Tomato (Solanum lycopersicum) is a premier global crop, celebrated not only for its economic importance but also as a fundamental “well-being food” that provides essential vitamins, minerals, and potent antioxidants. This review highlights the transformative impact of CRISPR/Cas9 and next-generation precision tools, such as base and prime editing, on modern tomato breeding. Beyond functional genomics, we focus on the strategic engineering of tomato to maximize productivity through fruit size optimization and the biofortification of high-value metabolites (e.g., GABA, lycopene, and vitamins). Furthermore, we examine recent advances in developing multi-stress resilience against both biotic and abiotic challenges. A significant emphasis is placed on re-designing plant architecture and developmental traits to tailor tomato varieties for future agricultural systems, particularly indoor and vertical farming. By advanced delivery methods, CRISPR technologies offer unprecedented potential to accelerate the development of “smart” tomato, ensuring sustainable agriculture and global food security in a changing climate.

In this study, molecular-genetic analyses were carried out to identify resistance to yellow rust (Puccinia striiformis f. sp. tritici) in soft wheat (Triticum aestivum L.) samples. Yellow rust is one of the most destructive diseases of wheat worldwide, causing significant yield losses and posing a serious threat to global food security, particularly under changing climatic conditions. The disease is also highly prevalent in Central Asian countries, including Uzbekistan and Tajikistan, where wheat is a staple crop and ensuring stable production is of strategic importance. A total of 68 wheat genotypes were examined and genotyped using 42 highly polymorphic DNA markers. Based on the obtained phenotypic and genotypic data, association analysis was performed using the TASSEL and STRUCTURE programs. To identify genetic associations, GLM (General Linear Model) and MLM (Mixed Linear Model) statistical models were applied. The analysis revealed that the following markers showed significant and reliable associations with yellow rust resistance: Barc0187 (p=0.0040), Gwm340 (p=0.0043), Barc008 (p=0.0132), and Gwm111 (p=0.0147). These markers are recommended as reliable molecular indicators for identifying yellow rust-resistant genotypes and for improving marker-assisted selection (MAS) strategies in future wheat breeding programs.

Patchouli is a plant that produces essential oil. One problem with patchouli is that production remains low due to virus attacks. To address this issue, virus-free seedlings can be produced through tissue culture. This measure requires examining the effectiveness of patchouli regeneration in vitro through histological observations and acclimatization, in as much as effective propagation supports healthy seedlings. The purpose of this study was to determine the optimal propagation for Aceh patchouli via in vitro propagation, through histological observation. It investigated the optimal acclimatization for patchouli to assist patchouli adaptation. The study was carried out in several stages, starting from shoot multiplication, root induction, and acclimatization. Shoot multiplication was carried out on MS medium supplemented with BAP : 0.25 mg/L, 0.50 mg/L, 0.75 mg/L, 1.00 mg/L, 1.25 mg/L, and 1.50 mg/L. Root induction was carried out on MS medium supplemented with NAA : 0 mg/L, 0.2 mg/L, 0.4 mg/L, 0.6 mg/L, and 0.8 mg/L. Finally, the acclimatization was performed on compost under covering treatment. The results demonstrated that the best shoot multiplication, taking place in 6.3 days, was obtained through the 0.25 mg/L BAP treatment. This treatment resulted in the highest shoot proliferation, with a mean of 68.5 shoots per explant, as well as the greatest shoot height (5.1 cm). The best root induction was obtained from NAA 0.2 mg/L, producing a plant length (18.27 cm), plant height (9.60 cm), root length (8.67 cm), and plant fresh weight (1.49 g). During the acclimatization stage, the 12-day covering treatment produced the best seedlings, as evinced by plant length (25.8 cm), shoot height (19.5 cm), root length (7.9 cm), fresh weight (1.85 g), leaf width (3.0 cm), and a survival rate of 100%.

Microalgae offer a sustainable platform for biotechnology due to their rapid growth and ability to accumulate high-value metabolites such as lipids, proteins, and carbohydrates. This study investigates the biochemical and morphological responses of Chlorella vulgaris and Scenedesmus incrassatulus across different growth phases and under nitrogen (N) and phosphorus (P) deficiency. Molecular identification and phylogenetic analysis confirmed the taxonomic status of both species. Scanning Electron Microscopy (SEM) combined with Energy Dispersive X-ray Spectroscopy (EDS) revealed species-specific surface structures and elemental composition. S. incrassatulus exhibited a compact, granular morphology, while C. vulgaris showed a smoother, colonial structure. EDS analysis demonstrated higher potassium and phosphorus levels in C. vulgaris, whereas S. incrassatulus presented elevated calcium and magnesium contents. Biochemical profiling indicated a metabolic shift during the stationary phase, with reduced protein synthesis and increased lipid and carbohydrate accumulation. Under nitrogen deficiency, C. vulgaris achieved the highest lipid content (53.68%), while S. incrassatulus reached 45.86%. Carbohydrate accumulation was also prominent during the stationary phase, with values of 49.18% for C. vulgaris and 47.99% for S. incrassatulus. Protein content was highest in the exponential phase and declined under nutrient stress. Elemental analysis via Inductively Coupled Plasma-Atomic Emission Spectroscopy (ICP-AES) confirmed species-specific macronutrient and trace element profiles, supporting EDS data. These findings highlight the adaptive biochemical and structural traits of the two microalgae species, reinforcing their potential in biofuel production, sustainable agriculture, bioremediation, and environmental applications. Future work should focus on optimizing cultivation conditions and exploring genetic approaches to maximize metabolite yields for industrial-scale applications.

Winged bean (Psophocarpus tetragonolobus L.) is a nutrient-rich tropical legume with considerable potential to improve food security in tropical regions. However, breeding programs for purple-podded winged bean remain limited due to insufficient information on key genetic parameters. This study aimed to assess heritability, expected genetic gain, trait correlations, and path analysis in advanced purple-podded winged bean lines. Ten breeding lines derived from crosses of Indonesian landraces were evaluated using a randomized complete block design with three replications. Traits observed included days to flowering, days to harvest, fruit set, pod width, pod length, pod weight, pod weight per plant, number of seeds per pod, and yield potential. The results revealed high broad-sense heritability (>0.5) for all traits, with the highest values observed for pod length (0.96), pod width (0.95), and fruit set (0.90). Expected genetic gain was highest for fruit set (35.20%), pod weight per plant (34.44%), and yield potential (34.44%). Correlation analysis indicated strong positive relationships between days to flowering and days to harvest (r = 0.90), while yield potential showed a perfect correlation with pod weight per plant (r = 1.00). Path analysis revealed positive direct effects of fruit set (0.478) and pod weight (0.310) on pod weight per plant, whereas number of seeds per pod had a negative direct effect (-0.429). Genotypes MNN 1122 and PLB 2324 exhibited the highest yield potentials (8.58 and 7.63 t ha^-1, respectively). These findings provide important genetic insights for the development of high-yielding purple-podded winged bean varieties.

Coix lacryma-jobi L. is a cereal crop belonging to the Poaceae family, valued for its nutritional, medicinal, and ornamental uses. Among its varieties, two prominent landraces, C. lacryma-jobi var. kiboa and var. tapol, are cultivated for their distinct grain morphologies and favorable agronomic traits. However, despite its economic importance, detailed cytogenetic and molecular phylogenetic studies remain limited. This study presents a cytogenetic and molecular phylogenetic analysis of C. lacryma-jobi L. var. kiboa and tapol. Partial cytogenomic characterization on the 45S and 5S rDNA loci as well as Arabidopsis- type telomeric repeats using pre-labeled oligomer probes for fluorescence in situ hybridization (PLOP-FISH) technique confirmed a diploid chromosome number of 2n = 20 in both varieties. The 45S and 5S rDNA loci were localized on the nucleolar organizer region (NOR) of the short arm of chromosome 1 and the long arm of chromosome 4, respectively, indicating conserved chromosomal arrangements. Additionally, Arabidopsis-type telomeric repeats were detected at the terminal regions of all chromosomes. Chromosome sizes ranged from 2.98 ± 0.07 to 3.74 ± 0.11 μm in var. kiboa and from 3.42 ± 0.08 to 4.12 ± 0.05 μm in var. tapol. Phylogenetic analyses based on the internal transcribed spacer (ITS1 and ITS4) genes revealed a close genetic relationship between the two varieties, supporting their shared evolutionary lineage. These findings enhanced our understanding of adlay genetic diversity and provide foundational insights for plant breeding improvement, conservation strategies, and future genomic research.

Cotton fiber development is a complex process regulated by multiple networks that involve various transcription factors (TFs). Recent studies (2020-2025) have elucidated the roles of TFs through silencing and overexpression experiments in cotton plants. We conducted a literature search in NCBI using the keywords ‘transcription factor, fiber elongation, cotton plant’ to identify relevant studies. This review focuses on studies published between 2020 and 2025 that were selected for review. We discussed various TFs and molecular mechanisms leading to altered fiber length. The research works included various analyses of transcription factors, genes, proteins, and metabolites as well as fiber quality results. The reviewed data highlight the complexity of fiber development networks, which involve extensive crosstalk among regulatory pathways. Despite the complexity, many novel TFs, modules, and tandems that participate in fiber elongation have been found. Their positive or negative regulatory roles in fiber formation stages promote a more profound understanding of fiber initiation and elongation.

Mungbean is one of the prominent pulse crops in Indonesia since the mungbean seeds are highly nutritious and has become an important part of the diet for the community. The black-seeded mungbean highly nutritious as it contains high anthocyanin content. We have developed a black-seeded mungbean lines that need to be evaluated for drought tolerance. Drought tolerance is important as mungbean is usually cultivated during the drought-prone dry season that leads to total loss. This study aimed to (1) determine the effectiveness of drought tolerance indices to select drought tolerance in black-seeded mungbean, (2) reveal the drought indices most suitable to select drought-tolerant, high- yielding black-seeded mungbean lines. This study was conducted during dry season in the Field Laboratory of Universitas Nusa Cendana. A Split-Plot design was employed, consisting of irrigation frequencies as the main plot and mungbean genotype as the sub- plot treatments. The main plot consisted of three levels, i.e. irrigation every day (I₁), every four days (I₂), and every seven days (I₃), and the subplot consisted of 23 mungbean genotypes. Seed yields under non-stress and stress conditions were used to calculate the drought indices. The data were subjected to ANOVA, PCA and correlation analysis. There were significant variations in seed yields among genotypes under different drought indices. The indices MP, GMP, STI, HARM, MRP, SSI, YSI, MSTIK1, and MSTIK2 are suitable for selection of drought-tolerant, high-yielding mungbean lines. V9.HT, V10.HT, V11.HT, V16.HT, V18.HT, V19.HT, V20.HT, V22.HT were potential for further evaluation as promising drought tolerant, high yielding varieties.

Garlic (Allium sativum L.) is an important Philippine crop, valued both as culinary ingredient and as alternative medicine. Its bioactivity is mainly attributed to organosulfur compounds such as alliin and allicin, with other metabolites such as phenolic compounds also playing a role. Despite this, limited biochemical data exist on Philippine garlic varieties. This study aimed to characterize 12 garlic accessions collected from Ilocos Norte by determining their alliin content and total phenolic content (TPC). Alliin was quantified through high-performance thin-layer chromatography (HPTLC) densitometry, while TPC was measured using the Folin-Ciocalteu assay. Results revealed differences in both alliin content and TPC, with “Ilocos Pink” consistently exhibiting the highest values (32.84 mg/g FW of alliin; 0.4985 mg GAE/g FW of TPC), suggesting strong potential for bioactivity. In contrast, “Miracle” (19.78 mg/g FW of alliin; 0.1806 mg GAE/g of TPC) and Tan Bolters (20.07 mg/g FW of alliin; 0.1658 mg GAE/g of TPC) had the lowest values for both alliin content and TPC. These findings highlight the varietal differences among accessions, providing a baseline for further studies on their bioactivity, breeding, and post-harvest utilization. This research underscores the importance of characterizing local garlic varieties to strengthen their competitive value and to promote their utilization in specialized applications.

Amylopectin branch-chain length distribution is a key determinant of rice starch functionality and eating quality, yet the genetic basis underlying specific chain fractions remains incompletely understood in diverse germplasm. In this study, amylopectin fine structure was quantified in 137 accessions of the Korean Rice Core Selection (KRICE_Core) using HPAEC-PAD, and genome-wide association studies were conducted with 2.1 million high-quality SNPs under the FarmCPU model. The short-chain distribution (SCD, DP 6-12) varied from 26.85% to 37.20%, whereas the intermediate-chain distribution (ICD, DP 12-24) ranged from 52.57% to 61.04%, and the two fractions showed a strong inverse correlation. GWAS identified two major loci on chromosomes 4 and 6, with the chromosome 6 region showing exceptionally strong association signals and co-localizing with Os06g0229800 (SSIIa). Haplotype analysis of SSIIa detected five non-synonymous SNPs defining five haplotypes. Hap1 and Hap5 were associated with increased SCD and reduced ICD, whereas indica-related haplotypes (Hap2-Hap4) showed the opposite trend, indicating that SSIIa allelic variation quantitatively shifts the balance between short and intermediate chain fractions. In a panel of 113 Korean-bred cultivars, Hap1 and Hap5 together accounted for > 99% of genotypes, suggesting strong directional selection for japonica-type SSIIa alleles during Korean breeding. These findings provide robust molecular targets for designing rice varieties with tailored starch architecture and cooking qualities.

Carbohydrates and genetic factors influence cell division in citrus fruits from ovule cultures. Here, we investigated the effects of various carbohydrate sources (sorbitol, maltose, galactose, and lactose) on cell proliferation, somatic embryogenesis, and plant regeneration in three Citrus unshiu cultivars (‘Miyagawa wase’ [MW], ‘Haryejosaeng’ [HW], and ‘Nankan 20 gou’ [NW]), and one C. reticulata cultivar (‘Ootaponkan’ [PM]). In PM, carbohydrate sources did not affect proliferation; MW showed a significant but marginal increase in media containing 300 mM mannitol. It also proliferated well in media supplemented with 300 mM sorbitol and a mixture of galactose and lactose. NW achieved the best rate with 100 mM mannitol and 146 mM lactose, whereas HW proliferated well with 100 mM mannitol alone. Phylogenetic analysis using 18 citrus varieties showed distinct genetic differences among the cultivars, suggesting that the differences in regeneration capacities in different carbohydrate sources could be attributed to their genetic differences. This study provides valuable insights for optimizing tissue culture protocols for mandarin varieties and may enhance the efficiency of citrus breeding and tissue culture applications.