Yoichi Sakata

Wheat is a major staple crop for over one-third of the world’s population, crucial for global food security, economic stability and cultural traditions. Recently, single-cell and spatial omics approaches have transformed biological discovery, primarily in medical and animal sciences, and they are now beginning to be applied in plant research. Here we summarize the technical innovations and feasibility of spatial omics applications in wheat research, particularly for understanding developmental and environmental responses, thereby potentially enhancing wheat breeding. We highlight how these tools can reveal spatial and temporal patterns in gene expression, cellular heterogeneity and tissue organization in wheat. Furthermore, we propose developing a spatially resolved single-cell atlas of wheat across its life cycle to facilitate breakthroughs in basic research and potential applications in breeding. To achieve these goals, we advocate for a Wheat Spatial Omics Consortium to foster worldwide collaboration for overcoming barriers and developing sustainable and climate-resilient wheat.

The emergence of land plants required adaptations to altered water availability and increased effective gravity. Bryophytes underwent major changes in physiology, anatomy, and growth during their emergence onto land. However, the link between gravity, photosynthesis, and genetic control remains unclear. Here, we show that leaf carbon dioxide diffusion enhanced photosynthesis in the model moss Physcomitrium patens under increased gravity (6 and 10 times Earth’s gravity), driven by increases in plant (gametophore) number and chloroplast size. RNA sequencing analysis showed that 10 gravity up-regulated several species-specific APETALA2/ethylene-responsive factor (AP2/ERF) transcription factors. Overexpression of one such AP2/ERF , ISSUNBOSHI1 ( IBSH1 ; gene ID = Pp3c1_32440 ), in P. patens phenocopied plants grown at 10 gravity, and the dominant repressor form of IBSH1 suppressed 10 gravity responses. These results provide evidence that the proliferation of AP2/ERF transcription factors and the establishment of a notable gene network may have been important in adaptation to the terrestrial environment during land plant evolution.

ETHYLENE INSENSITIVE 2 (EIN2) is an Nramp family transmembrane protein recognized as an essential component of ethylene signaling in angiosperms. However, its functions in other plant systems are not fully understood. Here, we demonstrate that ppein2ab mutants of the moss Physcomitrium patens, in which both EIN2-like genes have been disrupted, do not show a typical ethylene-mediated escape response following submergence. Interestingly, ppein2ab mutants showed reduced sensitivity to abscisic acid (ABA), a phytohormone that mediates drought stress responses. The ppein2ab plants were sensitive to hyperosmosis and freezing stress and exhibited reduced late embryogenesis abundant protein accumulation. Furthermore, ppein2ab mutants showed reduced activation of both SNF1-related protein kinase2 (SnRK2), the central activator of ABA and osmostress signaling, and the B3-RAF kinase ARK/PpCTR1L, a positive regulator of SnRK2. These results indicate that EIN2 is a dual function signaling component mediating both submergence and drought signaling in bryophytes. The diminished ABA responses in ppein2ab were restored by introduction of Arabidopsis EIN2 and the EIN2 orthologs of the Charophyceaen alga Chara braunii, suggesting functional conservation of EIN2 orthologs in Phragmoplastophyta.

Cell-to-cell communication is essential for multicellular organisms. Plasmodesmata (PD) are plant-specific nanopore structures pivotal for cell-to-cell communication and plant survival. However, how PD form and their structure, regulation, and evolution remain largely unknown. Here, we demonstrate that the exogenous supply of abscisic acid (ABA), a well-conserved phytohormone in land plants, reduces primary PD density in the moss Physcomitrium patens . This regulation requires all core components of the ABA signaling pathway. Furthermore, we reveal that ABA-INSENSITIVE 5, a well-conserved transcription factor in the ABA signaling pathway of land plants, plays a pivotal role in PD density regulation, whereas ABA-INSENSITIVE 3 does not. Our findings show that the ABA-induced reduction in primary PD density is mediated by these ABA-responsive factors in P. patens . Considering previous reports on ABA-dependent PD regulation in both moss and angiosperms, we propose that the ABA-mediated control of PD biogenesis and permeability represents a conserved mechanism in land plants, with critical implications for cell-to-cell communication and stress adaptation.

Locust bean (Ceratonia siliqua) accumulates the galactomannan (GM) locust bean gum (LBG) in its seeds. LBG is a major industrial raw material used as a food thickener and gelling agent, whose unique properties mean that it cannot be readily replaced by other GMs. Whereas much is known about GM accumulation and the genes associated with GM biosynthesis in legumes, the genes involved in GM biosynthesis in C. siliqua are largely unknown. Here, we present a genome-wide list of genes predicted to be associated with the GM biosynthesis pathway in C. siliqua. We confirmed high GM accumulation in endosperm using a newly established GM quantification method involving LC-MS/MS. Through de novo draft genome assembly, we comprehensively identified genes predicted to be related to the GM biosynthesis pathway in C. siliqua by identifying orthologous groups. In particular, we identified all genes predicted to encode mannan synthase (ManS) and galactomannan galactosyltransferase (GMGT), enzymes functioning in the final step of GM biosynthesis, from the C. siliqua draft genome. ManS and the GMGT paralogs were predominantly expressed in endosperm. The genome and transcriptome produced in this study should facilitate research examining why C. siliqua produces LBG, unlike other legumes.

Plants are often exposed not only to short-term (S-) but also to long-term (L-)heat stress over several consecutive days. A few Arabidopsis mutants defective in L-heat tolerance have been identified, but the molecular mechanisms are less understood for this tolerance than for S-heat stress tolerance. To elucidate the mechanisms of the former, we used a forward genetic screen for sensitive to long-term heat (sloh) mutants and isolated sloh3 and sloh63. The mutants were hypersensitive to L- but not to S-heat stress, and sloh63 was also hypersensitive to salt stress. We identified the causal genes, SLOH3 and SLOH63, both of which encoded splicing-related components of the MOS4-associated complex (MAC). This complex is widely conserved in eukaryotes and has been suggested to interact with spliceosomes. Both genes were induced by L-heat stress in a time-dependent manner, and some abnormal splicing events were observed in both mutants under L-heat stress. In addition, endoplasmic reticulum (ER) stress and subsequent unfolded protein response occurred in both mutants under L-heat stress and were especially prominent in sloh63, suggesting that enhanced ER stress is due to the salt hypersensitivity of sloh63. Splicing inhibitor pladienolide B led to concentration-dependent disturbance of splicing, decreased L-heat tolerance, and enhanced ER stress. These findings suggest that maintenance of precise mRNA splicing under L-heat stress by the MAC is important for L-heat tolerance and suppressing ER stress in Arabidopsis.

Natural genetic variation has facilitated the identification of genes underlying complex traits such as stress tolerances. We here evaluated the long-term (L-) heat tolerance (37°C for 5 days) of 174 Arabidopsis thaliana accessions and short-term (S-) heat tolerance (42°C, 50 min) of 88 accessions and found extensive variation, respectively. Interestingly, L-heat–tolerant accessions are not necessarily S-heat tolerant, suggesting that the tolerance mechanisms are different. To elucidate the mechanisms underlying the variation, we performed a chromosomal mapping using the F₂ progeny of a cross between Ms-0 (a hypersensitive accession) and Col-0 (a tolerant accession) and found a single locus responsible for the difference in L-heat tolerance between them, which we named Long-term Heat Tolerance 1 (LHT1). LHT1 is identical to MAC7, which encodes a putative RNA helicase involved in mRNA splicing as a component of the MOS4 complex. We found one amino acid deletion in LHT1 of Ms-0 that causes a loss of function. Arabidopsis mutants of other core components of the MOS4 complex—mos4-2, cdc5-1, mac3a mac3b, and prl1 prl2—also showed hypersensitivity to L-heat stress, suggesting that the MOS4 complex plays an important role in L-heat stress responses. L-heat stress induced mRNA processing–related genes and compromised alternative splicing. Loss of LHT1 function caused genome-wide detrimental splicing events, which are thought to produce nonfunctional mRNAs that include retained introns under L-heat stress. These findings suggest that maintaining proper alternative splicing under L-heat stress is important in the heat tolerance of A. thaliana.

Calcium (Ca²⁺) is a major ion in living organisms, where it acts as a second messenger for various biological phenomena. The Golgi apparatus retains a higher Ca²⁺ concentration than the cytosol and returns cytosolic Ca²⁺ to basal levels after transient elevation in response to environmental stimuli such as osmotic stress. However, the Ca²⁺ transporters localized in the Golgi apparatus of plants have not been clarified. We previously found that a wild-type (WT) salt-tolerant Arabidopsis (Arabidopsis thaliana) accession, Bu-5, showed osmotic tolerance after salt acclimatization, whereas the Col-0 WT did not. Here, we isolated a Bu-5 background mutant gene, acquired osmotolerance-defective 6 (aod6), which reduces tolerance to osmotic, salt, and oxidative stresses, with a smaller plant size than the WT. The causal gene of the aod6 mutant encodes CATION CALCIUM EXCHANGER4 (CCX4). The aod6 mutant was more sensitive than the WT to both deficient and excessive Ca²⁺. In addition, aod6 accumulated higher Ca²⁺ than the WT in the shoots, suggesting that Ca²⁺ homeostasis is disturbed in aod6. CCX4 expression suppressed the Ca²⁺ hypersensitivity of the csg2 (calcium sensitive growth 2) yeast (Saccharomyces cerevisiae) mutant under excess CaCl₂ conditions. We also found that aod6 enhanced MAP kinase 3/6 (MPK3/6)-mediated immune responses under osmotic stress. Subcellular localization analysis of mGFP-CCX4 showed GFP signals adjacent to the trans-Golgi apparatus network and co-localization with Golgi apparatus-localized markers, suggesting that CCX4 localizes in the Golgi apparatus. These results suggest that CCX4 is a Golgi apparatus-localized transporter involved in the Ca²⁺ response and plays important roles in osmotic tolerance, shoot Ca²⁺ content, and normal growth of Arabidopsis.