Agricultural Biotechnology Research Center, Academia Sinica

The semi-dwarf high-yielding rice (Oryza sativa) variety IR8 was the major modern line that gave rise to the “Green Revolution” in Asia approximately 60 years ago. Although the sd1 mutation in IR8 responsible for semi-dwarfism is well known, the sequence variation, evolutionary origins, and functional impacts of SD1 haplotypes remain incompletely characterized. By analyzing whole-genome sequences from the 3K Rice Genomes Project, Taiwanese landraces, and Asian wild rice, we classified SD1 into 12 haplotypes, including two newly identified loss-of-function alleles: a 1,279-bp deletion and an E100/R340 variant. Phylogenetic and nucleotide analyses traced the origins of several haplotypes, including the widely used 383-bp deletion (DGWG type), to the wild accession W1718 in southern China, from which they were later introgressed into landraces and subsequently brought to Taiwan. Protein structural modeling further revealed that distinct amino acid substitutions affect GA20ox-2 activity by altering the catalytic pocket or local protein stability. Screening of SD1 and Hd1 genotypes showed that most modern indica varieties carry loss-of-function alleles of both sd1 and hd1, reflecting strong post–Green Revolution selection for semi-dwarfism and early maturity. Our results clarify the evolutionary history and functional consequences of SD1 variation and highlight that the combined loss-of-function sd1–hd1 genotype was central to the development of high-yielding, lodging-resistant, and photoperiod-insensitive rice varieties. These findings provide a comprehensive framework for understanding key Green Revolution genes and offer guidance for future rice improvement and genome-editing strategies.

Phytosesquiterpene lactones deoxyelephantopin (DET) and its derivative DETD-35 are reported to induce oxidative stress towards inhibiting triple-negative breast cancer (TNBC) cell activities. This study aimed to elucidate how DET and DETD-35 affect mitochondrial function and systemic metabolism in TNBC cells. DET and DETD-35 promoted mitochondrial superoxide production by upregulating expression of SOD1 and SOD2, induced permeability transition pore opening, and attenuated intracellular ATP levels. Neither compound interfered with mitochondrial respiration/bioenergetics in normal mammary MCF-10A cells. Comparative mitochondrial proteome and bioinformatic analyses showed significant deregulation of proteins related to the oxidative phosphorylation, depolarization of mitochondria, and apoptosis signaling in DET- or DETD-35-treated TNBC cells, and primary metabolomics revealed that both compounds deregulated metabolites dynamics and the corresponding metabolic pathways in TNBC cells. Knockdown of the PRKCA gene/protein involved in inducing mitochondrial toxicity in TNBC cells reversed cytotoxicity, apoptosis, and the levels of several metabolites induced by DET or DETD-35 in the cancer cells. Integrated Pearson's correlation and IPA network analyses of differentially expressed proteins and metabolites revealed the networks of ATP synthesis, energy homeostasis, and respiration, depolarization, and transmembrane potential in mitochondria highly correlated to the compound effects. Notable, DET/DETD-35 inhibited mitochondrial ATPase activity, and molecular modeling further predicted the binding sites of either compound with ATP synthase at the subunits α/β and c/a interfaces. The overexpression of ATP synthase-related proteins ATP5A1 and ATP5C1 in the tumor microenvironment of MDA-MB-231 xenograft mice were also significantly suppressed by DET and DETD-35 treatments. In summary, this study identifies DETD-35 and DET as novel ATPase inhibitors which are attributed to disrupting mitochondrial biogenetics and cellular metabolism and networking in TNBC cells.

Rice roots develop aerenchyma, which transports oxygen from shoots to roots, facilitating adaptation to waterlogged conditions. This oxygen oxidizes ferrous ions into ferric compounds, forming iron plaque that mitigates iron toxicity. However, the molecular mechanisms linking aerenchyma and iron plaque formation remain poorly understood. Here we identified a rice mutant (AZ1302) defective in both aerenchyma and iron plaque formation, with the causal mutation mapped to the PHYTOENE SYNTHASE 2 (OsPSY2) gene. CRISPR–Cas9-induced psy2 mutants exhibited reduced levels of carotenoid-derived hormones, strigolactones and abscisic acid, in roots. In psy2 mutants, exogenous application of strigolactones rescued aerenchyma formation, while abscisic acid restored iron plaque deposition, providing evidence for distinct hormonal regulatory functions in the two processes. These findings revise the current understanding by dissociating the roles of aerenchyma and iron plaque formation, establishing a role for OsPSY2 in integrating hormonal signalling to drive root plasticity and offering new insights into plant adaptation under environmental stress.

Abstract Symbiotic associations enable species to integrate complementary traits and adapt to novel environments. However, how the host and endosymbiont exchange nutrients remains poorly understood in most cases. Previously Paramecium bursaria cells were shown to reorganize lipid droplets to accommodate endosymbiotic Chlorella cells and interfering with lipid metabolism reduced the endosymbiont number. Here, we combined transcriptomics, lipidomics, imaging mass spectrometry, and stable-isotope tracing to investigate organic nutrient exchange in this symbiotic system. Our results reveal that endosymbiotic algae undergo extensive reprogramming of lipid metabolic pathways and accumulate markedly higher levels of triglycerides than free-living algae. Isotope-labeling experiments demonstrate that at least some of these lipids originate from the host, providing direct evidence for organic carbon transfer from Paramecium to its algal endosymbionts. Together, our results show that the establishment of symbiosis fundamentally reshapes algal lipid metabolism and uncover an unexpected host-to-symbiont lipid provisioning mechanism—opposite to the canonical direction of carbon flow observed in most photosynthetic symbioses. This work provides new insight into the metabolic principles that sustain and stabilize endosymbiotic partnerships.

SUMMARYTransposable elements (TEs) significantly influence genomic diversity and gene regulation in plants. Brassica rapa and B. oleracea, with their distinct domestication histories, offer excellent models to explore TE dynamics. Here, we developed a refined TE classification method and systematically analyzed TEs across 12 B. rapa and B. oleracea genomes, identifying 1878 TE families. Approximately half (49.5%) of these TE families were shared between the two species, reflecting a common evolutionary origin, whereas species‐specific expansions, particularly among long‐terminal repeat (LTR) retrotransposons, underscore their roles in genomic differentiation. We notably characterized a heat‐responsive Ty1‐copia family (Copia0035) in B. oleracea roots, distinguished by low GC content and the absence of CG and CHG methylation motifs, sharing regulatory similarities with the Arabidopsis heat‐induced ONSEN element. Syntenic analyses of gene‐TE associations highlighted significant intraspecies TE insertion variability, with more accession‐specific insertions in B. rapa and more conserved insertions, often associated with distinct morphotypes in B. oleracea. Gene ontology enrichment indicated TE involvement in developmental, reproductive, and stress response pathways. Transcriptome analysis across diverse accessions revealed that genes proximal to TEs, particularly those regulating floral development and flowering time, exhibit increased expression variability. These findings advance our understanding of TE‐mediated genome evolution in Brassica species and underscore their potential utility in breeding and genome engineering strategies for crop improvement.

BackgroundCaenorhabditis elegans fed a high-glucose Escherichia coli OP50 diet exhibit reduced fecundity, but the underlying mechanisms remain unclear.MethodsA differential high-glucose diet paradigm was established using C. elegans fed two bacterial diets that produced distinct fecundity outcomes under high-glucose conditions. The effects of these diets in varying conditions were analyzed through transcriptomic, lipidomic, and metabolomic profiling to correlate with fecundity. Supplementation experiments were further performed to validate the links between changes in lipid metabolism and fecundity. By characterizing the gerlime phenotypes, we constructed a model to interpret how dietary inputs alter oogenesis signaling and, consequently, fecundity outcomes.ResultsC. elegans fed a high-glucose E. coli OP50 diet exhibit reduced fecundity, accompanied by disrupted lipid homeostasis characterized by decreased monounsaturated and increased cyclopropane fatty acids, reduced phosphatidylcholine and elevated triacylglycerols, and abnormal lipid droplet and vitellogenin accumulation in the intestine and oocytes. In contrast, worms fed a high-glucose Comamonas aquatica DA1877 diet maintain lipid balance and normal fecundity. We identified altered lipid metabolism strongly correlated with reproductive decline, whereas dietary signals from C. aquatica protected against glucose toxicity. Mechanistically, high-glucose diets appeared to rewire the choline–methionine axis, lowering PC levels and reducing RAS/ERK signaling in germline and gonadal sheath cells, thereby impairing oogenesis. Notably, vitamin B12 supplementation restored RAS/ERK signaling and rescued the diet-specific fecundity defects.ConclusionWe demonstrate that dietary cues under high-glucose conditions modulate a genetic network linking lipid homeostasis and signaling pathways, ultimately determining fecundity outcomes in C. elegans.

Outside Front Cover: The cover image is based on the article Optimised Ribosome Profiling Reveals New Insights Into Translational Regulation in Synchronised Chlamydomonas reinhardtii Cultures by Yen-Ling Lin et al., https://doi.org/10.1111/pce.15681.

• Developed an AIoT-enabled decision support system for precision irrigation management. • Using LSTM-based AI models, achieved 97–98 % accuracy in water stress detection. • Integrated PCA for dimensionality reduction of high-dimensional physiological datasets. • Utilised hyperspectral and point cloud data for robust crop water stress prediction. • Improved irrigation efficiency to promote sustainable agriculture under drought stress. Climate change has increased the severity of droughts, threatening global agricultural productivity. The implementation of information technology for enhancing smart agriculture has proven its great potential for supporting precision agriculture that can provide crops with the ability to defend themselves against environmental threats. Rice, which is a staple food crop in tropical and subtropical regions, is particularly sensitive to water stress during its critical growth stages. This study therefore focused on Tainung No. 67 rice, known for its drought resistance, to develop an intelligent AIoT-based plant watering decision support system. The proposed system aims to optimise water use and enhance agricultural resilience by integrating real-time monitoring, AI-driven analysis, and automated irrigation. Data were collected using hyperspectral imaging, point cloud analysis, and physiological indicators (measured by the LI-600 device), providing a comprehensive time-series dataset for model training. Principal component analysis (PCA) was used to reduce data dimensionality, and an LSTM-based AI framework was used to predict water stress severity. Experimental results showed high accuracy for all datasets, with the AI model achieving 97 % accuracy for point cloud data and 98 % accuracy for hyperspectral imagery. Scenarios with mixed missing data further validated the practicality and robustness of the system. This research highlights the potential to address drought-related challenges in agriculture through the integration of IoT, AI and advanced sensing technologies. The system not only optimises irrigation strategies but also contributes to sustainable farming practices through the preservation of water resources.

[[abstract]]In this article the affiliation details for Teng-Kuang Yeh were incorrectly given as “AltruBio Taiwan R&D Center, Taipei 114063, Taiwan” but should have been “Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Zhunan, Miaoli County 35053, Taiwan”. The original article has been corrected. In this article the e-mail address of the corresponding author Lun Kelvin Tsou was incorrect. The original article has been corrected.