randomized complete block design (RCBD) in a controlled growth chamber. The following nine parameters were recorded: germination pace (GP), germination percentage (G%), number of roots (NR), shoot length (SL), root length (RL), shoot-root length ratio (SRR), fresh biomass weight (FBW), dry biomass weight (DBW), and water content (WC). An analysis of variance (ANOVA) revealed highly significant differences ( p < 0.01) among the genotypes, treatments (PEG25%, PEG30%) and genotypes × treatment interaction, for all traits. The broad-sense heritability (H 2 ) estimates were very high in both concentrations. They ranged from 89.4 to 98.9% under PEG25% and from 70.8 to 98.7% under PEG30%. Citr15314 (Afghanistan) was among the best performing genotypes under both concentrations for most of the germination traits. Two KASP markers for TaDreb-B1 and Fehw3 genes were used to screen all genotypes and to study the effect of these on drought tolerance at the germination stage. All genotypes with Fehw3 (only) showed a better performance for most traits under both concentrations compared to other genotypes having TaDreb-B1 or having both genes. To our knowledge, this work is the first report showing the effect of the two genes on germination traits under severe drought stress conditions.

The number of genes encoding β-oxidation enzymes in Cupriavidus necator H16 (synonym, Ralstonia eutropha H16) is high, but only the operons A0459-A0464 and A1526-A1531, each encoding four genes for β-oxidation enzymes, were expressed during growth with long-chain-length fatty acids (LCFAs). However, we observed that C. necator ΔA0459-A0464 ΔA1526-A1531 and C. necator H16 showed the same growth behavior during growth with decanoic acid and shorter FAs. The negative effect of the deletion of these two operons increased with an increasing chain length of the utilized FAs. Transcriptome sequencing (RNA-Seq) revealed the expression profiles of genes involved in the catabolism of medium-chain-length fatty acids (MCFAs) in C. necator H16. Operon A0459-A0464 was expressed only during growth with nonanoic acid, whereas operon A1526-A1531 was highly expressed during growth with octanoic and nonanoic acid. The gene clusters B1187-B1192 and B0751-B0759 showed a log2 fold change in expression of up to 4.29 and 4.02, respectively, during growth with octanoic acid and up to 8.82 and 5.50, respectively, with nonanoic acid compared to sodium gluconate-grown cells. Several acyl-CoA ligases catalyze the activation of MCFAs with coenzyme A (CoA), but fadD3 (A3288), involved in activation of LCFAs, was not detected. The expression profiles of C. necator strain ΔA0459-A0464 ΔA1526-A1531 showed that the growth with nonanoic acid resulted in the expression of further β-oxidation enzyme-encoding genes. Additional insights into the transport of FAs in C. necator H16 revealed the complexity and putative involvement of the DegV-like protein encoded by A0463 in the transport of odd-chain-length FAs and of siderophore biosynthesis in the transport mechanism. IMPORTANCE Although Cupriavidus necator H16 has been used in several studies to produce polyhydroxyalkanoates from various lipids, the fatty acid metabolism is poorly understood. The β-oxidation of long-chain-length FAs has been investigated, but the tremendous number of homologous genes encoding β-oxidation enzymes hides the potential for variances in the expressed genes for catabolism of shorter FAs. The catabolism of medium-chain-length FAs and connected pathways has not been investigated yet. As more sustainable substrates such as lipids and the production of fatty acids and fatty acid derivates become more critical with the dependency on fossil-based substances, understanding the complex metabolism in this highly diverse workhorse for biotechnology, C. necator, is inevitable. For further metabolic engineering and construction of production strains, we investigated the metabolism during growth on medium-chain-length FAs by RNA-Seq.

Tiny aquatic plants from the Lemnaceae family, commonly known as duckweeds, are often regarded as detrimental to the environment because of their ability to quickly populate and cover the surfaces of bodies of water. Due to their rapid vegetative propagation, duckweeds have one of the fastest growth rates among flowering plants and can accumulate large amounts of biomass in relatively short time periods. Due to the high yield of valuable biomass and ease of harvest, duckweeds can be used as feedstock for biofuels, animal feed, and other applications. Thanks to their efficient absorption of nitrogen- and phosphate-containing pollutants, duckweeds play an important role in the restorative ecology of water reservoirs. Moreover, compared to other species, duckweed species and ecotypes demonstrate exceptionally high adaptivity to a variety of environmental factors; indeed, duckweeds remove and convert many contaminants, such as nitrogen, into plant biomass. The global distribution of duckweeds and their tolerance of ammonia, heavy metals, other pollutants, and stresses are the major factors highlighting their potential for use in purifying agricultural, municipal, and some industrial wastewater. In summary, duckweeds are a powerful tool for bioremediation that can reduce anthropogenic pollution in aquatic ecosystems and prevent water eutrophication in a simple, inexpensive ecologically friendly way. Here we review the potential for using duckweeds in phytoremediation of several major water pollutants: mineral nitrogen and phosphorus, various organic chemicals, and heavy metals.

Genetic information is stored in very long DNA molecules, which are folded to form chromatin, a similarly long polymer fibre that is ultimately organised into chromosomes. The organisation of chromatin is fundamental to many cellular functions, from the expression of the genetic information to cell division. As a long polymer, chromatin is very flexible and may adopt a myriad of shapes. Globally, the polymer physics governing chromatin dynamics is very well understood. But chromatin is not uniform and regions of it, with chemical modifications and bound effectors, form domains and compartments through mechanisms not yet clear. Polymer models have been successfully used to investigate these mechanisms to explain cytological observations and build hypothesis for experimental validation. Many different approaches to conceptualise chromatin in polymer models can be envisioned and each reflects different aspects. Here, we compare recent approaches that aim at reproducing prominent features of interphase chromatin organisation: the compartmentalisation into eu- and heterochromatin compartments, the formation of a nucleolus, chromatin loops and the rosette and Rabl conformations of interphase chromosomes. We highlight commonalities and contradictions that point to a modulation of the mechanisms involved to fine degree. Consolidating models will require the inclusion of yet hidden or neglected parameters., Competing Interests: The authors declare no conflict of interest., (© 2023 The Authors.)

The Astragalus subgenus Hypoglottis Bunge, which consists of several sections, is one of the taxonomically most complicated groups in the genus. The Astragalus section Stereothrix Bunge belongs to this subgenus and is a significant element of the Irano-Turanian floristic region. A molecular phylogenetic analysis of this section and its closely related taxa using nuclear ribosomal DNA internal transcribed spacers (ITS) and external transcribed spacer (ETS) regions as well as plastid mat K sequences were conducted. Parsimony analyses and Bayesian phylogenetic inference revealed that the section is not monophyletic in its current form, as some taxa belonging to closely related sections such as Hypoglottidei DC. and the Malacothrix Bunge group within the sect. Stereothrix render it paraphyletic. Moreover, species groups belonging to sect. Stereothrix are placed in different clades within the phylogenetic tree of subgenus Hypoglottis , which indicates polyphyly, i.e., multiple independent origins of taxa placed in the sect. Stereothrix . Molecular dating of the group estimated an age of 3.62 (1.73-5.62) My for this assemblage with the major diversification events happening during the last 2 My. Many species groups separated only within the last 0.5 to 1 My. Based on morphological and molecular data, we discuss the phylogenetic relationships of the groups and synonymy of species. In addition, the included taxa of sect. Hypoglottidei are not monophyletic and include species belonging to sects. Hololeuce , Koelziana , Malacothrix , Onobrychoideae, and Ornithodpodium group within the sect. Stereothrix taxa. We conclude that only an analysis including all groups and nearly all species of the sections within the Hypoglottis clade can finally result in an new evolutionary-based system for these taxa.

The European Search Catalogue for Plant Genetic Resources (EURISCO) is a central entry point for information on crop plant germplasm accessions from institutions in Europe and beyond. In total, it provides data on more than two million accessions, making an important contribution to unlocking the vast genetic diversity that lies deposited in >400 germplasm collections in 43 countries. EURISCO serves as the reference system for the Plant Genetic Resources Strategy for Europe and represents a significant approach for documenting and making available the world's agrobiological diversity. EURISCO is well established as a resource in this field and forms the basis for a wide range of research projects. In this paper, we present current developments of EURISCO, which is accessible at http://eurisco.ecpgr.org., (© The Author(s) 2022. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Nitrogen is an essential nutrient that affects all aspects of the growth, development and metabolic responses of plants. Here we investigated the influence of the two major sources of inorganic nitrogen, nitrate and ammonium, on the toxicity caused by excess of Mn in great duckweed, Spirodela polyrhiza . The revealed alleviating effect of ammonium on Mn-mediated toxicity, was complemented by detailed molecular, biochemical and evolutionary characterization of the species ammonium transporters (AMTs). Four genes encoding AMTs in S. polyrhiza , were classified as SpAMT1;1 , SpAMT1;2 , SpAMT1;3 and SpAMT2 . Functional testing of the expressed proteins in yeast and Xenopus oocytes clearly demonstrated activity of SpAMT1;1 and SpAMT1;3 in transporting ammonium. Transcripts of all SpAMT genes were detected in duckweed fronds grown in cultivation medium, containing a physiological or 50-fold elevated concentration of Mn at the background of nitrogen or a mixture of nitrate and ammonium. Each gene demonstrated an individual expression pattern, revealed by RT-qPCR. Revealing the mitigating effect of ammonium uptake on manganese toxicity in aquatic duckweed S. polyrhiza , the study presents a comprehensive analysis of the transporters involved in the uptake of ammonium, shedding a new light on the interactions between the mechanisms of heavy metal toxicity and the regulation of the plant nitrogen metabolism.

Pyrenophora tritici-repentis (Died.) Drechs., the causal agent of tan spot, is one of the most serious biotic diseases affecting wheat worldwide ( Triticum aestivum L.). Studying the interaction between different fungicide mixtures and nitrogen (N) rates under tan spot outbreaks is of key importance for reducing aboveground biomass and grain yield losses. Taking this into account, our study took a mechanistic approach to estimating the combined effect of different fungicides and N fertilization schemes on the severity of tan spot, green leaf area index, SPAD index, aboveground biomass dynamics, and yield in a wheat crop affected at the reproductive stage. Our results indicated that reductions in green leaf area, healthy area duration (HAD), and the chlorophyll concentration (SPAD index) due to increases in the percentage of damage led to decreases in biomass production (-19.2%) and grain yield (-48.1%). Fungicides containing triazole + strobilurin + carboxamides (TSC) or triazole + strobilurin (TS) combined with high N doses showed the most efficient disease control. The positive physiological effects of TSC fungicides, such as extending the green leaf area, are probably responsible for the greater production of aboveground biomass (+29.3%), as well as the positive effects on grain yield (+15.8%) with respect to TS. Both fungicide treatments increased grains per spike, kernel weight, spikes m -2 , grains m -2 and grain yield. The increase in biomass in the TSC tended to cause slighter non-significant increases in grains per spike, 1000-kernel weight and grain yield compared with TS. The linear regression revealed positive associations among the extension of HAD and biomass (+5.88 g.m , and grain yield. The increase in biomass in the TSC tended to cause slighter non-significant increases in grains per spike, 1000-kernel weight and grain yield compared with TS. The linear regression revealed positive associations among the extension of HAD and biomass (+5.88 g.m -2 .HAD -1 .day -1 ), grain yield (+38 kg.ha.HAD -1 ), and grain number (100.7 grains m -1 ), and grain number (100.7 grains m 2 .HAD -1 ), explained by the interactions of high N doses and fungicides. Our study is the first report of the positive effect of TSC fungicides with high N doses on grain yield related-traits under tan spot infections in wheat.-1 ), explained by the interactions of high N doses and fungicides. Our study is the first report of the positive effect of TSC fungicides with high N doses on grain yield related-traits under tan spot infections in wheat.

The FAIR data principle as a commitment to support long-term research data management is widely accepted in the scientific community. However, although many established infrastructures provide comprehensive and long-term stable services and platforms, a large quantity of research data is still hidden. Currently, high-throughput plant genomics and phenomics technologies are producing research data in abundance, the storage of which is not covered by established core databases. This concerns the data volume, for example, time series of images or high-resolution hyperspectral data; the quality of data formatting and annotation, e.g., with regard to structure and annotation specifications of core databases; uncovered data domains; or organizational constraints prohibiting primary data storage outside institutional boundaries. To share these potentially dark data in a FAIR way and master these challenges the ELIXIR Germany/de.NBI service Plant Genomic and Phenomics Research Data Repository (PGP) implements an on-premise approach, which allows research data to be kept in place and wrapped in FAIR-aware software infrastructure. In this chapter, the e!DAL infrastructure software and the PGP repository are presented as best practice on how to easily setup FAIR-compliant and intuitive research data services., (© 2023. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.)

Fluorescence live-cell microscopy is important in cell biology to perform artifact-free investigations. To analyze the dynamics of chromatin and centromeres at different stages of the cell cycle in nuclei and chromosomes, we performed simultaneous EYFP-CENH3/H2B-DsRed and single H2B-YFP transformations in Arabidopsis wild-type and cohesin T-DNA mutants. All constructs were under the control of the strong CaMV 35S promoter. While a strong silencing of fluorescence expression occurred differently in leaf and root tissues in the double transformants, nearly all single-transformed wild-type and most mutant cells showed H2B-YFP fluorescence. It seems that for an efficient co-expression of two fluorescence proteins, endogenous promoters and terminators should be used., (© 2023 S. Karger AG, Basel.)

Fluorescence in situ hybridization (FISH) has been widely used to visualize target DNA sequences in fixed chromosome samples by denaturing the dsDNA to allow complementary probe hybridization, thus damaging the chromatin structure by harsh treatments. To overcome this limitation, a CRISPR/Cas9-based in situ labeling method was developed, termed CRISPR-FISH. This method is also known as RNA-guided endonuclease-in situ labeling (RGEN-ISL). Here we present different protocols for the application of CRISPR-FISH on acetic acid: ethanol or formaldehyde-fixed nuclei and chromosomes as well as tissue sections for labeling repetitive sequences in a range of plant species. In addition, methods on how immunostaining can be combined with CRISPR-FISH are provided., (© 2023. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.)

The crop species barley is a genetic model for the small grain temperate cereals. Thanks to the availability of whole genome sequence and the development of customizable endonucleases, site-directed genome modification has recently revolutionized genetic engineering. Several platforms have been established in plants, with the most flexible one offered by the clustered regularly interspaced short palindromic repeats (CRISPR) technology. In this protocol, commercially available synthetic guide RNAs (gRNAs), Cas enzymes, or custom-generated reagents are used for targeted mutagenesis in barley. The protocol has been successfully used with immature embryo explants to generate site-specific mutations in regenerants. As the double-strand break-inducing reagents are customizable and can be efficiently delivered, pre-assembled ribonucleoprotein (RNP) complexes allow efficient generation of genome-modified plants., (© 2023. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.)

Varietal differences within a species with agronomic importance are often based on minor changes in the genomic sequence. For example, fungus-resistant and fungus-susceptible wheat varieties may vary in only one amino acid. The situation is similar with the reporter genes Gfp and Yfp where two base pairs cause a shift in the emission spectrum from green to yellow. Methods of targeted double-strand break induction now allow this exchange precisely with the simultaneous transfer of the desired repair template. However, these changes rarely lead to a selective advantage that can be used in generating such mutant plants. The protocol presented here allows a corresponding allele replacement at the cellular level using ribonucleoprotein complexes in combination with an appropriate repair template. The efficiencies achieved are comparable to other methods with direct DNA transfer or integration of the corresponding building blocks in the host genome. They are in the range of 35 percent, considering one allele in a diploid organism as barley and using Cas9 RNP complexes., (© 2023. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.)

Highly pathogenic avian influenza viruses (HPAIV) have been responsible for causing several severe outbreaks across the world. To protect poultry farms and to prevent the possible spread of new influenza pandemics, vaccines that are both efficacious and low-cost are in high demand. We produced stable, large hemagglutinin H5 oligomers in planta by the specific interaction between S•Tag and S•Protein. H5 oligomers combined via S•Tag::S•Protein interaction in plant crude extracts induced strong humoral immune responses, strong neutralizing antibody responses, and resistance in chickens after challenge with a wild type HPAIV H5 virus strain. In all three parameters, plant crude extracts with H5 oligomers induced better responses than crude extracts containing trimers. The neutralizing antibodies induced by by two-dose and one dose immunization with an adjuvanted crude extract containing H5 oligomer protected vaccinated chickens from two lethal H5N1 virus strains with the efficiency of 92% and 100%, respectively. Following housing vaccinated chickens together with ten non-immunized chickens, only one of these chickens had detectable levels of the H5N1 virus. To facilitate the easy storage of a candidate vaccine, the H5 oligomer crude extracts were mixed with adjuvants and stored for 3.5 and 5.5 months at 4 °C, and chickens were immunized with these crude extracts. All these vaccinated chickens survived after a lethal H5N1 virus challenge. H5 oligomer crude extracts are comparable to commercial vaccines as they also induce strong virus-neutralizing immune responses following the administration of a single dose. The cost-effective production of plant crude extract vaccine candidates and the high stability after long-term storage will enable and encourage the further exploration of this technology for veterinary vaccine development., (© 2022. The Author(s).)

Camelina sativa is an oil crop with low input costs and resistance to abiotic and biotic stresses. The presence of glucosinolates, plant metabolites with adverse health effects, restricts the use of camelina for human and animal nutrition. Cas9 endonuclease-based targeted mutagenesis of the three homeologs of each of the glucosinolate transporters CsGTR1 and CsGTR2 caused a strong decrease in glucosinolate amounts, highlighting the power of this approach for inactivating multiple genes in a hexaploid crop. Mutagenesis of the three homeologs of each of the transcription factors CsMYB28 and CsMYB29 resulted in the complete loss of glucosinolates, representing the first glucosinolate-free Brassicaceae crop. The oil and protein contents and the fatty acid composition of the csgtr1csgtr2 and csmyb28csmyb29 mutant seeds were not affected. The decrease and elimination of glucosinolates improves the quality of the oil and press cake of camelina, which thus complies with international standards regulating glucosinolate levels for human consumption and animal feeding., (© 2022 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.)

Phytohormones are supposed to contribute to the establishment of mutualistic Arbuscular mycorrhiza (AM) symbioses. However, their role in the acclimation of micropropagated plantlet inoculated with AM is still unknown. To address this question, we performed a hormone profiling during the acclimation of Satureja khuzistanica plantlets inoculated with Rhizoglomus fasciculatum. The levels of indoleacetic acid (IAA), methyl indole acetic acid, cis-zeatin, cis zeatin ribose, jasmonate, jasmonoyl isoleucine, salicylic acid, abscisic acid (ABA) were analyzed. Further, the relative gene expression of AOS (Allene oxide synthase) as a key enzyme of jasmonate biosynthesis, in either inoculated or non-inoculated micropropagated plantlets was evaluated during acclimation period. The concentrations of IAA and cis-zeatin increased in the plantlets inoculated by AM whereas the concentration of ABA decreased upon 60 days acclimation in the whole shoot of plantlets of S. khuzistanica. The relative expression of AOS gene resulted in an increase of isoleucine jasmonate, the bioactive form of jasmonate. Based on our results, IAA and cis-zeatin probably contribute to maintaining growth, and AM reduces transition stress by modifying ABA and jasmonate concentrations., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2022 Elsevier GmbH. All rights reserved.)

Enantioselective transamination of amino acids is a great challenge in biotechnology as suitable enzymes with wide substrate spectrum are rare. Here, we present a new transaminase from Variovorax boronicumulans (VboTA, Variovorax boronicumulans ω-transaminase) which is specific for β-amino acids. The amino acid sequence of VboTA is similar to an ω-transaminase from Variovorax paradoxus , for which a crystal-structure is available. This similarity is allowing us to classify VboTA as a fold type 1 ω-transaminase (ω-TA). Although both enzymes have a high sequence similarity (86% identities, 92% positives), there are differences in the active center, which allow VboTA to accept a broader substrate spectrum. Both enzymes have also a different temperature stability and temperature optimum. VboTA deaminates the D-form of aromatic β-amino acids, such as β-homophenylalanine and β-phenylalanine as well as aliphatic β-amino acids, such as β-homoalanine and β-leucine. The optimal reaction conditions turned out to be 32 °C and pH 9. Kinetic resolution lead to high enantiomeric excess of 86.6% to >99.9%, depending on the amino donor/acceptor pair. In contrast to many other ω-TAs, VboTA has a broad substrate spectrum and uses both aromatic or aliphatic amino acids. With γ-amino acids as substrates, VboTA showed no activity at all., Competing Interests: The authors declare no competing interests., (© 2023 The Authors.)

Background: Genebanks worldwide are transforming into biodigital resource centers, providing access not only to the plant material itself but also to its phenotypic and genotypic information. Adding information for relevant traits will help boost plant genetic resources' usage in breeding and research. Resistance traits are vital for adapting our agricultural systems to future challenges., Findings: Here we provide phenotypic data for the resistance against Blumeria graminis f. sp. tritici, the causal agent of wheat powdery mildew-a substantial risk to our agricultural production. Using a modern high-throughput phenotyping system, we infected and photographed a total of 113,638 wheat leaves of 7,320 winter wheat (Triticum aestivum L.) plant genetic resources of the German Federal ex situ Genebank for Agricultural and Horticultural Crops and 154 commercial genotypes. We quantified the resistance reaction captured by images and provide them here, along with the raw images., Conclusion: This massive amount of phenotypic data, combined with already published genotypic data, also provides a valuable and unique training dataset for the development of novel genotype-based predictions as well as mapping methods., (© The Author(s) 2023. Published by Oxford University Press GigaScience.)

Background: The sequencing of whole genomes is becoming increasingly affordable. In this context, large-scale sequencing projects are generating ever larger datasets of species-specific genomic diversity. As a consequence, more and more genomic data need to be made easily accessible and analyzable to the scientific community., Findings: We present DivBrowse, a web application for interactive visualization and exploratory analysis of genomic diversity data stored in Variant Call Format (VCF) files of any size. By seamlessly combining BLAST as an entry point together with interactive data analysis features such as principal component analysis in one graphical user interface, DivBrowse provides a novel and unique set of exploratory data analysis capabilities for genomic biodiversity datasets. The capability to integrate DivBrowse into existing web applications supports interoperability between different web applications. Built-in interactive computation of principal component analysis allows users to perform ad hoc analysis of the population structure based on specific genetic elements such as genes and exons. Data interoperability is supported by the ability to export genomic diversity data in VCF and General Feature Format 3 files., Conclusion: DivBrowse offers a novel approach for interactive visualization and analysis of genomic diversity data and optionally also gene annotation data by including features like interactive calculation of variant frequencies and principal component analysis. The use of established standard file formats for data input supports interoperability and seamless deployment of application instances based on the data output of established bioinformatics pipelines., (© The Author(s) 2023. Published by Oxford University Press GigaScience.)

Plant genetic resources (PGR) stored at genebanks are humanity's crop diversity savings for the future. Information on PGR contrasted with modern cultivars is key to select PGR parents for pre-breeding. Genotyping-by-sequencing was performed for 7,745 winter wheat PGR samples from the German Federal ex situ genebank at IPK Gatersleben and for 325 modern cultivars. Whole-genome shotgun sequencing was carried out for 446 diverse PGR samples and 322 modern cultivars and lines. In 19 field trials, 7,683 PGR and 232 elite cultivars were characterized for resistance to yellow rust - one of the major threats to wheat worldwide. Yield breeding values of 707 PGR were estimated using hybrid crosses with 36 cultivars - an approach that reduces the lack of agronomic adaptation of PGR and provides better estimates of their contribution to yield breeding. Cross-validations support the interoperability between genomic and phenotypic data. The here presented data are a stepping stone to unlock the functional variation of PGR for European pre-breeding and are the basis for future breeding and research activities., (© 2022. The Author(s).)

Common bunt (caused by Tilletia caries and T. Foetida ) is a major wheat disease. It occurs frequently in the USA and Turkey and damages grain yield and quality. Seed treatment with fungicides is an effective method to control this disease. However, using fungicides in organic and low-income fields is forbidden, and planting resistant cultivars are preferred. Due to the highly effective use of fungicides, little effort has been put into breeding resistant genotypes. In addition, the genetic diversity for this trait is low in modern wheat germplasm. Synthetic wheat genotypes were reported as an effective source to increase the diversity in wheat germplasm. Therefore, a set of 25 synthetics that are resistant to the Turkish common bunt race were evaluated against the Nebraska common bunt race. Four genotypes were found to be very resistant to Nebraska's common bunt race. Using differential lines, four isolines carrying genes, Bt10 , Bt11 , Bt12 , and Btp , were found to provide resistance against both Turkish and Nebraska common bunt races. Genotypes carrying any or all of these four genes could be used as a source of resistance in both countries. No correlation was found between common bunt resistance and some agronomic traits, which suggests that common bunt resistance is an independent trait.

High seed quality is key to agricultural production, which is increasingly affected by climate change. We studied the effects of drought and elevated temperature during seed production on key seed quality traits of two genotypes of malting barley ( Hordeum sativum L.). Plants of a "Hana-type" landrace (B1) were taller, flowered earlier and produced heavier, larger and more vigorous seeds that resisted ageing longer compared to a semi-dwarf breeding line (B2). Accordingly, a NAC domain-containing transcription factor (TF) associated with rapid response to environmental stimuli, and the TF ABI5, a key regulator of seed dormancy and vigour, were more abundant in B1 seeds. Drought significantly reduced seed yield in both genotypes, and elevated temperature reduced seed size. Genotype B2 showed partial thermodormancy that was alleviated by drought and elevated temperature. Metabolite profiling revealed clear differences between the embryos of B1 and B2. Drought, but not elevated temperature, affected the metabolism of amino acids, organic acids, osmolytes and nitrogen assimilation, in the seeds of both genotypes. Our study may support future breeding efforts to produce new lodging and drought resistant malting barleys without trade-offs that can occur in semi-dwarf varieties such as lower stress resistance and higher dormancy., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Nagel, Arc, Rajjou, Cueff, Bailly, Clément, Sanchez-Vicente, Bailly, Seal, Roach, Rolletschek, Lorenzo, Börner and Kranner.)

The generation of haploid plants accelerates the crop breeding process. One of the haploidization strategies is based on the genetic manipulation of endogenous centromere-specific histone 3 (CENH3). To extend the haploidization toolbox, we tested whether targeted in vivo degradation of CENH3 protein can be harnessed to generate haploids in Arabidopsis thaliana. We show that a recombinant anti-GFP nanobody fused to either heterologous F-box (NSlmb) or SPOP/BTB ligase proteins can recognize maternally derived enhanced yellow fluorescent protein (EYFP)-tagged CENH3 in planta and make it accessible for the ubiquitin-proteasome pathway. Outcrossing of the genomic CENH3-EYFP-complemented cenh3.1 mother with plants expressing the GFP-nanobody-targeted E3 ubiquitin ligase resulted in a haploid frequency of up to 7.6% in pooled F1 seeds. EYFP-CENH3 degradation occurred independently in embryo and endosperm cells. In reciprocal crosses, no haploid induction occurred. We propose that the uniparental degradation of EYFP-fused genomic CENH3 during early embryogenesis leads to a decrease in its level at centromeres and subsequently weakens the centromeres. The male-derived wild type CENH3 containing centromere outcompetes the CENH3-EYFP depleted centromere. Consequently, maternal chromosomes undergo elimination, resulting in haploids., (© The Author(s) 2022. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email: journals.permissions@oup.com.)

Background: As complete and accurate genome sequences are becoming easier to obtain, more researchers wish to get one or more of them to support their research endeavors. Reliable and well-documented sequence assembly workflows find use in reference or pangenome projects., Results: We describe modifications to the TRITEX genome assembly workflow motivated by the rise of fast and easy long-read contig assembly of inbred plant genomes and the routine deployment of the toolchains in pangenome projects. New features include the use as surrogates of or complements to dense genetic maps and the introduction of user-editable tables to make the curation of contig placements easier and more intuitive., Conclusion: Even maximally contiguous sequence assemblies of the telomere-to-telomere sort, and to a yet greater extent, the fragmented kind require validation, correction, and comparison to reference standards. As pangenomics is burgeoning, these tasks are bound to become more widespread and TRITEX is one tool to get them done. This technical guide is supported by a step-by-step computational tutorial accessible under https://tritexassembly.bitbucket.io/ . The TRITEX source code is hosted under this URL: https://bitbucket.org/tritexassembly ., (© 2022. The Author(s).)

Nucleus, chromatin, and chromosome organization studies heavily rely on fluorescence microscopy imaging to elucidate the distribution and abundance of structural and regulatory components. Three-dimensional (3D) image stacks are a source of quantitative data on signal intensity level and distribution and on the type and shape of distribution patterns in space. Their analysis can lead to novel insights that are otherwise missed in qualitative-only analyses. Quantitative image analysis requires specific software and workflows for image rendering, processing, segmentation, setting measurement points and reference frames and exporting target data before further numerical processing and plotting. These tasks often call for the development of customized computational scripts and require an expertise that is not broadly available to the community of experimental biologists. Yet, the increasing accessibility of high- and super-resolution imaging methods fuels the demand for user-friendly image analysis workflows. Here, we provide a compendium of strategies developed by participants of a training school from the COST action INDEPTH to analyze the spatial distribution of nuclear and chromosomal signals from 3D image stacks, acquired by diffraction-limited confocal microscopy and super-resolution microscopy methods (SIM and STED). While the examples make use of one specific commercial software package, the workflows can easily be adapted to concurrent commercial and open-source software. The aim is to encourage biologists lacking custom-script-based expertise to venture into quantitative image analysis and to better exploit the discovery potential of their images. Abbreviations: 3D FISH: three-dimensional fluorescence in situ hybridization; 3D: three-dimensional; ASY1: ASYNAPTIC 1; CC: chromocenters; CO: Crossover; DAPI: 4',6-diamidino-2-phenylindole; DMC1: DNA MEIOTIC RECOMBINASE 1; DSB: Double-Strand Break; FISH: fluorescence in situ hybridization; GFP: GREEN FLUORESCENT PROTEIN; HEI10: HUMAN ENHANCER OF INVASION 10; NCO: Non-Crossover; NE: Nuclear Envelope; Oligo-FISH: oligonucleotide fluorescence in situ hybridization; RNPII: RNA Polymerase II; SC: Synaptonemal Complex; SIM: structured illumination microscopy; ZMM (ZIP: MSH4: MSH5 and MER3 proteins); ZYP1: ZIPPER-LIKE PROTEIN 1.

Key Message: Genomic prediction of genebank accessions benefits from the consideration of additive-by-additive epistasis and subpopulation-specific marker effects. Wheat (Triticum aestivum L.) and other species of the Triticum genus are well represented in genebank collections worldwide. The substantial genetic diversity harbored by more than 850,000 accessions can be explored for their potential use in modern plant breeding. Characterization of these large number of accessions is constrained by the required resources, and this fact limits their use so far. This limitation might be overcome by engaging genomic prediction. The present study compared ten different genomic prediction approaches to the prediction of four traits, namely flowering time, plant height, thousand grain weight, and yellow rust resistance, in a diverse set of 7745 accession samples from Germany's Federal ex situ genebank at the Leibniz Institute of Plant Genetics and Crop Plant Research in Gatersleben. Approaches were evaluated based on prediction ability and robustness to the confounding influence of strong population structure. The authors propose the wide application of extended genomic best linear unbiased prediction due to the observed benefit of incorporating additive-by-additive epistasis. General and subpopulation-specific additive ridge regression best linear unbiased prediction, which accounts for subpopulation-specific marker-effects, was shown to be a good option if contrasting clusters are encountered in the analyzed collection. The presented findings reaffirm that the trait's genetic architecture as well as the composition and relatedness of the training set and test set are major driving factors for the accuracy of genomic prediction., (© 2022. The Author(s).)

Introduction: Legume crops are an important source of protein and oil for human health and in fixing atmospheric N 2 for soil enrichment. With an objective to accelerate much-needed genetic analyses and breeding applications, draft genome assemblies were generated in several legume crops; many of them are not high quality because they are mainly based on short reads. However, the superior quality of genome assembly is crucial for a detailed understanding of genomic architecture, genome evolution, and crop improvement., Objectives: Present study was undertaken with an objective of developing improved chromosome-length genome assemblies in six different legumes followed by their systematic investigation to unravel different aspects of genome organization and legume evolution., Methods: We employed in situ Hi-C data to improve the existing draft genomes and performed different evolutionary and comparative analyses using improved genome assemblies., Results: We have developed chromosome-length genome assemblies in chickpea, pigeonpea, soybean, subterranean clover, and two wild progenitor species of cultivated groundnut (A. duranensis and A. ipaensis). A comprehensive comparative analysis of these genome assemblies offered improved insights into various evolutionary events that shaped the present-day legume species. We highlighted the expansion of gene families contributing to unique traits such as nodulation in legumes, gravitropism in groundnut, and oil biosynthesis in oilseed legume crops such as groundnut and soybean. As examples, we have demonstrated the utility of improved genome assemblies for enhancing the resolution of "QTL-hotspot" identification for drought tolerance in chickpea and marker-trait associations for agronomic traits in pigeonpea through genome-wide association study. Genomic resources developed in this study are publicly available through an online repository, 'Legumepedia'., Conclusion: This study reports chromosome-length genome assemblies of six legume species and demonstrates the utility of these assemblies in crop improvement. The genomic resources developed here will have significant role in accelerating genetic improvement applications of legume crops., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2021. Production and hosting by Elsevier B.V.)

The B chromosome (B) is a dispensable component of the genome in many species. To evaluate the impact of Bs on the transcriptome of the standard A chromosomes (A), comparative RNA-seq analyses of rye and wheat anthers with and without additional rye Bs were conducted. In both species, 5-6% of the A-derived transcripts across the entire genomes were differentially expressed in the presence of  2Bs. The GO term enrichment analysis revealed that Bs influence A chromosome encoded processes like "gene silencing"; "DNA methylation or demethylation"; "chromatin silencing"; "negative regulation of gene expression, epigenetic"; "post-embryonic development"; and "chromosome organization." 244 B chromosome responsive A-located genes in + 2B rye and + B wheat shared the same biological function. Positively correlated with the number of Bs, 939 and 1391 B-specific transcripts were identified in + 2B and + 4B wheat samples, respectively. 85% of B-transcripts in + 2B were also found in + 4B transcriptomes. 297 B-specific transcripts were identified in + 2B rye, and 27% were common to the B-derived transcripts identified in + B wheat. Bs encode mobile elements and housekeeping genes, but most B-transcripts were without detectable similarity to known genes. Some of these genes are involved in cell division-related functions like Nuf2 and might indicate their importance in maintaining Bs. The transcriptome analysis provides new insights into the complex interrelationship between standard A chromosomes and supernumerary B chromosomes., (© 2022. The Author(s).)

Studying the probability distribution of replication initiation along a chromosome is a huge challenge. Drosophila polytene chromosomes in combination with super-resolution microscopy provide a unique opportunity for analyzing the probabilistic nature of replication initiation at the ultrastructural level. Here, we developed a method for synchronizing S-phase induction among salivary gland cells. An analysis of the replication label distribution in the first minutes of S phase and in the following hours after the induction revealed the dynamics of replication initiation. Spatial super-resolution structured illumination microscopy allowed identifying multiple discrete replication signals and to investigate the behavior of replication signals in the first minutes of the S phase at the ultrastructural level. We identified replication initiation zones where initiation occurs stochastically. These zones differ significantly in the probability of replication initiation per time unit. There are zones in which initiation occurs on most strands of the polytene chromosome in a few minutes. In other zones, the initiation on all strands takes several hours. Compact bands are free of replication initiation events, and the replication runs from outer edges to the middle, where band shapes may alter., (© 2022. The Author(s).)

Staphylococcus saccharolyticus, a coagulase-negative staphylococcal species, has some unusual characteristics for human-associated staphylococci, such as slow growth and its preference for anoxic culture conditions. This species is a relatively abundant member of the human skin microbiota, but its microbiological properties, as well as the pathogenic potential, have scarcely been investigated so far, despite being occasionally isolated from different types of infections including orthopedic implant-associated infections. Here, we investigated the growth and biofilm properties of clinical isolates of S. saccharolyticus and determined host cell responses. Growth assessments in anoxic and oxic conditions revealed strain-dependent outcomes, as some strains can also grow aerobically. All tested strains of S. saccharolyticus were able to form biofilm in a microtiter plate assay. Strain-dependent differences were determined by optical coherence tomography, revealing that medium supplementation with glucose and sodium chloride enhanced biofilm formation. Visualization of the biofilm by confocal laser scanning microscopy revealed the role of extracellular DNA in the biofilm structure. In addition to attached biofilms, S. saccharolyticus also formed bacterial aggregates at an early stage of growth. Transcriptome analysis of biofilm-grown versus planktonic cells revealed a set of upregulated genes in biofilm-embedded cells, including factors involved in adhesion, colonization, and competition such as epidermin, type I toxin-antitoxin system, and phenol-soluble modulins (beta and epsilon). To investigate consequences for the host after encountering S. saccharolyticus , cytokine profiling and host cell viability were assessed by infection experiments with differentiated THP-1 cells. The microorganism strongly triggered the secretion of the tested pro-inflammatory cyto- and chemokines IL-6, IL-8, and TNF-alpha, determined at 24 h post-infection. S. saccharolyticus was less cytotoxic than Staphylococcus aureus . Taken together, the results indicate that S. saccharolyticus has substantial pathogenic potential. Thus, it can be a potential cause of orthopedic implant-associated infections and other types of deep-seated infections., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Afshar, Møllebjerg, Minero, Hollensteiner, Poehlein, Himmelbach, Lange, Meyer and Brüggemann.)

Grain legumes were domesticated in parallel with cereals in several regions of the world and formed the economic basis of early farming cultures. Since then, legumes have played a vital role in human and animal diets and in fostering agrobiodiversity. Increasing grain legume cultivation will be crucial to safeguard nutritional security and the resilience of agricultural ecosystems across the globe. A better understanding of the molecular underpinnings of domestication and crop evolution of grain legumes may be translated into practical approaches in modern breeding programs to stabilize yield, which is threatened by evolving pathogens and changing climates. During recent decades, domestication research in all crops has greatly benefited from the fast progress in genomic technologies. Yet still, many questions surrounding the domestication and diversification of legumes remain unanswered. In this review, we assess the potential of genomic approaches in grain legume research. We describe the centers of origin and the crucial domestication traits of grain legumes. In addition, we survey the effect of domestication on both above-ground and below-ground traits that have economic importance. Finally, we discuss open questions in grain legume domestication and diversification and outline how to bridge the gap between the preservation of historic crop diversity and their utilization in modern plant breeding., (© The Author(s) 2022. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists.)

Spikelet abortion is a phenomenon where apical spikelet primordia on an immature spike abort. Regardless of the row-type, both apical and basal spikelet abortion occurs, and their extent decides the number of grain-bearing spikelets retained on the spike-thus, affecting the yield potential of barley. Reducing spikelet abortion, therefore, represents an opportunity to increase barley yields. Here, we investigated the variation for apical spikelet abortion along with 16 major spike, shoot, and grain traits in a panel of 417 six-rowed spring barleys. Our analyses showed a significantly large genotypic variation resulting in high heritability estimates for all the traits. Spikelet abortion (SA) varies from 13 to 51% depending on the genotype and its geographical origin. Among the seven spike traits, SA was negatively correlated with final spikelet number, spike length and density, while positively with awn length. This positive correlation suggests a plausible role of the rapidly growing awns during the spikelet abortion process, especially after Waddington stage 5. In addition, SA also showed a moderate positive correlation with grain length, grain area and thousand-grain weight. Our hierarchical clustering revealed distinct genetic underpinning of grain traits from the spike and shoot traits. Trait associations showed a geographical bias whereby European accessions displayed higher SA and grain and shoot trait values, whereas the trend was opposite for the Asian accessions. To study the observed phenotypic variation of SA explained by 16 other individual traits, we applied linear, quadratic, and generalized additive regression models (GAM). Our analyses of SA revealed that the GAM generally performed superior in comparison to the other models. The genetic interactions among traits suggest novel breeding targets and easy-to-phenotype "proxy-traits" for high throughput on-field selection for grain yield, especially in early generations of barley breeding programs., Competing Interests: Author QHM is employed by BASF Agricultural Solutions GmbH. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Kamal, Muqaddasi and Schnurbusch.)

Asexual reproduction results in offspring that are genetically identical to the mother. Among apomictic plants (reproducing asexually through seeds) many require paternal genetic contribution for proper endosperm development (pseudogamous endosperm). We examined phenotypic diversity in seed traits using a diverse panel of sexual and apomictic accessions from the genus Boechera . While genetic uniformity resulting from asexual reproduction is expected to reduce phenotypic diversity in seeds produced by apomictic individuals, pseudogamous endosperm, variable endosperm ploidy, and the deviations from 2:1 maternal:paternal genome ratio in endosperm can all contribute to increased phenotypic diversity among apomictic offspring. We characterized seed size variation in 64 diploid sexual and apomictic (diploid and triploid) Boechera lineages. In order to find out whether individual seed size was related to endosperm ploidy we performed individual seed measurements (projected area and mass) using the phenoSeeder robot system and flow cytometric seed screen. In order to test whether individual seed size had an effect on resulting fitness we performed a controlled growth experiment and recorded seedling life history traits (germination success, germination timing, and root growth rate). Seeds with triploid embryos were 33% larger than those with diploid embryos, but no average size difference was found between sexual and apomictic groups. We identified a maternal effect whereby chloroplast lineage 2 had 30% larger seeds than lineage 3, despite having broad and mostly overlapping geographic ranges. Apomictic seeds were not more uniform in size than sexual seeds, despite genetic uniformity of the maternal gametophyte in the former. Among specific embryo/endosperm ploidy combinations, seeds with tetraploid (automomous) endosperm were on average smaller, and the proportion of such seeds was highest in apomicts. Larger seeds germinated more quickly than small seeds, and lead to higher rates of root growth in young seedlings. Seed mass is under balancing selection in Boechera , and it is an important predictor of several traits, including germination probability and timing, root growth rates, and developmental abnormalities in apomictic accessions., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Paczesniak, Pellino, Goertzen, Guenter, Jahnke, Fischbach, Lovell and Sharbel.)

AMMONIUM TRANSPORTER/METHYLAMMONIUM PERMEASE/RHESUS (AMT) family members transport ammonium across membranes in all life domains. Plant AMTs can be categorized into AMT1 and AMT2 subfamilies. Functional studies of AMTs, particularly AMT1-type, have been conducted using model plants but little is known about the function of AMTs from crops. Sugarcane ( Saccharum spp.) is a major bioenergy crop that requires heavy nitrogen fertilization but depends on a low carbon-footprint for competitive sustainability. Here, we identified and functionally characterized sugarcane ScAMT2;1 by complementing ammonium uptake-defective mutants of Saccharomyces cerevisiae and Arabidopsis thaliana . Reporter gene driven by the ScAMT2;1 promoter in A. thaliana revealed preferential expression in the shoot vasculature and root endodermis/pericycle according to nitrogen availability and source. Arabidopsis quadruple mutant plants expressing ScAMT2;1 driven by the CaMV35S promoter or by a sugarcane endogenous promoter produced significantly more biomass than mutant plants when grown in NH 4 and showed more + N-ammonium uptake by roots and nitrogen translocation to shoots. In 15 N-ammonium uptake by roots and nitrogen translocation to shoots. In A. thaliana of 90.17 µM and V m of 338.99 µmoles h max of 338.99 µmoles h -1 root DW. Altogether, our results suggest that ScAMT2;1 is a functional high-affinity ammonium transporter that might contribute to ammonium uptake and presumably to root-to-shoot translocation under high NH -1 root DW. Altogether, our results suggest that ScAMT2;1 is a functional high-affinity ammonium transporter that might contribute to ammonium uptake and presumably to root-to-shoot translocation under high NH 4 + conditions., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Koltun, Maniero, Vitti, de Setta, Giehl, Lima and Figueira.)

Brassica rapa ( B. rapa ) and its subspecies contain many bioactive metabolites that are important for plant defense and human health. This study aimed at investigating the metabolite composition and variation among a large collection of B. rapa genotypes, including subspecies and their accessions. Metabolite profiling of leaves of 102 B. rapa genotypes was performed using ultra-performance liquid chromatography coupled with a photodiode array detector and quadrupole time-of-flight mass spectrometry (UPLC-PDA-QTOF-MS/MS). In total, 346 metabolites belonging to different chemical classes were tentatively identified; 36 out of them were assigned with high confidence using authentic standards and 184 were those reported in B. rapa leaves for the first time. The accumulation and variation of metabolites among genotypes were characterized and compared to their phylogenetic distance. We found 47 metabolites, mostly representing anthocyanins, flavonols, and hydroxycinnamic acid derivatives that displayed a significant correlation to the phylogenetic relatedness and determined four major phylometabolic branches; 1) Chinese cabbage, 2) yellow sarson and rapid cycling, 3) the mizuna-komatsuna-turnip-caitai; and 4) a mixed cluster. These metabolites denote the selective pressure on the metabolic network during B. rapa breeding. We present a unique study that combines metabolite profiling data with phylogenetic analysis in a large collection of B. rapa subspecies. We showed how selective breeding utilizes the biochemical potential of wild B. rapa leading to highly diverse metabolic phenotypes. Our work provides the basis for further studies on B. rapa metabolism and nutritional traits improvement., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Zheng, Szymański, Shahaf, Malitsky, Meir, Wang, Aharoni and Rogachev.)

Histone chaperones and chromatin remodelers control nucleosome dynamics, which are essential for transcription, replication, and DNA repair. The histone chaperone Anti-Silencing Factor 1 (ASF1) plays a central role in facilitating CAF-1-mediated replication-dependent H3.1 deposition and HIRA-mediated replication-independent H3.3 deposition in yeast and metazoans. Whether ASF1 function is evolutionarily conserved in plants is unknown. Here, we show that Arabidopsis ASF1 proteins display a preference for the HIRA complex. Simultaneous mutation of both Arabidopsis ASF1 genes caused a decrease in chromatin density and ectopic H3.1 occupancy at loci typically enriched with H3.3. Genetic, transcriptomic, and proteomic data indicate that ASF1 proteins strongly prefers the HIRA complex over CAF-1. asf1 mutants also displayed an increase in spurious Pol II transcriptional initiation and showed defects in the maintenance of gene body CG DNA methylation and in the distribution of histone modifications. Furthermore, ectopic targeting of ASF1 caused excessive histone deposition, less accessible chromatin, and gene silencing. These findings reveal the importance of ASF1-mediated histone deposition for proper epigenetic regulation of the genome., (© 2022. The Author(s).)

The predominantly vegetative propagating duckweeds are of growing commercial interest. Since clonal accessions within a respective species can vary considerably with respect to their physiological as well as biochemical traits, it is critical to be able to track the clones of species of interest after their characterization. Here, we compared the efficacy of five different genotyping methods for Spirodela polyrhiza , a species with very low intraspecific sequence variations, including polymorphic NB-ARC-related loci, tubulin-gene-based polymorphism (TBP), simple sequence repeat variations (SSR), multiplexed ISSR genotyping by sequencing (MIG-seq), and low-coverage, reduced-representation genome sequencing (GBS). Four of the five approaches could distinguish 20 to 22 genotypes out of the 23 investigated clones, while TBP resolved just seven genotypes. The choice for a particular method for intraspecific genotyping can depend on the research question and the project budget, while the combination of orthogonal methods may increase the confidence and resolution for the results obtained.

Apple (Malus × domestica Borkh.) cropping behavior, if not regulated, is often manifested by high yields of small-sized fruit in so called ON-years, which are usually followed by strongly reduced crop loads in OFF-years. Such cropping pattern is defined as biennial bearing and causes significant losses in apple production. The growth of apple fruit overlaps with the formation of flower buds, which remain dormant until the following spring. Earlier works proposed that some fruit-derived mobile compounds, as e.g., phytohormones, could suppress flower bud formation that thereby leads to biennial bearing. We addressed this hypothesis by analyzing 39 phytohormones in apple seeds, fruit flesh and by measuring phytohormone export from the fruits of the biennial bearing cultivar 'Fuji' and of the regular bearing cultivar 'Gala'. Moreover, we analyzed the same compounds in bourse buds from fruiting (ON-trees) and non-fruiting (OFF-trees) spurs of both apple cultivars over the period of flower bud formation. Our results showed that apple fruit exported at least 14 phytohormones including indole-3-acetic acid and gibberellin A3; however, their influence on flower bud formation was inconclusive. A gibberellin-like compound, which was detected exclusively in bourse buds, was significantly more abundant in bourse buds from ON-trees compared with OFF-trees. Cultivar differences were marked by the accumulation of trans-zeatin-O-glucoside in bourse buds of 'Gala' ON-trees, whereas the levels of this compound in 'Gala' OFF were significantly lower and comparable to those in 'Fuji' ON- and OFF-trees. Particular phytohormones including five cytokinin forms as well as abscisic acid and its degradation products had higher levels in bourse buds from OFF-trees compared with ON-trees and were therefore proposed as potential promotors of flower bud initiation. The work discusses regulatory roles of phytohormones in flower bud formation in apple based on the novel and to date most comprehensive phytohormone profiles of apple fruit and buds., (© The Author(s) 2022. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

Plant biotrophic pathogens employ secreted molecules, called effectors, to suppress the host immune system and redirect the host's metabolism and development in their favour. Putative effectors of the gall-inducing maize pathogenic fungus Ustilago maydis were analysed for their ability to induce auxin signalling in plants. Using genetic, biochemical, cell-biological, and bioinformatic approaches we functionally elucidate a set of five, genetically linked effectors, called Topless (TPL) interacting protein (Tips) effectors that induce auxin signalling. We show that Tips induce auxin signalling by interfering with central corepressors of the TPL family. CRISPR-Cas9 mutants and deletion strain analysis indicate that the auxin signalling inducing subcluster effectors plays a redundant role in virulence. Although none of the Tips seem to have a conserved interaction motif, four of them bind solely to the N-terminal TPL domain and, for Tip1 and Tip4, we demonstrate direct competition with auxin/indole-3-acetic acid transcriptional repressors for their binding to TPL class of corepressors. Our findings reveal that TPL proteins, key regulators of growth-defence antagonism, are a major target of the U. maydis effectome., (© 2022 The Authors. New Phytologist © 2022 New Phytologist Foundation.)

Breeding has increasingly altered the genetics of crop plants since the domestication of their wild progenitors. It is postulated that the genetic diversity of elite wheat breeding pools is too narrow to cope with future challenges. In contrast, plant genetic resources (PGRs) of wheat stored in genebanks are valuable sources of unexploited genetic diversity. Therefore, to ensure breeding progress in the future, it is of prime importance to identify the useful allelic diversity available in PGRs and to transfer it into elite breeding pools. Here, a diverse collection consisting of modern winter wheat cultivars and genebank accessions was investigated based on reduced-representation genomic sequencing and an iSelect single nucleotide polymorphism (SNP) chip array. Analyses of these datasets provided detailed insights into population structure, levels of genetic diversity, sources of new allelic diversity, and genomic regions affected by breeding activities. We identified 57 regions representing genomic signatures of selection and 827 regions representing private alleles associated exclusively with genebank accessions. The presence of known functional wheat genes, quantitative trait loci, and large chromosomal modifications, i.e., introgressions from wheat wild relatives, provided initial evidence for putative traits associated within these identified regions. These findings were supported by the results of ontology enrichment analyses. The results reported here will stimulate further research and promote breeding in the future by allowing for the targeted introduction of novel allelic diversity into elite wheat breeding pools., (© 2022 Julius Kuehn-Institute and The Authors. The Plant Journal published by Society for Experimental Biology and John Wiley & Sons Ltd.)

Root nodules of legume plants are primarily inhabited by rhizobial nitrogen-fixing bacteria. Here, we propose two new Rhizobiales species isolated from root nodules of common sainfoin (Onobrychis viciifolia), as shown by core-gene phylogeny, overall genome relatedness indices, and pan-genome analysis. Mesorhizobium onobrychidis sp. nov. actively induces nodules and achieves atmospheric nitrogen and carbon dioxide fixation. This species appears to be depleted in motility genes and is enriched in genes for direct effects on plant growth performance. Its genome reveals functional and plant growth-promoting signatures, like a large unique chromosomal genomic island with high density of symbiotic genetic traits. Onobrychidicola muellerharveyae gen. nov. sp. nov. is described as a type species of the new genus Onobrychidicola in Rhizobiaceae . This species comprises unique genetic features and plant growth-promoting traits (PGPTs), which strongly indicate its function in biotic stress reduction and motility. We applied a newly developed bioinformatics approach for in silico prediction of PGPTs (PGPT-Pred), which supports the different lifestyles of the two new species and the plant growth-promoting performance of M. onobrychidis in the greenhouse trial. IMPORTANCE The intensive use of chemical fertilizers has a variety of negative effects on the environment. Increased utilization of biological nitrogen fixation (BNF) is one way to mitigate those negative impacts. In order to optimize BNF, suitable candidates for different legume species are required. Despite intensive search for new rhizobial bacteria associated with legumes, no new rhizobia have recently been identified from sainfoin (Onobrychis viciifolia). Here, we report on the discovery of two new rhizobial species associated with sainfoin, which are of high importance for the host and may help to increase sustainability in agricultural practices. We employed the combination of in silico prediction and in planta experiments, which is an effective way to detect promising plant growth-promoting bacteria.

Genetic diversity in wheat has been depleted due to domestication and modern breeding. Wild relatives are a valuable source for improving drought tolerance in domesticated wheat. A QTL region on chromosome 2BS of wild emmer wheat ( Triticum turgidum ssp. dicoccoides ) , conferring high grain yield under well-watered and water-limited conditions, was transferred to the elite durum wheat cultivar Uzan ( T. turgidum ssp. durum ) by a marker-assisted backcross breeding approach. The 2B introgression line turned out to be higher yielding but also exhibited negative traits that likely result from trans-, cis-, or linkage drag effects from the wild emmer parent. In this study, the respective 2BS QTL was subjected to fine-mapping, and a set of 17 homozygote recombinants were phenotyped at BC 4 F 5 generation under water-limited and well-watered conditions at an experimental farm in Israel and at a high-throughput phenotyping platform (LemnaTec-129) in Germany. In general, both experimental setups allowed the identification of sub-QTL intervals related to culm length, kernel number, thousand kernel weight, and harvest index. Sub-QTLs for kernel number and harvest index were detected specifically under either drought stress or well-watered conditions, while QTLs for culm length and thousand-kernel weight were detected in both conditions. Although no direct QTL for grain yield was identified, plants with the sub-QTL for kernel number showed a higher grain yield than the recurrent durum cultivar Uzan under well-watered and mild drought stress conditions. We, therefore, suggest that this sub-QTL might be of interest for future breeding purposes., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Deblieck, Szilagyi, Andrii, Saranga, Lauterberg, Neumann, Krugman, Perovic, Pillen and Ordon.)

Most of the freshwaters worldwide are used for agriculture. Freshwater sources are expected to decline and will not suffice to support the food production needed for the growing population. Therefore, growing crops with seawater might constitute a solution. However, very little work has been done on the effect of seawater stress on wheat, an important cereal crop. The present study aimed to determine whether particular wheat genotypes provided better resistance to seawater stress. A set of 80 highly diverse spring wheat genotypes collected from different countries in Europe, Asia, Africa, North and South America was exposed to 50% seawater stress at the early growth stage. Four seeding shoot and root traits were scored for all genotypes. High genetic variations were found among all genotypes for the epicotyl length (EL), hypocotyl length (HL), number of radicles (NOR), and fresh weight (FW). Eight genotypes with high-performance scores of seedling traits were selected. The correlation analyses revealed highly significant correlations among all traits scored in this study. The strongest correlation was found between the NOR and the other seeding traits. Thus, the NOR might be an important adaptive trait for seawater tolerance. The genetic diversity among all genotypes was investigated based on genetic distance. A wide range of genetic distances among all genotypes was found. There was also a great genetic distance among the eight selected genotypes. In particular, the genetic distance between ATRI 5310 (France) and the other seven genotypes was the greatest. Such high genetic diversity might be utilized to select highly divergent genotypes for crossing in a future breeding program. The present study provides very useful information on the presence of different genetic resources in wheat for seawater tolerance., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Amro, Harb, Youssef, Ali, Mohammed, Mourad, Afifi, Börner and Sallam.)

Drought events or the combination of drought and heat conditions are expected to become more frequent due to global warming, and wheat yields may fall below their long-term average. One way to increase climate-resilience of modern high-yielding varieties is by their genetic improvement with beneficial alleles from crop wild relatives. In the present study, the effect of two beneficial QTLs introgressed from wild emmer wheat and incorporated in the three wheat varieties BarNir, Zahir and Uzan was studied under well-watered conditions and under drought stress using non-destructive High-throughput Phenotyping (HTP) throughout the life cycle in a single pot-experiment. Plants were daily imaged with RGB top and side view cameras and watered automatically. Further, at two time points, the quantum yield of photosystem II was measured with a top view FluorCam. The QTL carrying near isogenic lines (NILs) were compared with their corresponding parents by t -test for all non-invasively obtained traits and for the manually determined agronomic and yield parameters. Data quality of phenotypic traits (repeatability) in the controlled HTP experiment was above 85% throughout the life cycle and at maturity. Drought stress had a strong effect on growth in all wheat genotypes causing biomass reduction from 2% up to 70% at early and late points in the drought period, respectively. At maturity, the drought caused 47-55% decreases in yield-related traits grain weight, straw weight and total biomass and reduced TKW by 10%, while water use efficiency (WUE) increased under drought by 29%. The yield-enhancing effect of the introgressed QTLs under drought conditions that were previously demonstrated under field/screenhouse conditions in Israel, could be mostly confirmed in a greenhouse pot experiment using HTP. Daily precision phenotyping enabled to decipher the mode of action of the QTLs in the different genetic backgrounds throughout the entire wheat life cycle. Daily phenotyping allowed a precise determination of the timing and size of the QTLs effect (s) and further yielded information about which image-derived traits are informative at which developmental stage of wheat during the entire life cycle. Maximum height and estimated biovolume were reached about a week after heading, so experiments that only aim at exploring these traits would not need a longer observation period. To obtain information on different onset and progress of senescence, the CVa curves represented best the ongoing senescence of plants. The QTL on 7A in the BarNir background was found to improve yield under drought by increased biomass growth, a higher photosynthetic performance, a higher WUE and a "stay green effect.", Competing Interests: CK was employed by company BASF SE. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Lauterberg, Saranga, Deblieck, Klukas, Krugman, Perovic, Ordon, Graner and Neumann.)