DeCASA in AgriVerse: Parallel Agriculture for Smart Villages in Metaverses

The demand for food is tremendously increasing with the growth of the world population,which necessitates the development of sustainable agriculture under the impact of various factors,such as climate change.To fulfill this challenge,we are developing Metaverses for agriculture,referred to as Agri Verse,under our Decentralized Complex Adaptive Systems in Agriculture(De CASA)project,which is a digital world of smart villages created alongside the development of Decentralized Sciences(De Sci)and Decentralized Autonomous Organizations(DAO)for Cyber-Physical-Social Systems(CPSSs).Additionally,we provide the architectures,operating modes and major applications of De CASA in AgriVerse.For achieving sustainable agriculture,a foundation model based on ACP theory and federated intelligence is envisaged.Finally,we discuss the challenges and opportunities.

Multi-year analyses on three populations reveal the first stable QTLs for tolerance to rain-induced fruit cracking in sweet cherry (Prunus avium L.)

Rain-induced fruit cracking is a major problem in sweet cherry cultivation.Basic research has been conducted to disentangle the physiological and mechanistic bases of this complex phenomenon,whereas genetic studies have lagged behind.The objective of this work was to disentangle the genetic determinism of rain-induced fruit cracking.We hypothesized that a large genetic variation would be revealed,by visual field observations conducted on mapping populations derived from well-contrasted cultivars for cracking tolerance.Three populations were evaluated over 7–8 years by estimating the proportion of cracked fruits for each genotype at maturity,at three different areas of the sweet cherry fruit:pistillar end,stem end,and fruit side.An original approach was adopted to integrate,within simple linear models,covariates potentially related to cracking,such as rainfall accumulation before harvest,fruit weight,and firmness.We found the first stable quantitative trait loci(QTLs)for cherry fruit cracking,explaining percentages of phenotypic variance above 20%,for each of these three types of cracking tolerance,in different linkage groups,confirming the high complexity of this trait.For these and other QTLs,further analyses suggested the existence of at least two-linked QTLs in each linkage group,some of which showed confidence intervals close to 5 cM.These promising results open the possibility of developing marker-assisted selection strategies to select cracking-tolerant sweet cherry cultivars.Further studies are needed to confirm the stability of the reported QTLs over different genetic backgrounds and environments and to narrow down the QTL confidence intervals,allowing the exploration of underlying candidate genes.

Ecosystems and Biodiversity Research

The common goals and the almost perfect complement of the initiatives taken in parallel at Kunming and at several Max Planck sites could serve as valuable starting points for further promoting the CAS/MPS partnership in all matching areas of ecological research.

Time for a Nuclear Meeting： Protein Trafficking and Chromatin Dynamics Intersect in the Plant Circadian System

Circadian clocks mediate adaptation to the 24-h world. In Arabidopsis, most circadian-clock components act in the nucleus as transcriptional regulators and generate rhythmic oscillations of transcript accumulation. In this review, we focus on post-transcriptional events that modulate the activity of circadian-clock components, such as phosphorylation, ubiquitination and proteasome-mediated degradation, changes in cellular localization, and protein-protein interactions. These processes have been found to be essential for circadian function, not only in plants, but also in other circadian systems. Moreover, light and clock signaling networks are highly interconnected. In the nucleus, light and clock compo- nents work together to generate transcriptional rhythms, leading to a general control of the timing of plant physiological processes.

Additive QTLs on three chromosomes control flowering time in woodland strawberry(Fragaria vesca L.)

Flowering time is an important trait that affects survival,reproduction and yield in both wild and cultivated plants.Therefore,many studies have focused on the identification of flowering time quantitative trait locus(QTLs)in different crops,and molecular control of this trait has been extensively investigated in model species.Here we report the mapping of QTLs for flowering time and vegetative traits in a large woodland strawberry mapping population that was phenotyped both under field conditions and in a greenhouse after flower induction in the field.The greenhouse experiment revealed additive QTLs in three linkage groups(LG),two on both LG4 and LG7,and one on LG6 that explain about half of the flowering time variance in the population.Three of the QTLs were newly identified in this study,and one co-localized with the previously characterized FvTFL1 gene.An additional strong QTL corresponding to previously mapped PFRU was detected in both field and greenhouse experiments indicating that gene(s)in this locus can control the timing of flowering in different environments in addition to the duration of flowering and axillary bud differentiation to runners and branch crowns.Several putative flowering time genes were identified in these QTL regions that await functional validation.Our results indicate that a few major QTLs may control flowering time and axillary bud differentiation in strawberries.We suggest that the identification of causal genes in the diploid strawberry may enable fine tuning of flowering time and vegetative growth in the closely related octoploid cultivated strawberry.

Structure, biochemical function, and signaling mechanism of plant NLRs

To counter pathogen invasion,plants have evolved a large number of immune receptors,including membrane-resident pattern recognition receptors(PRRs)and intracellular nucleotide-binding and leucine-rich repeat receptors(NLRs).Our knowledge about PRR and NLR signaling mechanisms has expanded significantly over the past few years.Plant NLRs form multi-protein complexes called resistosomes in response to pathogen effectors,and the signaling mediated by NLR resistosomes converges on Ca2+-permeable channels.Ca2+-permeable channels important for PRR signaling have also been identified.These findings highlight a crucial role of Ca2+in triggering plant immune signaling.In this review,we first discuss the structural and biochemical mechanisms of non-canonical NLR Ca2+channels and then summarize our knowledge about immune-related Ca2+-permeable channels and their roles in PRR and NLR signaling.We also discuss the potential role of Ca2+in the intricate interaction between PRR and NLR signaling.

A versatile Tn7 transposon-based bioluminescence tagging tool for quantitative and spatial detection of bacteria in plants

Investigation of plant-bacteria interactions requires quantification of in planta bacterial titers by means of cumbersome and time-consuming colony-counting assays.Here,we devised a broadly applicable tool for bioluminescence-based quantitative and spatial detection of bacteria in plants.We developed vectors that enable Tn7 transposon-mediated integration of the luxCDABEluciferase operon into a specific genomic location found ubiquitously across bacterial phyla.These vectors allowed for the generation of bioluminescent transformants of various plant pathogenic bacteria from the genera Pseudomonas,Rhizobium(Agrobacterium),and Ralstonia.Direct luminescence measurements of plant tissues inoculated with bioluminescent Pseudomonas syringae pv.tomato DC3000(Pto-lux)reported bacterial titers as accurately as conventional colony-counting assays in Arabidopsis thaliana,Solanum lycopersicum,Nicotiana benthamiana,and Marchantia polymorpha.We further showed the usefulness of our vectors in converting previously generated Pto derivatives to isogenic bioluminescent strains.Importantly,quantitative bioluminescence assays using these Pto-lux strains accurately reported the effects of plant immunity and bacterial effectors on bacterial growth,with a dynamic range of four orders of magnitude.Moreover,macroscopic bioluminescence imaging illuminated the spatial patterns of Pto-lux growth in/on inoculated plant tissues.In conclusion,our vectors offer untapped opportunities to develop bioluminescence-based assays for a variety of plant-bacteria interactions.

Gene Tagging by Activating DNA Transposon nDart in Indica Rice

As International Rice Genome sequencing Project (2005) demonstrated, the rice genome contains various transposons and about 13% of the genome is occupied by DNA transposons. So far, only a few DNA

Internalized and Newly Synthesized Arabidopsis PIN- FORMED2 Pass through Brefeldin A Compartments： A New Insight into Intracellular Dynamics of the Protein by Using the Photoconvertible Fluorescence Protein Dendra2 as a Tag

Dear Editor, Plasma membrane （PM）-Iocalized PIN-FORMED （PIN） auxin efflux carriers were shown to cycle rapidly and con- tinuously between PM and the endomembrane system and this cycling is affected by many exogenous factors and endogenous programs （Grunewald and Friml, 2010）. The fungal lactone metabolite Brefeldin A （BFA） is believed to interrupt the continuous cycling of PINs and other PM proteins by inhibiting their re-secretion （Kleine-Vehn and Friml, 2008）.

Structural insight into chitin perception by chitin elicitor receptor kinase 1 of Oryza sativa

Plants have developed innate immune systems to fight against pathogenic fungi by monitoring pathogenic signals known as pathogen-associated molecular patterns(PAMP)and have established endo symbiosis with arbuscular mycorrhizal(AM)fungi through recognition of mycorrhizal(Myc)factors.Chitin elicitor receptor kinase 1 of Oryza sativa subsp.Japonica(OsC ERK1)plays a bifunctional role in mediating both chitin-triggered immunity and symbiotic relationships with AM fungi.However,it remains unclear whether OsC ERK1 can directly recognize chitin molecules.In this study,we show that OsC ERK1 binds to the chitin hexamer((NAG)6)and tetramer((NAG)4)directly and determine the crystal structure of the OsC ERK1-(NAG)6complex at 2?.The structure shows that one OsC ERK1 is associated with one(NAG)6.Upon recognition,chitin hexamer binds OsC ERK1 by interacting with the shallow groove on the surface of LysM 2.These structural findings,complemented by mutational analyses,demonstrate that LysM 2 is crucial for recognition of both(NAG)6and(NAG)4.Altogether,these findings provide structural insights into the ability of OsC ERK1 in chitin perception,which will lead to a better understanding of the role of OsCERK1 in mediating both immunity and symbiosis in rice.

Conserved Functions of Arabidopsis and Rice CC-Type Glutaredoxins in Flower Development and Pathogen Response

Glutaredoxins （GRXs） are ubiquitous oxidoreductases that play a crucial role in response to oxidative stress by reducing disulfides in various organisms. In planta, three different GRX classes have been identified according to their active site motifs. CPYC and CGFS classes are found in all organisms, whereas the CC-type class is specific for higher land plants. Recently, two Arabidopsis CC-type GRXs, ROXY1 and ROXY2, were shown to exert crucial functions in petal and anther initiation and differentiation. To analyze the function of CC-type GRXs in the distantly related monocots, we isolated and characterized OsROXY1 and OsROXY2-two rice homologs of ROXY1. Both genes are expressed in vegetative and reproductive stages. Although rice flower morphology is distinct from eudicots, OsROXY1/2 floral expression patterns are similar to their Arabidopsis counterparts ROXY1/2. Complementation experiments demonstrate that OsROXY1 and OsROXY2 can fully rescue the roxyl floral mutant phenotype. Overexpression of OsROXY1, OsROXY2, and ROXY1 in Arabidopsis causes similar vegetative and reproductive plant developmental defects. ROXY1 and its rice homologs thus exert a conserved function during eudicot and monocot flower development. Strikingly, overexpression of these CC-type GRXs also leads to an increased accumulation of hydrogen peroxide levels and hyper-susceptibility to infection from the necrotrophic pathogen Botrytis cinerea, revealing the importance of balanced redox processes in flower organ develop- ment and pathogen defence.

From Decision to Commitment： The Molecular Memory of Flowering

During the floral transition the shoot apical meristem changes its identity from a vegetative to an inflorescence state. This change in identity can be promoted by external signals, such as inductive photoperiod conditions or vernalization, and is accompanied by changes in expression of key developmental genes. The change in meristem identity is usually not reversible, even if the inductive signal occurs only transiently. This implies that at least some of the key genes must possess an intrinsic memory of the newly acquired expression state that ensures irreversibility of the process. In this review, we discuss different molecular scenarios that may underlie a molecular memory of gene expression.

Repression of the Auxin Response Pathway Increases Arabidopsis Susceptibility to Necrotrophic Fungi

In plants, resistance to necrotrophic pathogens depends on the interplay between different hormone systems, such as those regulated by salicylic acid （SA）, jasmonic acid （JA）, ethylene, and abscisic acid. Repression of auxin signaling by the SA pathway was recently shown to contribute to antibacterial resistance. Here, we demonstrate that Arabidopsis auxin signaling mutants axrl, axr2, and axr6 that have defects in the auxin-stimulated SCF （Skpl-Cullin- F-box） ubiquitination pathway exhibit increased susceptibility to the necrotrophic fungi Plectosphaerella cucumerina and Botrytis cinerea. Also, stabilization of the auxin transcriptional repressor AXR3 that is normally targeted for removal by the SCF-ubiquitin/proteasome machinery occurs upon P. cucumerina infection. Pharmacological inhibition of auxin transport or proteasome function each compromise necrotroph resistance of wild-type plants to a similar extent as in non-treated auxin response mutants. These results suggest that auxin signaling is important for resistance to the necrotro- phic fungi P. cucumerina and B. cinerea. SGTlb （one of two Arabidopsis SGT1 genes encoding HSP90/HSC70 co-chaperones） promotes the functions of SCF E3-ubiquitin ligase complexes in auxin and JA responses and resistance conditioned by certain Resistance （R） genes to biotrophic pathogens. We find that sgtlb mutants are as resistant to P. cucumerina as wild-type plants. Conversely, auxin/SCF signaling mutants are uncompromised in RPP4-triggered resistance to the obligate biotrophic oomycete, Hyaloperonospora parasitica. Thus, the predominant action of SGTlb in R gene-conditioned resis- tance to oomycetes appears to be at a site other than assisting SCF E3-ubiquitin ligases. However, genetic additivity of sgtlb axrl double mutants in susceptibility to H. parasitica suggests that SCF-mediated ubiquitination contributes to lim- iting biotrophic pathogen colonization once plant-pathogen compatibility is established.

Roles of Arabidopsis Patatin-Related Phospholipases A in Root Development Are Related to Auxin Responses and Phosphate Deficiency

Phospholipase A enzymes cleave phospho- and galactolipids to generate free fatty acids and lysolipids that function in animal and plant hormone signaling. Here, we describe three Arabidopsis patatin-related phospholipase A （pPLA） genes AtPLAIVA, AtPLAIVB, and AtPLAIVC and their corresponding proteins. Loss-of-function mutants reveal roles for these pPLAs in roots during normal development and under phosphate deprivation. AtPLAIVA is expressed strongly and exclusively in roots and AtplalVA-null mutants have reduced lateral root development, characteristic of an impaired auxin response. By contrast, AtPLAIVB is expressed weakly in roots, cotyledons, and leaves but is transcriptionally induced by auxin, although AtplalVB mutants develop normally. AtPLAIVC is expressed in the floral gynaecium and is induced by abscisic acid （ABA） or phosphate deficiency in roots. While an AtplalVC-1 loss-of-function mutant displays ABA respon- siveness, it exhibits an impaired response to phosphate deficiency during root development. Recombinant AtPLA proteins hydrolyze preferentially galactolipids and, less efficiently, phospholipids, although these enzymes are not localized in chloroplasts. We find that AtPLAIVA and AtPLAIVB are phosphorylated by calcium-dependent protein kinases in vitro and this enhances their activities on phosphatidylcholine but not on phosphatidylglycerol. Taken together, the data reveal novel functions of pPLAs in root development with individual roles at the interface between phosphate deficiency and auxin signaling.

Recently duplicated sesterterpene(C25) gene clusters in Arabidopsis thaliana modulate root microbiota

Land plants co-speciate with a diversity of continually expanding plant specialized metabolites(PSMs) and root microbial communities(microbiota).Homeostatic interactions between plants and root microbiota are essential for plant survival in natural environments.A growing appreciation of microbiota for plant health is fuelling rapid advances in genetic mechanisms of controlling microbiota by host plants.PSMs have long been proposed to mediate plant and single microbe interactions.However,the effects of PSMs,especially those evolutionarily new PSMs,on root microbiota at community level remain to be elucidated.Here,we discovered sesterterpenes in Arabidopsis thaliana,produced by recently duplicated prenyltransferase-terpene synthase(PT-TPS) gene clusters,with neo-functionalization.A single-residue substitution played a critical role in the acquisition of sesterterpene synthase(sesterTPS) activity in Brassicaceae plants.Moreover,we found that the absence of two root-specific sesterterpenoids,with similar chemical structure,significantly affected root microbiota assembly in similar patterns.Our results not only demonstrate the sensitivity of plant microbiota to PSMs but also establish a complete framework of host plants to control root microbiota composition through evolutionarily dynamic PSMs.

Small Ubiquitin-Like Modifier Conjugating Enzyme with Active Site Mutation Acts as Dominant Negative Inhibitor of SUMO Conjugation in Arabidopsis

Small ubiquitin-like modifier （SUMO） conjugation affects a broad range of processes in plants, including growth, flower initiation, pathogen defense, and responses to abiotic stress. Here, we investigate in vivo and in vitro a SUMO conjugating enzyme with a Cys to Ser change in the active site, and show that it has a dominant negative effect. In planta expression significantly perturbs normal development, leading to growth retardation, early flowering and gene expression changes. We suggest that the mutant protein can serve as a probe to investigate sumoylation, also in plants for which poor genetic infrastructure precludes analysis via loss-of-function mutants.

SNARE-RNAi Results in Higher Terpene Emission from Ectopically Expressed Caryophyllene Synthase in Nicotiana benthamiana

Plants produce numerous terpenes and much effort has been dedicated to the identification and charac- terization of the terpene biosynthetic genes. However, little is known about how terpenes are transported within the cell and from the cell into the apoplast. To investigate a putative role of vesicle fusion in this pro- cess, we used Agrobacterium tumefaciens-mediated transient coexpression in Nicotiana benthamiana of an MtVAMP721e-RNAi construct （Vi） with either a caryophyllene synthase or a linalool synthase, respec- tively. Headspace analysis of the leaves showed that caryophyllene or linalool emission increased about five-fold when N. benthamiana VAMP72 function was blocked. RNA sequencing and protein ubiquitination analysis of the agroinflltrated N. benthamiana leaf extracts suggested that increased terpene emissions may be attributed to proteasome malfunction based on three observations： leaves with TPS＋Vi showed （1） a higher level of a DsRed marker protein, （2） a higher level of ubiquitinated proteins, and （3） coordinated induced expression of multiple proteasome genes, presumably caused by the lack of proteasome- mediated feedback regulation. However, caryophyllene or linalool did not inhibit proteasome-related pro- tease activity in the in vitro assays. While the results are not conclusive for a role of vesicle fusion in terpene transport, they do show a strong interaction between inhibition of vesicle fusion and ectopic expression of certain terpenes. The results have potential applications in metabolic engineering.

Shedding Light on Large-Scale Chromatin Reorganization in Arabidopsis thaliana

Plants need to respond quickly and appropriately to various types of light signals from the environment to optimize growth and development. The immediate response to shading, reduced photon flux （low light）, and changes in spectral quality involves changes in gene regulation. In the case of more persistent shade, the plant shows a dramatic change in the organization of chromatin. Both plant responses are controlled via photoreceptor signaling proteins. Re- cently, several studies have revealed similar features of chromatin reorganization in response to various abiotic and biotic signals, while others have unveiled intricate molecular networks of light signaling towards gene regulation. This opinion paper briefly describes the chromatin （de）compaction response from a light-signaling perspective to provide a link be- tween chromatin and the molecular network of photoreceptors and E3 ubiquitin ligase complexes.

Alternative splicing enhances transcriptome complexity in desiccating seeds

Before being dispersed in the environment, mature seeds need to be dehydrated. The survival of seeds after dispersal depends on their low hydration in combination with high desiccation tolerance. These characteristics are estab- lished during seed maturation. Some key seed maturation genes have been reported to be regulated by alternative splicing （AS）. However, so far AS was described only for single genes and a comprehensive analysis of AS during seed maturation has been lacking. We investigated gene expression and AS during Arabidopsis thaliana seed development at a global level, before and after desiccation. Bioinformatics tools were developed to identify differentially spliced regions within genes. Our data suggest the importance and shows the peculiar features of AS during seed desiccation. We identified AS in 347o of genes that are expressed at both timepoints before and after desiccation. Most of these AS transcript variants had not been found before in other tissues. Among the AS genes some seed master regulators could be found. Interestingly, 6% of all expressed transcripts were not transcriptionally regulated during desiccation, but only modified by AS. We propose that AS should be more routinely taken into account in the analysis of transcriptomic data to prevent overlooking potentially important regulators.

XAANTAL2 （AGL14） Is an Important Component of the Complex Gene Regulatory Network that Underlies Arabidopsis Shoot Apical Meristem Transitions

In Arabidopsis thaliana, multiple genes involved in shoot apical meristem （SAM） transitions have been char- acterized, but the mechanisms required for the dynamic attainment of vegetative, inflorescence, and floral meristem （VM, IM, FM） cell fates during SAM transitions are not well understood. Here we show that a MADS-box gene, XAANTAL2 （XAL2/AGL14）, is necessary and sufficient to induce flowering, and its regula- tion is important in FM maintenance and determinacy, xal2 mutants are late flowering, particularly under short-day （SD） condition, while XAL2 overexpressing plants are early flowering, but their flowers have vege- tative traits. Interestingly, inflorescences of the latter plants have higher expression levels of LFY, AP1, and TFL1 than wild-type plants. In addition we found that XAL2 is able to bind the TFL1 regulatory regions. On the other hand, the basipetal carpels of the 35S：：XAL2 lines lose determinacy and maintain high levels of WUS expression under SD condition. To provide a mechanistic explanation for the complex roles of XAL2 in SAM transitions and the apparently paradoxical phenotypes of XAL2 and other MADS-box （SOCl, AGL24） over- expressors, we conducted dynamic gene regulatory network （GRN） and epigenetic landscape modeling. We uncovered a GRN module that underlies VM, IM, and FM gene configurations and transition patterns in wild- type plants as well as loss and gain of function lines characterized here and previously. Our approach thus provides a novel mechanistic framework for understanding the complex basis of SAM development.