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.

Perspectives of CRISPR/Cas-mediated cisengineering in horticulture:unlocking the neglected potential for crop improvement

Directed breeding of horticultural crops is essential for increasing yield,nutritional content,and consumer-valued characteristics such as shape and color of the produce.However,limited genetic diversity restricts the amount of crop improvement that can be achieved through conventional breeding approaches.Natural genetic changes in cisregulatory regions of genes play important roles in shaping phenotypic diversity by altering their expression.Utilization of CRISPR/Cas editing in crop species can accelerate crop improvement through the introduction of genetic variation in a targeted manner.The advent of CRISPR/Cas-mediated cis-regulatory region engineering(cis-engineering)provides a more refined method for modulating gene expression and creating phenotypic diversity to benefit crop improvement.Here,we focus on the current applications of CRISPR/Cas-mediated cis-engineering in horticultural crops.We describe strategies and limitations for its use in crop improvement,including de novo cis-regulatory element(CRE)discovery,precise genome editing,and transgene-free genome editing.In addition,we discuss the challenges and prospects regarding current technologies and achievements.CRISPR/Cas-mediated cis-engineering is a critical tool for generating horticultural crops that are better able to adapt to climate change and providing food for an increasing world population.

Molecular and genetic regulations of fleshy fruit shape and lessons from Arabidopsis and rice

Fleshy fruit shape is an important external quality trait influencing the usage of fruits and consumer preference.Thus,modification of fruit shape has become one of the major objectives for crop improvement.However,the underlying mechanisms of fruit shape regulation are poorly understood.In this review we summarize recent progress in the genetic basis of fleshy fruit shape regulation using tomato,cucumber,and peach as examples.Comparative analyses suggest that the OFP-TRM(OVATE Family Protein-TONNEAU1 Recruiting Motif)and IQD(IQ67 domain)pathways are probably conserved in regulating fruit shape by primarily modulating cell division patterns across fleshy fruit species.Interestingly,cucumber homologs of FRUITFULL(FUL1),CRABS CLAW(CRC)and 1-aminocyclopropane-1-carboxylate synthase 2(ACS2)were found to regulate fruit elongation.We also outline the recent progress in fruit shape regulation mediated by OFP-TRM and IQD pathways in Arabidopsis and rice,and propose that the OFP-TRM pathway and IQD pathway coordinate regulate fruit shape through integration of phytohormones,including brassinosteroids,gibberellic acids,and auxin,and microtubule organization.In addition,functional redundancy and divergence of the members of each of the OFP,TRM,and IQD families are also shown.This review provides a general overview of current knowledge in fruit shape regulation and discusses the possible mechanisms that need to be addressed in future studies.

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.

弗里德里希·哈伯兰德教授--欧洲大豆业的先驱

对于弗里德里希·哈伯兰德（Friedrich Haber-landt）教授将大豆引进到欧洲所带来的巨大影响,无论给予多高的评价都不过分。他是19世纪奥匈帝国一位极具影响力的跨国界学者。1873年,当首次认知大豆后,他成为欧洲进行大豆系统试验的第一人,并向多国专家和用户传播大豆知识。

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

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.

CONSTANS alters the circadian clock in Arabidopsis thaliana

Plants are sessile organisms that have acquired highly plastic developmental strategies to adapt to the environment.Among these processes,the floral transition is essential to ensure reproductive success and is finelyregulated by several internal andexternal genetic networks.The photoperiodic pathway,which controls plant response to day length,is one of the most important pathways controlling flowering.In Arabidopsis photoperiodic flowering,CONSTANS(CO)is the central gene activating the expression of the florigen FLOWERING LOCUS T(FT)in the leaves at the end of a long day.The circadian clock strongly regulates Co expression.However,to date,no evidence has been reported regarding a feedbackloop from the photoperiod pathway back to the circadian clock.Using transcriptional networks,we have identified relevant network motifs regulating the interplay between the circadian clock and the photoperiod pathway.Gene expression,chromatin immunoprecipitation experiments,and phenotypic analysis allowed us to elucidate the role of Co over the circadian clock.Plants with altered cO expression showed a different internal clock period,measured by daily leaf rhythmic movements.We showed that co upregulates the expression of key genes related to the circadian clock,such as CCA1,LHY,PRR5,and Gl,at the end of a long day by bindingto specific sites on their promoters.Moreover,a high numberof PRR5-repressed target genes are upregulated by CO,and this could explain the phase transition promoted by CO.The CO-PRR5 complex interacts with the bZiP transcriptionfactor HY5andhelps to localize the complex in the promoters of clock genes.Taken together,our results indicate that there may be a feedback loop in which co communicates back to the circadian clock,providing seasonal information to the circadian system.

The RNA binding protein EHD6 recruits the m^(6)A reader YTH07 and sequesters OsCOL4 mRNA into phase-separated ribonucleoprotein condensates to promote rice flowering

N6-Methyladenosine(m^(6)A)is one of the most abundant modifications of eukaryotic mRNA,but its comprehensive biological functionality remains further exploration.In this study,we identified and characterized a new flowering-promoting gene,EARLY HEADING DATE6(EHD6),in rice.EHD6 encodes an RNA recognition motif(RRM)-containing RNA binding protein that is localized in the non-membranous cytoplasm ribonucleoprotein(RNP)granules and can bind both m^(6)A-modified RNA and unmodified RNA indiscriminately.We found that EHD6 can physically interact with YTH07,a YTH(YT521-B homology)domain-containing m^(6)A reader.We showed that their interaction enhances the binding of an m^(6)A-modified RNA and triggers relocation of a portion of YTH07 from the cytoplasm into RNP granules through phase-separated condensation.Within these condensates,the mRNA of a rice flowering repressor,CONSTANS-like 4(OsCOL4),becomes sequestered,leading to a reduction in its protein abundance and thus accelerated flowering through the Early heading date 1 pathway.Taken together,these results not only shed new light on the molecular mechanism of efficient m^(6)A recognition by the collaboration between an RNA binding protein and YTH family m^(6)A reader,but also uncover the potential for m^(6)A-mediated translation regulation through phaseseparated ribonucleoprotein condensation in rice.

Hordedane diterpenoid phytoalexins restrict Fusarium graminearum infection but enhance Bipolaris sorokiniana colonization of barley roots

Plant immunity is a multilayered process that includes recognition of patterns or effectors from pathogens to elicit defense responses.These include the induction of a cocktail of defense metabolites that typically restrict pathogen virulence.Here,we investigate the interaction between barley roots and the fungal pathogens Bipolaris sorokiniana(Bs)and Fusarium graminearum(Fg)at the metabolite level.We identify hordedanes,a previously undescribed set of labdane-related diterpenoids with antimicrobial properties,as critical players in these interactions.Infection of barley roots by Bs and Fg elicits hordedane synthesis from a 60o-kb gene cluster.Heterologous reconstruction of the biosynthesis pathway in yeast and Nicotiana benthamiana produced several hordedanes,including one of the most functionally decorated products 19-β-hydroxy-hordetrienoic acid(19-OH-HTA).Barley mutants in the diterpene synthase genes of this cluster are unable to produce hordedanes but,unexpectedly,show reduced Bs colonization.By contrast,colonization by Fusarium graminearum,another fungal pathogen of barley and wheat,is 4-fold higher in the mutants completely lacking hordedanes.Accordingly,19-OH-HTA enhances both germination and growth of Bs,whereas it inhibits other pathogenic fungi,including Fg.Analysis of microscopy and transcriptomics data suggest that hordedanes delay the necrotrophic phase of Bs.Taken together,these results show that adapted pathogens such as Bs can subvert plant metabolic defenses to facilitate root colonization.

Molecular actions of NLR immune receptors in plants and animals

NLRs constitute intracellular immune receptors in both plants and animals. Direct or indirect ligand recognition results in formation of oligomeric NLR complexes to mediate immune signaling. Over the past 20 years, rapid progress has been made in our understanding of NLR signaling. Structural and biochemical studies provide insight into molecular basis of autoinhibition,ligand recognition, and resistosome/inflammasome formation of several NLRs. In this review, we summarize these studies focusing on the structural aspect of NLRs. We also discuss the analogies and differences between plant and animal NLRs in their mechanisms of action and how the available knowledge may shed light on the signaling mechanisms of other NLRs.

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.

Microbe-induced coordination of plant iron-sulfur metabolism enhances high-light-stress tolerance of Arabidopsis

High-light stress strongly limits agricultural production in subtropical and tropical regions owing to photo-oxidative damage,decreased growth,and decreased yield.Here,we investigated whether beneficial mi-crobes can protect plants under high-light stress.We found that Enterobacter sp.SA187(SA187)supports the growth of Arabidopsis thaliana under high-light stress by reducing the accumulation of reactive oxygen species and maintaining photosynthesis.Under high-light stress,SA187 triggers dynamic changes in the expression of Arabidopsis genes related to fortified iron metabolism and redox regulation,thereby enhancing the antioxidative glutathione/glutaredoxin redox system of the plant.Genetic analysis showed that the enhancement of iron and sulfur metabolism by SA187 is coordinated by ethylene signaling.In sum-mary,beneficial microbes could be an effective and inexpensive means of enhancing high-light-stress tolerance in plants.

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.