Fine mapping and characterization of stripe rust resistance gene YrAYH in near-isogenic lines derived from a cross involving wheat landrace Anyuehong

Stripe rust,caused by Puccinia striiformis f.sp.tritici(Pst),is a devastating disease in wheat worldwide.Discovering and characterizing new resistance genes/QTL is crucial for wheat breeding programs.In this study,we fine-mapped and characterized a stripe rust resistance gene,YRAYH,on chromosome arm 5BL in the Chinese wheat landrace Anyuehong(AYH).Evaluations of stripe rust response to prevalent Chinese Pst races in near-isogenic lines derived from a cross of Anyuehong and Taichung 29 showed that YrAYH conferred a high level of resistance at all growth stages.Fine mapping using a large segregating population of 9748 plants,narrowed the YRAYH locus to a 3.7 Mb interval on chromosome arm 5BL that included 61 annotated genes.Transcriptome analysis of two NIL pairs identified 64 upregulated differentially expressed genes(DEGs)in the resistant NILs(NILs-R).Annotations indicated that many of these genes have roles in plant disease resistance pathways.Through a combined approach of fine-mapping and transcriptome sequencing,we identified a serine/threonine-protein kinase SRPK as a candidate gene underlying YrAYH.A unique 25 bp insertion was identified in the NILs-R compared to the NILs-S and previously published wheat genomes.An InDel marker was developed and co-segregated with YrAYH.Agronomic trait evaluation of the NILs suggested that YrAYH not only reduces the impact of stripe rust but was also associated with a gene that increases plant height and spike length.

The Arabidopsis pattern recognition receptor EFR enhances fire blight resistance in apple

Fire blight disease,caused by the bacterium Erwinia amylovora(E.amylovora),is responsible for substantial losses in cultivated apples worldwide.An important mechanism of plant immunity is based on the recognition of conserved microbial molecules,named pathogen-associated or microbe-associated molecular patterns(PAMPs or MAMPs),through pattern recognition receptors(PRRs),leading to pattern-triggered immunity(PTI).The interspecies transfer of PRRs represents a promising strategy to engineer broad-spectrum and durable disease resistance in crops.EFR,the Arabidopsis thaliana PRR for the PAMP elf18 derived from the elongation factor thermal unstable(EF-Tu)proved to be effective in improving bacterial resistance when expressed into Solanaceae and other plant species.In this study,we tested whether EFR can affect the interaction of apple with E.amylovora by its ectopic expression in the susceptible apple rootstock M.26.Stable EFR expression led to the activation of PAMP-triggered immune response in apple leaves upon treatment with supernatant of E.amylovora,as measured by the production of reactive oxygen species and the induction of known defense genes.The amount of tissue necrosis associated with E.amylovora infection was significantly reduced in the EFR transgenic rootstock compared to the wild-type.Our results show that the expression of EFR in apple rootstock may be a valuable biotechnology strategy to improve the resistance of apple to fire blight.

The challenge of defining rare genetic programs by single-cell RNA sequencing:Insights from phloem studies

Single-cell RNA sequencing technology provides unprecedented opportunities to capture the spatiotemporal aspects of genetic programs that drive cell differentiation.Phloem is a subtype of vascular tissue that is crucial for transporting sugars,proteins,and other organic molecules.Its critical role in the redistribution of carbon between photosynthetically active“source”organs(leaves,shoots)and“sink”tissues/organs incapable of fixing carbon(wood,storage organs,root system,etc.)has made phloem development and its transcriptional regulation a prime research focus.

Grafting vigour is associated with DNA de-methylation in eggplant

In horticulture,grafting is a popular technique used to combine positive traits from two different plants.This is achieved by joining the plant top part(scion)onto a rootstock which contains the stem and roots.Rootstocks can provide resistance to stress and increase plant production,but despite their wide use,the biological mechanisms driving rootstock-induced alterations of the scion phenotype remain largely unknown.Given that epigenetics plays a relevant role during distance signalling in plants,we studied the genome-wide DNA methylation changes induced in eggplant(Solanum melongena)scion using two interspecific rootstocks to increase vigour.We found that vigour was associated with a change in scion gene expression and a genome-wide hypomethylation in the CHH context.Interestingly,this hypomethylation correlated with the downregulation of younger and potentially more active long terminal repeat retrotransposable elements(LTR-TEs),suggesting that graft-induced epigenetic modifications are associated with both physiological and molecular phenotypes in grafted plants.Our results indicate that the enhanced vigour induced by heterografting in eggplant is associated with epigenetic modifications,as also observed in some heterotic hybrids.

Breaking the biotrophic interfacial complex:How genome editing can lead to rice blast resistance

Genome editing is a transformational technology—by precisely altering the coding or regulatory sequence of a specific gene,it is now possible to change specific traits within a wide variety of organisms.As a consequence,plant breeding can be taken to a new level of precision,and many countries are moving rapidly to adopt new legislation to permit genome editing(Greenwood et al.,2023).However,genome editing has so far seldom been used to develop disease-resistant crops.This is because plant immunity often depends on single dominant resistance genes,which encode immune receptors that recognize secreted effectors deployed by plant pathogens(Jones and Dangl,2006).In this context,genetic modification has proven to be a much more powerful technology so far to introduce these genes from distinct varieties,or even different species,to develop disease resistant crop species(Greenwood et al.,2023),especially when multiple disease-resistance loci can be introduced together to provide more durable resistance(Luo et al.,2021).Genome editing can be used in an innovative way to resurrect previously effective resistance genes(Contreras et al.,2023),but it has been less effective at introducing new forms of disease resistance to crops.

Zig, Zag, and ’Zyme: leveraging structural biology to engineer disease resistance

Dynamic host–pathogen interactions determine whether disease will occur.Pathogen effector proteins are central players in such disease development.On one hand,they improve susceptibility by manipulating host targets;on the other hand,they can trigger immunity after recognition by host immune receptors.A major research direction in the study of molecular plant pathology is to understand effector-host interactions,which has informed the development and breeding of crops with enhanced disease resistance.Recent breakthroughs on experiment-and artificial intelligence-based structure analyses significantly accelerate the development of this research area.Importantly,the detailed molecular insight of effector–host interactions enables precise engineering to mitigate disease.Here,we highlight a recent study by Xiao et al.,who describe the structure of an effector-receptor complex that consists of a fungal effector,with polygalacturonase(PG)activity,and a plant-derived polygalacturonase-inhibiting protein(PGIP).PGs weaken the plant cell wall and produce immune-suppressive oligogalacturonides(OGs)as a virulence mechanism;however,PGIPs directly bind to PGs and alter their enzymatic activity.When in a complex with PGIPs,PGs produce OG polymers with longer chains that can trigger immunity.Xiao et al.demonstrate that a PGIP creates a new active site tunnel,together with a PG,which favors the production of long-chain OGs.In this way,the PGIP essentially acts as both a PG receptor and enzymatic manipulator,converting virulence to defense activation.Taking a step forward,the authors used the PG-PGIP complex structure as a guide to generate PGIP variants with enhanced long-chain OG production,likely enabling further improved disease resistance.This study discovered a novel mechanism by which a plant receptor plays a dual role to activate immunity.It also demonstrates how fundamental knowledge,obtained through structural analyses,can be employed to guide the design of proteins with desired functions in agriculture.

Transcriptional Regulation of the Ambient Temperature Response by H2A.Z Nucleosomes and HSF1 Transcription Factors in Arabidopsis

Temperature influences the distribution, range, and phenology of plants. The key transcriptional activators of heat shock response in eukaryotes, the heat shock factors （HSFs）, have undergone large-scale gene amplification in plants. While HSFs are central in heat stress responses, their role in the response to ambient temperature changes is less well understood. We show here that the warm ambient temperature transcriptome is dependent upon the HSFA1 clade ofArabidopsis HSFs, which cause a rapid and dynamic eviction of H2A.Z nucleosomes at target genes. A transcriptional cascade results in the activation of multiple downstream stress-responsive transcription factors, triggering large-scale changes to the transcriptome in response to elevated temperature. H2A.Z nucleosomes are enriched at temperature-responsive genes at non-inducible temperature, and thus likely confer inducibility of gene expression and higher responsive dynamics. We propose that the antagonistic effects of H2A.Z and HSF1 provide a mechanism to activate gene expression rapidly and precisely in response to temperature, while preventing leaky transcription in the absence of an activation signal.

Arabidopsis SWC4 Binds DNA and Recruits the SWR1 Complex to Modulate Histone H2A.Z Deposition at Key Regulatory Genes

Deposition of the H2A.Z histone variant by the SWR1 complex （SWRI-C） in regulatory regions of specific loci modulates transcription. Characterization of mutations in Arabidopsis thaliana homologs of yeast SWRI-C has revealed a role for H2A.Z exchange in a variety of developmental processes. Nevertheless, the exact composition of plant SWRI-C and how it is recruited to target genes remains to be established. Here we show that SWC4, the Arabidopsis homolog of yeast SANT domain protein Swc4/Eaf2, is a DNA-binding protein that interacts with SWR1-C subunits. We demonstrate that the swc4-1 knockout mutant is embryo- lethal, while SWC4 RNAi knockdown lines display pleiotropic phenotypic alterations in vegetative and repro- ductive traits, including acceleration of flowering time, indicating that SWC4 controls post-embryonic processes. Transcriptomic analyses and genome-wide profiling of H2A.Z indicate that SWC4 represses tran- scription of a number of genes, including the floral integrator FT and key transcription factors, mainly by modulating H2A.Z deposition. Interestingly, SWC4 silencing does not affect H2A.Z deposition at the FLC locus nor expression of this gene, a master regulator of flowering previously shown to be controlled by SWR1-C. Importantly, we find that SWC4 recognizes specific AT-rich DNA elements in the chromatin regions of target genes and that SWC4 silencing impairs SWRI-C binding at FT. Collectively, our data suggest that SWC4 regulates plant growth and development by aiding SWR1-C recruitment and modulating H2A.Z deposition.

Interplay between ABA and GA Modulates the Timing of Asymmetric Cell Divisions in the Arabidopsis Root Ground Tissue

In multicellular organisms, controlling the timing and extent of asymmetric cell divisions （ACDs） is crucial for correct patterning. During post-embryonic root development in Arabidopsis thaliana, ground tissue （GT） maturation involves an additional ACD of the endodermis, which generates two different tissues： the endo- dermis （inner） and the middle cortex （outer）. It has been reported that the abscisic acid （ABA） and gibberellin （GA） pathways are involved in middle cortex （MC） formation. However, the molecular mechanisms under- lying the interaction between ABA and GA during GT maturation remain largely unknown. Through transcriptome analyses, we identified a previously uncharacterized C2H2-type zinc finger gene, whose expression is regulated by GA and ABA, thus named GAZ （GA- AND ABA-RESPONSIVE ZINC FINGER）. Seedlings ectopically overexpressing GAZ （GAZ-OX） were sensitive to ABA and GA during MC formation, whereas GAZ-SRDX and RNAi seedlings displayed opposite phenotypes. In addition, our results indicated that GAZ was involved in the transcriptional regulation of ABA and GA homeostasis. In agreement with pre- vious studies that ABA and GA coordinate to control the timing of MC formation, we also confirmed the unique interplay between ABA and GA and identified factors and regulatory networks bridging the two hor- mone pathways during GT maturation of the Arabidopsis root.

Pm21 from Haynaldia villosa Encodes a CC-NBS- LRR Protein Conferring Powdery Mildew Resistance in Wheat

Dear Editor Wheat powdery mildew, caused by Blumeria graminis f. sp. tritici （Bgt）, is a destructive disease of wheat throughout the world. One of the most important environmental-friendly and economical methods to reduce wheat loss caused by Bgt is to develop highly resistant varieties （Kuraparthy et al., 2007）. Pm21 from the wild species Haynaldia villosa （also known as Dasypyrum villosum） confers high resistance to Bgt in wheat throughout all growth stages. It has now become one of the most highly effective genetic loci introgressed into wheat from wild species, and the commercial varieties harboring Pm21 have been widely used in wheat production with more than 4 million hectares in China.

Intra-strain Elicitation and Suppression of Plant Immunity by Ralstonia solanacearum Type-III Effectors in Nicotiana benthamiana

Effector proteins delivered inside plant cells are powerful weapons for bacterial pathogens,but this exposes the pathogen to potential recognition by the plant immune system.Therefore,the effector repertoire of a given pathogen must be balanced for a successful infection.Ralstonia solanacearum is an aggressive pathogen with a large repertoire of secreted effectors.One of these effectors,RipE1,is conserved in most R.solanacearum strains sequenced to date.In this work,we found that RipE1 triggers immunity in N.benthamiana,which requires the immune regulator SGT1,but not EDS1 or NRCs.Interestingly,RipE1-triggered immunity induces the accumulation of salicylic acid(SA)and the overexpression of several genes encoding phenylalanine-ammonia lyases(PALs),suggesting that the unconventional PALmediated pathway is responsible for the observed SA biosynthesis.Surprisingly,RipE1 recognition also induces the expression of jasmonic acid(JA)-responsive genes and JA biosynthesis,suggesting that both SA and JA may act cooperatively in response to RipE1.We further found that RipE1 expression leads to the accumulation of glutathione in plant cells,which precedes the activation of immune responses.R.solanacearum secretes another effector,RipAY,which is known to inhibit immune responses by degrading cellular glutathione.Accordingly,RipAY inhibits RipE1-triggered immune responses.This work shows a strategy employed by R.solanacearum to counteract the perception of its effector proteins by plant immune system.

Requirement of a Homolog of Glucosidase Ⅱ β-Subunit for EFR-Mediated Defense Signaling in Arabidopsis thaliana

EFR is a plasma-membrane resident receptor responsible for recognition of microbial elongation factorTu （EF-Tu） and thus triggering plant innate immunity to fend off phytopathogens. Functional EFR must be subject to the endoplasmic reticulum quality control （ERQC） machinery for the correct folding and proper assembly in order to reach its final destination. Genetic studies have demonstrated that ERD2b, a counterpart of the yeast or mammalian HDEL receptor ERD2 for retaining proteins in the endoplasmic reticulum （ER） lumen, is required for EFR function in plants （Li et al., 2009）. In this study, we characterized the Arabidopsis glucosidase Ⅱ β--subunit via the H DEL motif against the non-redundant protein database. Data mining also revealed that the glucosidase Ⅱ β--subunit gene has a highly similar expression pattern to ERD2b and the other known ERQC components involved in EFR biogenesis. Importantly, the T-DNA insertion lines of the glucosidase Ⅱ β-subunit gene showed that EFR-controlled responses were substantially reduced or completely blocked in these mutants. The responses include seedling growth inhibition, induction of marker genes, MAP kinase activation, and callose deposition, trigged by peptide elf18, a full mimic of E F-Tu. Taken together, ourdata indicate a requirement of the glucosidase Ⅱ β-subunitfor EFR function.

A potato late blight resistance gene protects against multiple Phytophthora species by recognizing a broadly conserved RXLR-WY effector

Species of the genus Phytophthora,the plant killer,cause disease and reduce yields in many crop plants.Although many Resistance to Phytophthora infestans(Rpi)genes effective against potato late blight have been cloned,few have been cloned against other Phytophthora species.Most Rpi genes encode nucleotide-binding domain,leucine-rich repeat-containing(NLR)immune receptor proteins that recognize RXLR(Arg-X-Leu-Arg)effectors.However,whether NLR proteins can recognize RXLR effectors from multiple Phytophthora species has rarely been investigated.Here,we identified a new RXLR-WY effector AVRamr3 from P.infestans that is recognized by Rpi-amr3 from a wild Solanaceae species Solanum americanum.Rpi-amr3 associates with AVRamr3 in planta.AVRamr3 is broadly conserved in many different Phytophthora species,and the recognition of AVRamr3 homologs by Rpi-amr3 activates resistance against multiple Phytophthora pathogens,including the tobacco black shank disease and cacao black pod disease pathogens P.parasitica and P.palmivora.Rpi-amr3 is thus the first characterized resistance gene that acts against P.parasitica or P.palmivora.These findings suggest a novel path to redeploy known R genes against different important plant pathogens.

Vacuole Integrity Maintained by DUF300 Proteins Is Required for Brassinosteroid Signaling Regulation

Brassinosteroid （BR） hormone signaling controls multiple processes during plant growth and development and is initiated at the plasma membrane through the receptor kinase BRASSINOSTEROID INSENSITIVE1 （BRI1） together with co-receptors such as BRI1-ASSOClATED RECEPTOR KINASE1 （BAK1）. BRI1 abun- dance is regulated by endosomal recycling and vacuolar targeting, but the role of vacuole-related proteins in BR receptor dynamics and BR responses remains elusive. Here, we show that the absence of two DUF300 domain-containing tonoplast proteins, LAZARUS1 （LAZl） and LAZl HOMOLOG1 （LAZlH1）, causes vacuole morphology defects, growth inhibition, and constitutive activation of BR signaling. Intriguingly, tonoplast accumulation of BAK1 was substantially increased and appeared causally linked to enhanced BRI1 trafficking and degradation in lazl lazlhl plants. Since unrelated vacuole mutants exhibited normal BR responses, our findings indicate that DUF300 proteins play distinct roles in the regulation of BR signaling by maintaining vacuole integrity required to balance subcellular BAK1 pools and BR receptor distribution.

Sequence-Independent Identification of Active LTR Retrotransposons in Arabidopsis

Dear Editor,LTR retrotransposons （LTR-TEs） are mobile genetic elements that often comprise a large portion of the host genome and are particularly abundant in genomes of plants （Lisch, 2013）. They transpose through an RNA transcript that is reverse transcribed to an extrachromosomal DNA （ecDNA） of the original element that can insert at a new genomic location （Wicker et al., 2007）.

Calcium signaling primes RNA interference during viral infection

Plants resist viral infection through multiple mechanisms.These include physical barriers,activation of NUCLEOTIDE-BINDING LEUGINE-RICH REPEAT PROTEINS(NLRs),autophagy,biosyn-thesis of defense-related phytohormones,and RNA interference(RNAi).RNAI suppresses the expression of viral RNA and is conserved across several eukaryotic kingdoms.During infection,RNA-DEPENDENT RNA POLYMERASES(RDRs)amplify viral RNA fragments into double-stranded RNAs(dsRNAs).

RNA Splicing:A Novel Pathogen Effector Target

Potato late blight caused by the notorious oomycete pathogen Phytophthora infestans led to the Irish famine in the 1840s.To date,this disease still remains a challenge for potato production(Figure 1).Effector proteins help P.infestans to infect their host plants,including potato and tomato.In summer 2004,in the Joint Genome Institute(Walnut Creek,California),some Phytophthora researchers gathered at an"Effector table,"and by aligning the amino acid sequences of many unpublished effector proteins from Phytophthora pathogens,revealed that all of them possess conserved Arg-any residue-Leu-Arg(RXLR)and Glu-Glu-Arg(EER)motifs post signal peptides(Govers and Gijzen,2006).In 2009,the genome sequence of P.infestans strain T30-4 was published and 563 RXLR effectors were predicted.Since then,many high-throughput"effectoromics"screening strategies were carried out and effectors were identified that trigger a hypersensitive response(HR)on some host genotypes,or that function as cell death repressors or RNA silencing suppressors.However,the function of most RXLR effectors remains unknown.

Crip21:Alert from Dodder to Crops

Together with pathogenic microbes and herbivorous insects,parasitic plants are emerging as aggressive threats on agriculture worldwide.Among them,Cuscuta(dodder),a stem holoparasite,extracts nutrients and water from host plants through phloem feeding.Dodder is parasitic on a very wide variety of plants,including a number of important agricultural and horticultural crops such as alfalfa,clover,tomatoes,and potatoes.Dodder in-festations cause major economic concerns,including crop yield reduction and cost increase of crop harvesting.Understanding resistance mechanisms against dodder can provide potential so-lutions to effectively control dodder infestations.

FERONIA-Goddess receptor in plants

Receptor-like kinases,representing the largest transmembrane receptor family in plants,contribute to different aspects of the plant life cycle.During the past decade,a number of studies have highlighted FERONIA(FER)as a versatile receptor playing important roles in plant growth and stress responses(Zhang et al.,2020).