Ryohei Terauchi

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.

Background: Plant organ shape is an important trait in terms of economic efficiency in agriculture. The club-like or spindle-shaped underground tubers of Chinese yam ( Dioscorea polystachya Turcz.) impede mechanical harvest resulting in unprofitable cultivation. Results: We performed genome-wide DNA methylation sequencing of two closely related Chinese yam tuber shape variants F60 (long, thin) and F2000 (short, thick) to investigate potential epigenetic effects on tuber development and shaping. Analysis of differentially methylated regions (DMRs) led to the identification of 1,513 hyper- or hypomethylated regions in 763 DMR-associated genes of which the majority were detected in the CHG methylation context. Gene Ontology (GO) term analysis revealed enriched DMR-associated genes related to anatomical structure development, hormone response, and photomorphogenesis. DMRs in brassinosteroid (BR) pathway-related genes, in particular BR signaling genes, were detected. We further identified hyperDMRs and hypoDMRs in putative circadian rhythm-related genes such as DpVOZ1 , DpPIE1 and DpSPA1 as well as several putative organ shape-related genes ( DpIQD13, DpTCPs ). Conclusion: A potential network consisting of components of the BR signaling pathway, and circadian clock as well as microtubule-associated proteins was suggested to coordinate tuberization and affect tuber shape of Chinese yam.

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.

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 describe 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 read coverage analysis of the sex chromosomes revealed X - and Y -specific regions in putative pericentromeric chromosome regions. Within the Y -specific region, we identified two candidate genes that are likely involved in sex determination: BLH9 , encoding a homeobox protein, and HSP90 , encoding a molecular chaperone. BLH9 has similar functions to AtBLH9 in Arabidopsis thaliana . BLH9 is thought to suppress female organ development, whereas HSP90 might be required for pollen development. These results shed light on the complex evolution of dioecy in plants. Author summary: Sexual reproduction is a nearly universal, indispensable feature of evolution in eukaryotes. The molecular mechanisms underlying sex determination vary depending on the taxon. However, most information about this process was derived from studies of model organisms and/or domesticated species. To elucidate the diversity and evolution of sex determination, we need to expand the taxonomic breadth of these investigations. Here, we focused on the monocot genus Dioscorea , which contains species with multiple sex-determination systems, suggesting that frequent evolutionary transitions occur between the different sex-determination systems. We investigated the genetics of sex determination in Dioscorea tokoro , a dioecious wild yam endemic to East Asia. Whole-genome assembly and genetic analysis, along with transcriptome analysis, suggested that this species employs a male heterogametic sex determination ( XY ) system, with two Y -chromosome-specific genes that might be involved in male and female differentiation. These findings enhance our understanding of the complex evolution of dioecy.