Motoki Shimizu

Plant-derived peptides regulate immunity and host–microbe interactions, but whether fungal pathogens exploit endogenous plant peptides for infection-site selection remains largely unknown. Rapid alkalinization factors (RALFs) are a family of plant peptide hormones that contribute to plant development, reproduction, stress responses, and cell-wall organization. Here, we show that OsRALF7, which is an immune-activating peptide in rice ( Oryza sativa ), is co-opted by the rice blast fungus Magnaporthe oryzae as a host-derived cue for appressorium formation, specialized infection structures required for host penetration. While synthetic OsRALF7 peptide induced defense responses in rice suspension cells, the same peptide induced appressorium formation in M. oryzae . OsRALF7-induced appressorium formation was associated with activation of the cAMP/PKA and Pmk1 MAPK pathways and required a hydrophobic surface. M. oryzae inoculated onto Osralf7 knockout plants formed fewer appressoria, and the positioning of these appressoria relative to the boundaries between two adjacent plant epidermal cells was altered. These findings suggest that OsRALF7 provides positional information for infection initiation for M. oryzae . OsRALF7 localized to the plasma membrane and cell wall in rice, and its appressorium-inducing activity required a conserved YISY motif and cysteine residues. This activity was not conserved in Colletotrichum higginsianum , as RALF23 from Arabidopsis thaliana did not induce appressorium formation but instead showed antifungal activity. Together, these findings uncover a dual function of endogenous plant immune-modulating RALF peptides at the plant–pathogen interface, where they can be exploited by M. oryzae as a host-derived cue for infection initiation while also retaining antifungal activity against other fungal species.

The complete genome sequence of a relatively weak virulent tobacco pathogen, Pseudomonas syringae pv. tabaci 8018 ( Pta 8018) was determined to elucidate key genetic elements that cause disease. Genome comparison of Pta 8018 to the previously available P. syringae pv. tabaci strains revealed that Pta 8018 and Pta 11528 had high genome synteny, with an approximately 5 Mb chromosome inversion in Pta 6605. Furthermore, Pta 8018 had lost the pathogenicity island GI‐1 including a tabtoxin biosynthesis gene cluster and showed weak virulence on Nicotiana tabacum ‘Xanthi NC’ (Xanthi). When inoculated into several tobacco cultivars, Pta 8018 caused leaf angular spot not only in Xanthi but also in N. tabacum cultivars Burley21 and N509, while Pta 6605 did not cause disease in Burley21 and N509 due to the presence of avirulence factor HopAZ1. We found that a mutation in hopAZ1 allows Pta 8018 to avoid recognition in these cultivars. Introduction of intact hopAZ1 of Pta 6605 into Pta 8018 rendered it avirulent to N509 and Burley21, revealing that effector HopAZ1 is a key virulence determinant of P. syringae pv. tabaci . Our data show that although Pta 8018 has reduced virulence strength by the loss of GI‐1 in Xanthi, it expanded its host range to two other cultivars through mutation of hopAZ1 .

Plants often produce unstable sex phenotypes; however, the underlying evolutionary and molecular mechanisms are unclear. In white Guinea yam ( Dioscorea rotundata ), the most economically important tuber crop, genetic improvement is critical for food security but remains constrained by dioecy and complex sex phenotypes. White Guinea yam has a ZZ/ZW sex determination system in which ZZ individuals are consistently male, whereas ZW individuals can be female, male, or monoecious. Here we show that chromosome 11 is the sex chromosome, featuring a 1.2-Mb inversion between the Z and W chromosomes. A 170-kb W-specific region carries the microRNA gene dro-MIR432, likely involved in sex switching. The recent emergence of this miRNA-mediated ZZ/ZW system, distinct from the XY/XX system within Dioscorea , underscores the dynamic evolution of plant sex determination.

Although plant pan-genome studies have revealed extensive copy number variations, their phenotypic consequences remain poorly understood. Here, we manipulated the copy number of OsMADS18 in rice (Oryza sativa) cv 'Hitomebore' using the CRISPR/Cas9 system. We established rice lines harboring one to three tandem copies of OsMADS18, as identified by quantitative PCR and sequencing. The presence of one to three OsMADS18 tandem copies was reflected in stepwise increases in transcript levels and concomitant agronomic trait values. These results demonstrate that manipulating gene copy number can fine-tune important quantitative traits, providing a novel breeding strategy for crop improvement.

Dioecious plants, which have distinct male and female individuals, constitute ~5% of angiosperm species and have emerged frequently and independently from hermaphroditic ancestors. Although recent molecular studies of sex determination have started to reveal the diversity of the genetic systems underlying dioecy, research on the evolution of dioecy is limited, especially in monocots. Here, we explore the molecular basis of sex determination in the monocot Dioscorea tokoro , a dioecious wild yam endemic to East Asia. Chromosome-scale and haplotype-resolved genome assemblies and linkage analysis suggested that this plant has a male heterogametic sex-determination (XY) system, with sex-determination regions located on chromosome 3. Sequence comparison between the X- and Y-chromosomes and read coverage analysis revealed X- and Y-specific regions in putative pericentromeric chromosome regions. Within the Y-specific region, we propose two candidate genes that are likely involved in sex determination: BLH9 , encoding a homeobox protein, and HSP90 , encoding a molecular chaperone . BLH9 functions in a similar way as AtBLH9 in Arabidopsis thaliana . BLH9 could be involved in suppression of female organ development, whereas HSP90 might be required for pollen development. These results shed light on the complex evolution of dioecy in plants.

Genomics-based breeding is a promising approach to generate crops with high yield and quality in a short timeframe. However, this approach is currently not suitable for simultaneously controlling multiple traits, necessitating development of a more efficient methodology. Here, we present a quick breeding strategy employing interpretable genomic prediction models generated using a large-scale recombinant population, which enables optimizing multiple traits in cultivars. To validate our strategy, we developed a nested association mapping population in rice ( Oryza sativa ) and generated its associated genomic models, which allowed rapid improvement of high-yielding rice cultivars. Our genomic breeding strategy provides a general framework to quickly breed high-yielding cultivars capable of coping with the challenges caused by a rapidly changing environment.

β-1,3-glucan-binding proteins (GBPs) play crucial roles in cell wall integrity, host– pathogen interactions, and stress responses in fungi, making them essential for fungal survival and virulence. Here, we show that a GBP of the causal agent for blast fungus, Magnaporthe oryzae , is involved in multipartite coevolutionary arms race with rice ( Oryza sativa ). The rice thaumatin-like pathogenesis-related protein 5 (OsPR5) binds to M. oryzae GBP and sequesters it from the fungal cell wall to confer immunity, but this interaction is counteracted by thaumatin-binding proteins secreted by the fungus to suppress apoplastic immunity. Moreover, a rice receptor kinase located at the cell surface has evolved a thaumatin-like domain to detect the fungal GBP and activate immunity. Our findings reveal that GBPs and thaumatin-domain-containing proteins are engaged in intricate coevolutionary dynamics in the rice apoplast. Given the conservation of thaumatin across plants, we propose a general defense mechanism against fungal pathogens.

Plants recognize pathogen-associated molecular patterns (PAMPs) via pattern recognition receptors, leading to the activation of pattern-triggered immunity in response to pathogen attack. P hytophthora infestans cer amide D (Pi-Cer D) is a sphingolipid from the oomycete pathogen P. infestans . Pi-Cer D is cleaved by the plant extracellular ceramidase NEUTRAL CERAMIDASE 2 (NCER2), and the resulting 9-methyl-branched sphingoid base is recognized by the plant receptor RESISTANT TO DFPM-INHIBITION OF ABSCISIC ACID SIGNALING 2 (RDA2) at the plasma membrane to transduce a defense signal. However, additional components are likely involved in sphingolipid recognition, which remain to be identified. Here, we employed a screen based on Lumi-Map technology to look for Arabidopsis ( Arabidopsis thaliana ) mutants with altered defense responses to Pi-Cer D. We identified three mutants showing diminished responses to Pi-Cer D and elf18, each carrying mutations in STAUROSPORIN AND TEMPERATURE SENSITIVE 3-LIKE A ( STT3A ), which encodes an oligosaccharyltransferase. The stt3a mutants exhibited higher susceptibility to the pathogen Colletotrichum higginsianum than the wild type and displayed alterations in NCER2 protein modifications. These findings suggest that STT3A contributes to plant immunity via post-translational modification of proteins including NCER2.

Although recent plant pan-genome studies have revealed extensive copy number variations, there are limited studies addressing the phenotypic consequences of these variations. Here, we manipulated the copy number of OsMADS18 in rice (Oryza sativa) through gene editing and evaluated the effects. OsMADS18, which encodes a MADS-box transcription factor known to regulate plant development, is tandemly duplicated in the elite rice cultivar ‘Hitomebore’ as a natural variant. We therefore edited the OsMADS18 copy number using a basic CRISPR/Cas9 system and established rice lines harboring one to three tandem copies of OsMADS18, as identified through high throughput qPCR screening. The presence of one to three OsMADS18 tandem copies was reflected in stepwise increases in transcript levels and concomitant trait values for leaf blade length and culm length. These results demonstrate that manipulating gene copy number can fine-tune important agronomic traits, providing a novel breeding strategy for crop improvement.