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Main conclusion: Comparative metabolic profiling of new genetic multiple flavonoid r2r3-myb mutants show that different types of R2R3-MYBs activate the early flavonoid biosynthesis genes. A revised model for flavonoid biosynthesis in Arabidopsis thaliana is proposed that integrates the regulatory roles of these R2R3-MYBs across early and late biosynthetic steps. Flavonoids are a large group of specialized plant metabolites. Their biosynthesis is mainly transcriptionally regulated by a sophisticated network of different transcription factors from various families, with R2R3-MYB factors being the main determinant of specific flavonoid class formation. The early biosynthetic steps, leading to the formation of non-visible flavonoids, have been proposed to be regulated by three R2R3-MYBs, PRODUCTION OF FLAVONOL GYLCOSIDE1-3 (PFG1-3), while the later biosynthetic steps leading to the formation of visible anthocyanin and proanthocyanidin pigments are reported to be regulated by four R2R3-MYBs, PRODUCTION OF ANTHOCYANIN PIGMENT1-4 (PAP1-4) and TRANSPARENT TESTA2 (TT2), respectively. Several studies have indicated that this model for the transcriptional regulation of flavonoid biosynthesis may be incomplete. To address this issue, especially regarding the regulation of the early biosynthesis genes by PAP1-4 and TT2, we generated several multiple r2r3-myb mutant lines. We characterized the pfg1-3, pfg1-3 tt2 and pfg1-3 pap1-4 mutants and did comparative metabolite profiling. This revealed that only the pfg1-3 tt2 mutant was deficient in proanthocyanidins and only the pfg1-3 pap1-4 mutant was deficient in anthocyanins. We demonstrate that PAP and TT2 R2R3-MYBs are also capable of activating the early biosynthesis genes required for dihydroflavonol formation. Our results provide evidence that the traditional view of distinct branch-specific R2R3-MYB regulators in flavonoid biosynthesis is overly simplistic. We, therefore, propose a revised model for the transcriptional regulation of flavonoid biosynthesis.

Main conclusions: Giant genomes in Alstroemeria have maintained structural conservation for ~18.4 million years, whereas satellite DNA amplification and elimination constitutes the main dynamic force underlying heterochromatin diversification and longitudinal chromosomal differentiation. Repetitive sequences are major components of plant genomes and play key roles in genome size evolution and structural variation. Alstroemeria L. is a genus of monocotyledonous plants with giant genomes (1C ≈ 25 Gb), native to the Americas and distributed into two distinct lineages: the Brazilian/Argentinean clade and the Chilean grade. Despite their ancient separation and differences in heterochromatin distribution, all species share a highly conserved chromosome number (2n = 16), with only minor variation in chromosome morphology. Here, we characterized the repetitive DNA fraction of six Chilean species, one Argentinean species, and two Brazilian species, and mapped the most abundant repeats on representative chromosomes from each lineage. LTR Ty3/gypsy Tekay retrotransposons were the predominant repetitive elements, accounting for 30.63-39.91% of the genome across all analyzed species and largely explaining genome size variation. Notably, despite their giant size, Alstroemeria genomes exhibited a relatively low overall proportion of repetitive DNA (up to ~68%), consistent with slow repeat removal and the accumulation of degraded sequences, as predicted for genomes of this size. Satellite DNA represented 0.23-3.42% of the genome, with most satellite families shared between the Brazilian and Chilean species. Nevertheless, despite the divergence of the Brazilian lineage approximately 9.2 million years ago, marked differences in satellite abundance and chromosomal distribution were observed. Our results indicate that giant genome evolution in Alstroemeria is characterized by long-term conservation of karyotype structure and transposable element composition, whereas satellite DNA constitutes a key dynamic component associated with heterochromatin diversification and longitudinal chromosomal differentiation between the Chilean and Brazilian lineages.

Main conclusion: These results highlight irradiated Ch-NPs as a promising, eco-friendly, and sustainable component of integrated disease management strategies, offering a viable alternative to conventional chemical fungicides for controlling Fusarium oxysporum f. sp. sesami in sesame cultivation. Fusarium wilt, caused by Fusarium oxysporum f. sp. sesami, poses a major limitation to sesame productivity. To develop a more efficient control approach, chitosan nanoparticles (Ch-NPs) were synthesized and exposed to 24 kGy of gamma irradiation, a process that improves their structural uniformity and enhances their functional properties. The antifungal activity was tested under laboratory, greenhouse, and field conditions, either alone or in combination with Trichoderma reesei, Bacillus subtilis, and the commercial fungicide Maxim-XL. The nanoparticles were characterized using UV, FTIR, and TEM analysis. UV analysis confirmed the nanoparticle spectrum with a maximum absorbance at 224 nm. Using transmission electron microscopy, it was found that by gamma irradiation, Ch-NP size was reduced from 89.08-113.63 nm to 48.11-56.22 nm, which, in turn, made it more uniform and bioactive. Irradiated Ch-NPs (250 µL L⁻¹) demonstrated the ability of almost complete inhibition of F. oxysporum growth in vitro, along with controlling the disease incidence and severity in greenhouse and field tests, which is equal to that of Maxim-XL. Among the biological agents tried, T. reesei was the best in giving an antagonism of 76.3% inhibition. Treatment with irradiated Ch-NPs and T. reesei enhanced sesame growth and productivity, reflected in greater plant height, more capsules, and higher seed yield, and also elevated the activities of defense-related enzymes-peroxidase, polyphenol oxidase, chitinase, and phenylalanine ammonia-lyase. The study therefore sought to assess the effectiveness of gamma-irradiated chitosan nanoparticles, used in combination with biological control agents, as eco-friendly alternatives to chemical fungicides for managing the disease.

Main conclusion: Selaginella moellendorffii myosins retain conserved intracellular functions of known plant myosins, while lycophytes possess a unique myosin VIII with an extended neck domain. Research on plant myosins has primarily focused on model species, such as green algae, mosses, and seed plants. Here, we identified and cloned the myosin genes in Selaginella moellendorffii for the first time in the lycophytes. S. moellendorffii possessed two myosin XI genes and two myosin VIII genes. The cloned S. moellendorffii myosin (Sm myosin) VIII contained a neck domain approximately twice as long as those of previously identified plant myosin VIIIs. A BLASTP search using OneKP indicates that this myosin VIII is conserved throughout lycophytes. Transient expression of Sm myosin in Arabidopsis thaliana cultured cells and Nicotiana benthamiana leaves suggests that Sm myosin XI-2 is orthologous to A. thaliana myosin XI-K, which provides a motive force for cytoplasmic streaming. Sm myosin VIII was localized to the plasmodesmata, consistent with A. thaliana myosin VIII, ATM1 localization. This suggests the plasmodesmata-associated function of myosin VIII is conserved among vascular plants. Cis-regulatory elements and expression analyses further indicate that Sm myosin responds to environmental stress and participates in spore reproduction. Cumulatively, the intracellular and physiological functions of plant myosins are highly conserved in land plants, whereas myosin VIII exhibits structural characteristics unique to lycophytes. These findings provide valuable insights into the conservation and diversification of plant myosins, contributing to a better understanding of their evolutionary dynamics in vascular plants.

Main conclusion: Over 2 decades ago, antisense rbcS tobacco lines with a progressive decrease in Rubisco abundance allowed network analysis of the regulation of photosynthesis, metabolism, and whole plant allocation. In the 1970 and 1980s, the study of the regulation of metabolism and growth was largely descriptive. Conceptual frameworks had been formulated that would allow a more rigorous approach, for example, to generate a small decrease in enzyme abundance and measure the resulting change in pathway flux. The lack of suitable mutants, however, made this approach practically impossible. This changed drastically when Agrobacterium-mediated transformation made it possible to alter expression of enzymes and other proteins at will. (Quick et al. in Planta 183:542-554, 1991a) and subsequent papers used antisense lines with a progressive decrease in Rubisco abundance to show that the contribution of Rubisco to the control of photosynthesis varies greatly, depending on the conditions in which photosynthesis is occurring and the conditions in which the plants had been grown. Analogous experiments by us and others on other Calvin-Benson cycle enzymes showed that they could also exert control and that the distribution of control depended on the conditions. We also used the rbcS antisense lines to, first, show that small decrease in Rubisco abundance is often accommodated by the photosynthetic apparatus to minimize the inhibition of photosynthesis and, second, explore how a larger decrease in Rubisco abundance and the resulting inhibition of photosynthesis impacts on central carbon and nitrogen metabolism, specialized metabolism, and whole plant architecture. This approach anticipated future developments like network analysis and system biology, is still relevant to designing strategies to improve crop photosynthesis, and can provide insights into photosynthetic performance and trade-offs in the field in a fluctuating environment.

Main conclusion: Weeds, especially purple nutsedge, are not just alternative hosts but highly susceptible host that drive the persistence and spread of rice root-knot nematodes. This study provides a comprehensive assessment of the host status of eight plant species, including rice and common rice-associated weeds, to the root-knot nematode Meloidogyne graminicola. By integrating quantitative infection assays with confocal laser scanning microscopy, we combined whole-plant measurements of nematode development with cellular-level visualization of feeding-site structures to characterize host suitability more precisely. The results revealed a continuum of responses ranging from weakly supportive to highly susceptible hosts. Purple nutsedge (Cyperus rotundus) showed the highest susceptibility under controlled conditions, with a reproduction factor (Rf = 77.25) exceeding that of rice (Oryza sativa, Rf = 15.45) and jungle rice (Echinochloa colona, Rf = 19.81). Digitaria sanguinalis also supported considerable nematode multiplication (Rf = 10.92). Confocal imaging provided temporal snapshots of feeding-site formation, giant cell development and gall progression in C. rotundus, complementing the quantitative findings. Several species, including Glinus oppositifolius and Stellaria media, supported minimal development, indicating limited suitability as hosts. Overall, the study demonstrates that multiple weeds commonly present in rice ecosystems can sustain M. graminicola development to varying degrees under experimental conditions. These results highlight the importance of considering weed species when evaluating nematode population dynamics and designing integrated management strategies for rice-based agroecosystems.

Over 50% of global arable soils are acidic; acidic soil-induced aluminum (Al) phytotoxicity primarily inhibits root elongation, thereby reducing the plant's absorption of water and nutrients, which suppresses crop yield. Gibberellic acid (GA), a class of critical plant hormones, acts as a core regulator of plant development and growth mechanisms and contributes to the physiological adaptation of plants under stress conditions. In this study, we selected the rice variety Nipponbare (Nip) to investigate whether GA exerts an effect on alleviating Al toxicity and to explore the underlying mechanisms in rice. This study shows that Al stress quickly elevated the endogenous GA content in rice root tissues, consequently alleviating Al-induced suppression of root development. Exogenous GA application increased the expression of the Oryza sativa Cysteine-rich Peptide (Peptide with Cysteine-rich TDIF motif) 3 (OsCDT3) and Oryza sativa Ferric Reductase Defective Like 4 (OsFRDL4) genes, which reduce the toxicity of Al to plants and conversely decreased the expression of the Oryza sativa Natural Resistance-Associated Macrophage Protein 1 for Aluminum Transport (OsNRAT1) gene, which transports Al ions from the extracellular environment to the intracellular space. Furthermore, exogenous GA treatment modified the hemicellulose and pectin levels, therefore decreasing the absorption of Al. Further research shows that GA reduced the endogenous nitric oxide (NO) levels; nevertheless, the application of an exogenous nitric oxide donor sodium nitroprusside (SNP) offset the alleviatory role of GA. In conclusion, GA accelerated the cell wall Al exclusion mechanism, probably improving rice tolerance to Al toxicity via regulating the accumulation of NO.

Nitrogen (N) is an essential macronutrient that plays a central role in photosynthesis, metabolism, and crop productivity. Accurate and non-destructive evaluation of plant N status is essential for improving N use efficiency and sustainable fertilization. Bioimpedance spectroscopy (BIS) has emerged as a promising tool for in vivo assessment of plant physiological state; however, its application to nutrient monitoring remains limited. Previous studies show that N deficiency significantly alters extracellular and intracellular fluid resistances and reduces cell membrane capacitance, reflecting impaired ion conductivity, loss of membrane integrity, and changes in vacuole storage. These alterations can be detected in vivo within specific frequency ranges and often correlate with leaf N content, but most studies considered only total N and did not account for inorganic nitrate (NO₃⁻) forms or water-related effects. Future research should combine BIS with direct apoplastic NO₃⁻ measurements and factorial N and water experiments to distinguish nutrient-specific responses from drought-induced changes. Applying advanced equivalent circuit models, such as the Double-Shell (DBS) model, could strengthen physiological interpretation and associate impedance parameters with cellular functions. Addressing these issues will enable BIS to become a reliable, non-destructive diagnostic method for N monitoring.

Key message: This study characterizes wild-type and mutants of rice for culm strength at morphological, histological, and molecular levels, identifying key genes and genomic regions that govern the strong culm trait. Strong culm trait in rice has gained importance for sustainability in the realm of climate change. The mutants having economic important traits have become a potential source for the identification of genomic regions. The present study aimed to characterize rice mutants having strong culms and to identify genomic regions through conventional as well as NGS-based mapping approaches. Morphological characterization of Samba Mahsuri mutants with strong culms showed that they had a greater culm diameter and physical strength than the wild type. Histological analysis confirmed the morphological parameters, which included increased thickness in culm tissue, wider intervascular bundle spacing, and thicker lignified epi- and sub-epidermal layers, as well as parenchymal layers. Exploring one of the chemically mutagenized Samba Mahsuri mutants, SB170-B having strong culm, a genetic linkage map was constructed and identified four novel QTLs: qSC-5 (chromosome 5), qSC-6a (chromosome 6), qSC-6b (chromosome 6), and qSC-10 (chromosome 10), explaining 23.76%, 21.60%, 15.40%, and 40.50% of the phenotypic variance for strong culm, respectively. MutMap, an NGS-based analysis of the weak and strong culm pools from the F₂ population derived from SB170-B×BPT 5204, also identified a genomic region (27.0-29.6 Mb) which was corresponding to the qSC-5. This genomic region comprised of 17 genic SNPs, which converted into kompetitive allele-specific PCR (KASP) assays. Among those, one KASP marker, KASP 5-2 (chr5:27972606; C/T), located in the gene LOC_Os05g48810, which encodes a DNA/J-binding protein was shown strong co-segregation with the strong culm trait, indicating its potential to use in improvement of strong culm trait through molecular breeding.