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.

BackgroundThis study explores the continuity and transformation of wild plant foraging practices in Biella, Piedmont (northwestern Italy), over the past 55 years. The aim was to assess how cultural, economic, and environmental shifts have shaped local ethnobotanical knowledge and practices, using a 1970 survey as a baseline for comparison. Ethnobotanical fieldwork was conducted with 15 local informants to document current wild plant uses for food and herbal teas.ResultsThe resulting dataset of 82 species was compared with a historical record of 93 species to identify patterns of continuity, loss, and innovation. Three main patterns emerged: (1) the disappearance of certain traditionally foraged plants, not due to ecological absence but largely because of socio-economic changes like the decline of pastoralism and the loss of daily interaction with mountain environments (2) the emergence of new foraging practices involving species that grow near settlements, linked to evolving lifestyles and land use; and (3) a relatively robust preservation of traditional ecological knowledge when compared to other Alpine areas. This resilience is attributed to the area’s geographic marginality, the socio-economic aftermath of the textile industry’s collapse, and the strength of local traditions such as home gardening and communal land use.ConclusionWild plant foraging remains a living tradition in Biella, marked by both persistence and adaptation. The findings underscore the dynamic nature of ethnobotanical knowledge and its potential role in sustainability, food security, and cultural heritage preservation amid rural and peri-urban change.

Trechispora (Hydnodontaceae) comprises a diverse group of wood- and soil-inhabiting fungi, primarily functioning as saprotrophs, with some species forming symbiotic associations with plants and animals. Despite the recognition of over 100 species worldwide, its diversity in Taiwan remains understudied. This study presents the first comprehensive taxonomic revision of Trechispora in Taiwan, integrating morphological and phylogenetic analyses based on sequence data from the nuc rDNA internal transcribed spacer ITS1-5.8S-ITS2 (ITS) region and the nuc 28S rDNA (28S). We describe four new species (Trechispora acerosa, T. floralis, T. formosana, and T. orchidophila) and report seven newly recorded species for Taiwan (T. crystallina, T. dentata, T. latehypha, T. mollusca, T. odontioidea, T. subsinensis, and T. wenshanensis). T. sinensis is synonymized under T. odontioidea. Morphological and phylogenetic analyses support their taxonomic placements, and an identification key to accepted Trechispora species in Taiwan is provided. This study expands the known diversity of Trechispora in Taiwan to 17 species, highlighting their ecological significance and potential interactions with plants in Taiwan's forest ecosystems.

AlphaFold 3 (AF3), an artificial intelligence (AI)-based software for protein complex structure prediction, represents a significant advancement in structural biology. Its flexibility and enhanced scalability have unlocked new applications in various fields, specifically in plant science, including improving crop resilience and predicting the structures of plant-specific proteins involved in stress responses, signalling pathways, and immune responses. Comparisons with existing tools, such as ClusPro and AlphaPulldown, highlight AF3’s unique strengths in sequence-based interaction predictions and its greater adaptability to various biomolecular structures. However, limitations persist, including challenges in modelling large complexes, protein dynamics, and structures from underrepresented plant proteins with limited evolutionary data. Additionally, AF3 encounters difficulties in predicting mutation effects on protein interactions and DNA binding, which can be improved with molecular dynamics and experimental validation. This review presents an overview of AF3’s advancements, using examples in plant and fungal research, and comparisons with existing tools. It also discusses current limitations and offers perspectives on integrating molecular dynamics and experimental validation to enhance its capabilities.

BackgroundDue to global warming and gradual climate change, plants are subjected to a wide range of environmental stresses, adversely affecting plant growth and production worldwide. Plants have developed various mechanisms to overpower these abiotic stresses, including salt stress, drought, and high light intensity. Apart from their own defense strategies, plants can get help from the beneficial endophytic bacteria inside host plants and assist them in enduring severe growth conditions. A previously isolated plant endophytic bacteria, Burkholderia seminalis 869T2, from vetiver grass can produce auxin, synthesize siderophore, and solubilize phosphate. The B. seminalis 869T2 can colonize inside host plants and increase the growth of bananas, Arabidopsis, and several leafy vegetables.ResultsWe further demonstrated that different growth parameters of Arabidopsis and pak choi plants were significantly increased after inoculating the B. seminalis 869T2 under normal, salt, and drought stress conditions compared to the mock-inoculated plants. Both transcriptome analysis and quantitative real-time PCR results showed that expression levels of genes related to phytohormone signal transduction pathways, including auxin, gibberellin, cytokinin, and abscisic acid were altered in Arabidopsis plants after inoculated with the strain 869T2 under salt stress, in comparison to the mock-inoculated control with salt treatments. Furthermore, the accumulation levels of hydrogen peroxide (H2O2), electrolyte leakage (EL), and malondialdehyde (MDA) were lower in the 869T2-inoculated Arabidopsis and pak choi plants than in control plants under salt and drought stresses.ConclusionsThe plant endophytic bacterium strain B. seminalis 869T2 may affect various phytohormone responses and reduce oxidative stress damage to increase salt and drought stress tolerances of host plants.

BackgroundLarge-scale coral bleaching events have become increasingly frequent in recent years. This process occurs when corals are exposed to high temperatures and intense light stress, leading to an overproduction of reactive oxygen species (ROS) by their endosymbiotic dinoflagellates. The ROS buildup prompts corals to expel these symbiotic microalgae, resulting in the corals’ discoloration. Reducing ROS production and enhancing detoxification processes in these microalgae are crucial to prevent the collapse of coral reef ecosystems. However, research into the cell physiology and genetics of coral symbiotic dinoflagellates has been hindered by challenges associated with cloning these microalgae.ResultsA procedure for cloning coral symbiotic dinoflagellates was developed in this study. Several species of coral symbionts were successfully cloned, with two of them further characterized. Experiments with the two species isolated from Turbinaria sp. showed that damage from light intensity at 340 μmol photons/m2/s was more severe than from high temperature at 36 °C. Additionally, preincubation in high salinity conditions activated their endogenous tolerance to bleaching stress. Pretreatment at 50 ppt salinity reduced the percentage of cells stained for ROS by 59% and 64% in the two species under bleaching stress compared to those incubated at 30 ppt. Furthermore, their Fv’/Fm’ during the recovery period showed a significant improvement compared to the controls.ConclusionsThese findings suggest that intense light plays a more important role than high temperatures in coral bleaching by enhancing ROS generation in the symbiotic dinoflagellates. The findings also suggest the genomes of coral symbiotic dinoflagellates have undergone evolutionary processes to develop mechanisms, regulated by gene expression, to mitigate damages caused by high temperature and high light stress. Understanding this gene expression regulation could contribute to strengthening corals’ resilience against the impact of global climate change.

BackgroundTrichoderma species, known as biocontrol agents against plant diseases, contain diverse compounds, especially terpenoids, with various bioactivities. To facilitate the exploration of bioactive secondary metabolites of Trichoderma harzianum NTU2180, the OSMAC approach MS/MS molecular networking was applied in the current study.ResultsThe feature-based molecular networking (FBMN) analysis showed that T. harzianum NTU2180 fermented on germinated brown rice (GBR) produced more terpenoids. Here, two new acorane-sesequiterpenes, trichospirols A (1) and B (2), and 12 known compounds (3 − 14) were isolated from the EtOAc layer of T. harzianum NTU2180 fermentation on GBR. Structures of these compounds were determined through NMR, UV, IR, and MS analyses. The absolute configuration of trichospirols A (1) was also elucidated by x-ray with Cu K-α radiation. Among them, six compounds (1, 2, 3, 4, 5, and 11) were annotated as terpenoids by the NPClassifier on FBMN. 5-Hydroxy-3-hydroxmethyl-2-methyl-7-methoxychromone (7) and ergosterol peroxide (11) showed significant anti-angiogenic activity in ex vivo experiments with respective 0.57 ± 0.12- and 0.20 ± 0.12-fold changes. In addition, compound 11 displayed cytotoxicity against Y79 retinoblastoma cells with IC50 value of 35.3 ± 6.9 µM.ConclusionsThe current study utilizes FBMN concept with OSMAC approach to accelerate the exploration of potential metabolites of the fungus Trichoderma harzianum NTU2180. Through a series of FBMN-guided isolation and purification, two new acorane-sesequiterpenes and 12 known compounds were obtained. The ex vivo and in vitro experiments were evaluated to assess anticancer isolates. It is worth noting that compound 11 was identified as a dual inhibitor targeting both angiogenesis and proliferation of retinoblastomas. Altogether, the results revealed the novel potential of T. harzianum for developing natural therapeutics against retinoblastomas.

BackgroundThe research aims to assess the effectiveness of artificial intelligence models in predicting the risk level in tulip greenhouses using different varieties. The study was conducted in 2022 in the Almaty region, Panfilov village.ResultsTwo groups of 10 greenhouses each (area 200 m2) were compared: the control group used standard monitoring methods, while the experimental group employed AI-based monitoring. We applied ANOVA, regression analysis, Bootstrap, and correlation analysis to evaluate the impact of factors on the risk level. The results demonstrate a statistically significant reduction in the risk level in the experimental group, where artificial intelligence models were employed, especially the recurrent neural network “Expert-Pro.” A comparison of different tulip varieties revealed differences in their susceptibility to risks. The results provide an opportunity for more effective risk management in greenhouse cultivation.ConclusionsThe high accuracy and sensitivity exhibited by the “Expert-Pro” model underscore its potential to enhance the productivity and resilience of crops. The research findings justify the theoretical significance of applying artificial intelligence in agriculture and its practical applicability for improving risk management efficiency in greenhouse cultivation conditions.

BackgroundThe button mangrove (Conocarpus erectus L.) is regarded as a peripheral species within mangrove communities. This particular species has the ability to thrive in regions that are arid or semiarid, where there is limited availability of nutrients. This study provides evidence of the ecological dominance of Conocarpus erectus across various habitats, highlighting its adaptability and success throughout the country of Pakistan. We collected twelve populations from four distinct ecological regions, including artificial forest plantations, agricultural fields, roadsides, and wastelands, offering a comprehensive assessment of C. erectus adaptability across diverse environmental contexts.ResultsForest plantation populations exhibited impressive shoot growth and moderate root lengths, with plants generally tall and well-weighted. Physiologically, they had moderate chlorophyll content and low carotenoid levels, with a balanced chlorophyll a/b ratio, indicating stable photosynthetic activity. Anatomically, these populations had thicker epidermal and cortical root layers but smaller vascular bundles and phloem regions. Stem and leaf structures were generally moderate in size, with thicker midribs and cortical layers in the leaves. Agricultural field populations showed robust shoot and root systems with balanced fresh and dry biomass. They exhibited high chlorophyll and carotenoid levels, indicating strong photosynthetic capacity. Root and stem anatomy revealed larger root areas, thicker cortex, and wide vascular bundles, reflecting enhanced structural development. Leaves from these populations had moderate midrib and cortical thickness, with larger stomatal areas, promoting efficient gas exchange. Roadside populations displayed deeper roots and reduced biomass production. These populations adapted to environmental stress through leaf expansion, with high leaf numbers and areas. Physiologically, populations had high chlorophyll content, with a high chlorophyll a/b ratio. Root and stem anatomy showed compact structures with smaller vascular bundles, indicating adaptation to harsher conditions. Leaf anatomy was moderate, with smaller vascular bundles and reduced water transport capacity. Wasteland populations exhibited poor growth and high shoot biomass despite small leaves. Physiologically, these populations had the highest total soluble protein and proline contents, reflecting stress adaptation. Anatomically, root and stem structures were variable, with some populations showing reduced cortical cell areas and smaller vascular bundles, indicating limited resource transport. Leaf structures had thicker lamina, thinner epidermal layers, and lower stomatal densities, reflecting adaptation to nutrient-poor soils.ConclusionThis study reveals the adaptability and thriving potential of Conocarpus erectus across varied habitats, providing key insights into its resilience and survival strategies. Understanding these adaptive traits can support habitat restoration, conservation planning, and improve species management in diverse environmental conditions, especially in response to climate change and habitat degradation.

BackgroundThe tropical legume Mucuna pruriens (L.) DC. can meet three agricultural needs: low-cost protein, high-value medicines, and green manure or cover crops. But like other underutilized crops, it needs more modern breeding resources. Identifying marker-trait associations (MTAs) can facilitate marker-assisted breeding and crop improvement. Recent studies have demonstrated the feasibility of identifying MTAs using a small number of accessions (< 100). We have characterized a panel of 70 M. pruriens accessions across two consecutive years and performed association analysis for 16 phenotypic traits related to seed (seed length, seed width, seed thickness, seed yield per plant, hundred seed weight); pod (pod length, pod width, number of pods per cluster, number of pods per plant); inflorescence (inflorescence length, flower buds per inflorescence, flower length, pedicel length), and biochemical attributes (L-DOPA, total protein, total carbohydrate), using 66 genic-microsatellite markers following mixed linear model.ResultsThe results showed significant phenotypic (P < 0.05) and genetic diversity (Shannon’s information index, I = 0.62) in our germplasm collection. Many tested traits were highly heritable (broad-sense heritability ranging from 42.86 to 99.93%). A total of 15 MTAs was detected at an adjusted significance level of P < 5.55 × 10− 3 for nine traits (seed length, seed thickness, seed width, hundred seed weight, seed yield per plant, inflorescence length, flower buds per inflorescence, flower length, and petiole length), contributed by 10 SSR markers (MPU_19, MPU_42, MPU_54, MPU_57, MPU_58, MPU_83, MPU_89, MPU_108, MPU_111, and MPU_122.) with phenotypic variance explained (PVE) ranging from 14.7 to 31.1%. Out of the ten trait-associated markers, the BLAST analysis revealed putative functions of seven markers, except MPU_57, MPU_58, and MPU_83.ConclusionFifteen MTAs identified for important traits with phenotypic variance explained > 10% from mixed linear model offer a solid resource base for improving this crop. This is the first report on association mapping in M. pruriens and our results are expected to assist with marker-assisted breeding and identifying candidate genes in this promising legume.