Hokkaido is located in a subarctic area of Japan, where attempts have been made to produce leafy vegetables with high Brix values in winter under cold-stress conditions. Kale has recently become popular due to its high nutritional value. ‘Winterbor’, a cold-tolerant cultivar of borecole, a type of kale, grows without any cold stress damage in unheated plastic greenhouses at temperatures as low as −7°C. In this study, it was found that the growth rate of ‘Winterbor’ in winter was less than that of the collard kale cultivar ‘Hi-Crop’ and had a higher dry matter ratio and Brix value. The air temperature within the greenhouse was lowered by approximately 2°C by removing some of the insulation layer on the greenhouse under the winter cultivation. As a result, neither leaf emergence nor overall plant weight was affected. As the air temperature continued to fall with the approach of winter, the dry matter ratio, Brix value, and sucrose content increased in ‘Winterbor’ leaves. The dry matter ratio, Brix value, and combined content of fructose, glucose, and sucrose tended to be higher under cold management (less insulation) than under standard management. Statistical analysis based on the air temperature conditions during the cultivation period indicated that leaf emergence and plant weight reached constant values at approximately 5°C and 3°C daily mean air temperature, respectively. However, the dry matter ratio, Brix value and total soluble sugar content (three soluble sugars) increased by 1.1%, 1.1, and 7.3 mg·g⁻¹ fresh weight (FW) with every 1°C drop from the average daily minimum air temperature for 10 days before harvest, starting at approximately 6°C. These results suggest the possibility of estimating and controlling borecole plant growth and quality parameters and could contribute to the systematic production and distribution of highly valuable borecoles grown in unheated plastic greenhouses in winter in Hokkaido.

The domestication of chili peppers (Capsicum spp.) across diverse environments has generated a wide range of cultivars that constitute valuable reservoirs of allelic diversity. Single nucleotide polymorphism (SNPs) markers are particularly useful for characterizing this diversity due to their high abundance in plants and environmental stability. However, the latest methods such as multiplexed inter-simple sequence repeats genotyping by sequencing (MIG-seq) and genotyping by sequencing (GBS) face limitations in terms of efficiency and costs, respectively. To address these challenges, we applied the novel, cost-effective, degenerate oligonucleotide primer MIG-seq (dpMIG-seq) method to assess genetic diversity in 65 Capsicum accessions from South America and Asia, representing C. annuum, C. chinense, C. frutescens, and C. baccatum. Sequencing generated a total of 78,673 SNPs, of which 11,557 high-quality markers were retained. Principal component analysis and neighbor-joining phylogenetic method resolved two major genetic pools corresponding to C. annuum and C. baccatum complexes, further dividing the collection into four clusters. C. baccatum formed a distinct branch, while C. chinense and C. frutescens occupied intermediate positions, suggesting their potential role as genetic bridges between C. annuum and C. baccatum. Population structure analysis (K = 5) confirmed species-level clustering and revealed admixture among C. frutescens and C. chinense for unclassified Capsicum spp. accessions. Because of the overall low interspecific gene flow, it is necessary to incorporate novel alleles into breeding programs. Using dpMIG-seq for SNP discovery and genetic analysis in Capsicum expands the study of phylogenetic relationships, germplasm characterization, and breeding strategies for crop improvement and biodiversity conservation.

This study investigated the effects of chitosomes, sweet basil oil, and sweet basil oil-chitosomes on oxidative stress and disease resistance in ‘Nam Dok Mai No. 4’ mangoes stored at room temperature (27 ± 2°C) for 8 days. Untreated fruits developed disease rapidly, with incidence reaching 100% by day 6, while all treatments delayed symptom development. Notably, sweet basil oil-chitosomes completely suppressed disease throughout storage. Hydrogen peroxide (H₂O₂) levels increased sharply in control and chitosome-treated fruits, while sweet basil oil and its encapsulated form significantly reduced H₂O₂ accumulation, with the encapsulated treatment maintaining the lowest levels in both peel and pulp. Both treatments slowed a decline in total phenolic content and ascorbic acid, with sweet basil oil-chitosomes offering the most effective preservation. Antioxidant enzyme activities (catalase and ascorbate peroxidase) were lowest in controls, moderately increased by chitosomes, and strongly enhanced by sweet basil oil. The encapsulated treatment showed the highest enzyme activities, with 4.02- and 8.02-fold increases in peel, and 10.8- and 4.96-fold increases in pulp. Pearson’s correlation indicated that sweet basil oil-chitosomes most effectively stabilized the antioxidant network and minimized oxidative stress, followed by chitosomes and free basil oil, while the control exhibited the weakest defense, consistent with its higher anthracnose susceptibility. Principal component analysis further confirmed that sweet basil oil-chitosomes offered the greatest protection by sustaining both enzymatic and non-enzymatic antioxidants. These results demonstrate that sweet basil oil-chitosomes, as an innovative nanocarrier delivery system, offer a promising natural strategy for enhanced postharvest disease management and quality preservation in mangoes.

DNA methylation is a key epigenetic modification essential for gene regulation, transposable element (TE) silencing, and genome stability. Genome-wide methylation profiling is now widely used in plant research, with whole-genome bisulfite sequencing (WGBS) being the most established method. However, bisulfite treatment can degrade DNA and introduce coverage bias. The recently developed enzymatic methyl-seq (EM-seq) minimizes DNA damage, while Oxford Nanopore Technologies (ONT) nanopore sequencing allows direct detection of methylated bases via ionic current shifts. Here, we applied WGBS, EM-seq, and ONT to identical genomic DNA extracted from an inbred line of Brassica rapa and compared methylation profiles across platforms. ONT exhibited the highest mapping rate and the most uniform genome coverage, especially in repetitive and GC-rich TE regions. WGBS showed biased coverage toward highly methylated regions, whereas EM-seq achieved the highest cytosine site depth despite the lowest mapping rate. Non-conversion analysis confirmed extremely low rates for both WGBS and EM-seq, while ONT showed a high false-positive rate for methylation calling, highlighting the need for improved signal-processing models. Although genome-wide methylation trends were broadly similar across platforms, ONT consistently reported lower CHH methylation levels in TE-rich heterochromatin. This likely reflects more accurate mapping in repetitive regions by ONT long reads, in contrast to WGBS’s overestimation in non-CG contexts. Pairwise correlation was high between WGBS and EM-seq, but substantially lower for ONT, particularly at CHH sites. Differentially methylated region (DMR) analysis further emphasized platform-specific biases, with the largest number of DMRs detected between WGBS and ONT. Together, our results highlight the distinct strengths and limitations of each platform and provide practical guidance for selecting optimal methylome profiling methods in future epigenomic studies of horticultural crops.

Optimizing both the fresh weight of the bulb and the overall yield is crucial to achieve profitable onion production. This study aimed to examine the effects of cultivar, plant density, and the amount of light interception on bulb weight and total yield. Two yellow onion cultivars, ‘Momiji No. 3’ and ‘Totana’, were grown at plant densities ranging from 10.4 to 31.2 plants per m² (with plant spacings of 24, 16, 12, and 8 cm at a fixed row spacing of 24 cm) over two years. Bulb fresh weight increased as plant spacing widened, whereas total yield per unit area increased with plant density. This shows a trade-off between individual bulb size and yield. ‘Totana’ consistently produced larger bulbs and higher yield than ‘Momiji No. 3’ at each plant density. For both cultivars, regardless of plant density, the amount of integrated light interception post-transplantation strongly correlated with bulb fresh weight and dry matter production. High light interception is driven primarily by a greater leaf area index (LAI) and canopy development. Among tested conditions, plant densities of 10.4–20.8 plants per m², with plant spacings of 24, 16, and 12 cm, in ‘Totana’ provided the optimal balance between bulb weight and yield, with bulbs exceeding 300 g per plant and total yields surpassing 4.0 kg·m⁻². For ‘Momiji No. 3’, wider plant spacing (16–24 cm) increased bulb weight, and bulbs exceeding 300 g may be achieved under favorable environmental conditions. The results of this study suggest that optimizing the combination of cultivar selection and plant density, while considering light interception capacity, can simultaneously improve bulb size and yield under field conditions.

In terms of the sensory characteristics of tomato, fruit texture is important for consumer acceptance. The fruit texture can be measured with instruments like texture profile analyzers or through sensory evaluation, and depends on several factors, including salt stress and cultivar. Additionally, alterations in pectin composition and metabolizing enzymes contributes to changes in fruit texture. However, cultivar differences regarding pectin content and pectin-metabolizing enzymes, the effect of salt stress on fruit texture and their relationships are often overlooked. This study tested whether the effect of salt stress on consumers’ evaluation of hardness, fruit texture, and pectin metabolism varied between three tomato cultivars; a cherry-type ‘cf Kosuzu’, a large-type ‘cf Momotaro Fight’, and a medium-large type ‘Celeb Sweet’. Salt stress was applied by adding 100 mM NaCl to the nutrient solution. The salt-induced changes in consumer evaluations of hardness and fruit texture depending on the cultivar; the evaluation of the large tomato type was higher than that of the cherry and medium-large types. Salt-stressed fruits of the large type exhibited increased pectin content and pectin-metabolizing enzymes, including pectin methylesterase (PME) and polygalacturonase (PG), compared to the cherry and medium-large types. Additionally, in a correlation network, PME and PG were connected by the consumers’ evaluations of hardness. Our results indicate that consumers’ evaluation of hardness, texture profile, and pectin metabolism varied across the three tomato cultivars. We infer that salt stress had a greater impact on the texture attributes of large-type fruits. Furthermore, pectin metabolism may contribute to cultivar variations in the effects of salt stress on fruit texture and the sensory evaluation of hardness.

In Japan, wholesale prices of strawberries fluctuate markedly, making the timing of peak harvest with periods of high market value a critical issue. Consequently, there is a strong demand for technologies that enable harvest control. We aimed to achieve harvest control with fruit maturation management using environmental control. Harvest control requires accurate prediction of fruit yield, which predicts fruit size and harvest date. In this study, we focused on predicting fruit size. To construct an early prediction model of fruit size as the foundation for harvest control decisions, we attempted predictions using only floral and environmental parameters available at the time of flowering. From the collected parameters, variable selection based on the variance inflation factor was performed to mitigate the effects of multicollinearity. To avoid overfitting, a 4-fold cross-validation was applied, and a multiple regression model was constructed to predict fruit weight. As a result of variable selection, six parameters were selected as explanatory variables: flowering order within the inflorescence, receptacle area, pedicel diameter, flowering day, average air temperature, and direction of inflorescence. The multiple regression model achieved an R² of 0.775. Additionally, the feasibility of substituting future temperature data with historical data or target set-point temperatures was demonstrated. Furthermore, a flower thinning experiment showed that the influence of post-flowering source–sink balance on fruit size was minimal, indicating that it does not need to be incorporated into the model. These results demonstrate that fruit size can be predicted with reasonable accuracy using data available at flowering, and will play an important role in early yield prediction systems that will be developed in the future.

Uncontrolled lighting, occlusion, and variations in viewing angles make it difficult to perform high-frequency, non-destructive monitoring of grape (Vitis vinifera L.) berry growth in the field. Instead of tracking absolute millimeter-level size, a biology-informed pipeline based on YOLOv8 to track relative growth trends is presented. A biology-informed, monotonicity-constrained smoothing step (F-smoothed) is integrated into a workflow that also includes object detection, pixel-to-centimeter conversion using an in-frame 1-cm ruler, preliminary smoothing (outlier removal, interpolation, moving average), and double-sigmoid fitting to summarize phase timing. Images of the ‘Kerner’ and ‘Zweigelt’ clusters in Yoichi, Hokkaido (2024 season; 10 clusters; 1–3-day intervals) were examined as a field case study. On a hold-out validation set, the trained YOLOv8s model demonstrated stable identification (mAP50 = 0.931; mAP50–95 = 0.704; Precision = 0.906; Recall = 0.875). In an independent laboratory validation using detached berries from the 2025 season imaged on a white background, image-derived diameters closely agreed with manual caliper measurements over a range of approximately 0.3–2.3 cm (n = 89; mean absolute error = 0.08 cm; root mean square error = 0.09 cm; mean absolute percentage error = 7.2%; bias = +0.07 cm; R² = 0.97). Biologically credible trajectories were obtained by applying F-smoothed, averaged cultivar curves followed a double-sigmoid pattern with clear timing features. Such relative temporal indicators are directly relevant for viticultural decisions such as scheduling field inspections and harvest windows and for designing sampling strategies for berry composition and quality. Although destructive sampling of the 2024 field clusters was not undertaken, the combination of a validated measurement module and biology-informed smoothing provides reliable phase timing and relative trend tracking in real-world scenarios. With only a handheld camera and conventional computing, this approach offers a practical methodology for non-destructive growth monitoring that emphasizes temporal dynamics while retaining interpretable links to physical berry size.