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.

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.

Cotton is a globally important fiber crop, but many elite cultivars are recalcitrant to in vitro regeneration. We developed a callus-mediated plant regeneration protocol for the local G. barbadense L. cultivar Surkhan-106. Sterilized seeds were germinated in vitro, and hypocotyl and cotyledon explants were cultured on Murashige and Skoog (MS) medium with various auxin/cytokinin combinations. Robust callus induction was achieved from hypocotyl explants within 2–3 weeks. Somatic embryogenesis was induced from callus after approximately 12–14 weeks on medium supplemented with indole-3-butyric acid (IBA), 2,4-dichlorophenoxyacetic acid (2,4-D), kinetin, and 6-benzylaminopurine (BAP). Embryogenic callus was periodically subcultured to prevent browning, and torpedo-stage somatic embryos were matured on hormone-free medium. These embryos germinated into plantlets within 10–15 days on MS medium. The entire regeneration cycle, from seed to plantlet, was completed in about 4–5 months. Hypocotyl explants showed significantly higher callus formation frequency (85%) and regeneration efficiency than cotyledon explants (60%) (ANOVA, p < 0.05). This study establishes the first efficient callus-based regeneration system for Surkhan-106, an important Uzbek cotton variety. The optimized protocol can facilitate rapid clonal propagation and genetic transformation of Surkhan-106 and other recalcitrant cotton cultivars, accelerating breeding programs for improved stress tolerance and yield.

Citations

Citations to this article as recorded by  

• Molecular and physiological indicators of heat tolerance in upland cotton ( Gossypium hirsutum L.)
  Abrorjon Y. Kurbonov, Mohigul Abdullayeva, Feruza F. Mamedova, Muxammad-Latif M. Nazirov, Naima Sh. Khojaqulova, Sanjar Sh. Djumaev, Yashin Babayev, Sayfulla Boboyev
  Journal of Plant Interactions.2026;[Epub]     CrossRef
• Molecular Characterization of Fusarium Wilt Resistance in Naturally Colored and Elite Upland Cotton Germplasm
  Abrorjon Y. Kurbonov, Feruza F. Mamedova, Sanjar Sh. Djumayev, Mukhammad Latif M. Nazirov, Naima Sh. Xojakulova, Maftuna U. Makhmudova, Ozod S. Turaev
  Journal of Natural Fibers.2026;[Epub]     CrossRef

This study aimed to enhance the Inpari 42 rice variety by integrating the aromatic trait through Marker-Assisted Backcrossing (MAB) while improving key agronomic characteristics in the BC₁F₁ generation. The aromatic gene from Merah Wangi was successfully introgressed into BC₁F₁ plants, confirmed through molecular analysis using the Bradbury marker, which detects mutations in the BADH2 gene responsible for fragrance in rice. Thirty BC₁F₁ plants with a heterozygous mutation in BADH2 were identified, demonstrating the reliability of MAB in maintaining the aromatic trait across generations. Agronomic evaluations revealed that BC₁F₁ plants exhibited intermediate flowering time, increased plant height, and longer panicles compared to the parental lines. Additionally, BC₁F₁ plants showed enhanced tillering capacity, more productive tillers, and higher grain yield per plant, indicating the successful integration of desirable traits from both parents. The next step in this research is to conduct further backcrosses with Inpari 42 to develop a stable aromatic variety, combining the high-yielding characteristics of Inpari 42 with the aromatic traits of Merah Wangi. These findings highlight the potential of BC₁F₁ lines for developing high-yielding aromatic rice varieties suitable for diverse agricultural settings.

Pre-harvest sprouting is a major physiological problem in rice caused by prolonged rainfall and high humidity during the harvest period, and it is one of the most important targets in current rice breeding programs. In this study, the effect of cold and freezing storage on the pre-harvest sprouting rate was investigated using ten rice varieties under four different treatments. The result showed storage treatments of panicle samples used for germinate evaluation had no significant influence on the pre-harvest sprouting rate. These findings may enhance the efficiency of mass screening for pre-harvest sprouting and support the development of tolerant rice varieties.

Salicylic acid (SA) is a plant hormone that has a significant role in many biochemical processes involved in cotton plant resistance against biotic and abiotic stress factors. Exogenous SA has been shown to have effects on plant growth and development, resistance to fungi and insects, and mitigation of abiotic stress factors. Treating cotton seedlings or plants with SA in a culture medium or spraying them with SA has enabled scientists to identify genes responsible for this chemical, associated with several biological functions. SA has been established as part of the defense system in cotton plants: antifungal resistance and insect resistance. Besides, it is a part of plant growth and development as well as fiber development. Identifying SA-responsive genes and understanding their roles in plant resistance enables the development of stress-resistant genotypes. This paper reviews scientific data resulting from the treatment of cotton plants with exogenous SA. In the first section, we discussed antifungal resistance-related data linked to SA treatment, which makes up the highest content of the review. We highlighted its significant role in cotton plant antifungal resistance. The second section deals with SA-responsive genes and metabolites linked with insect resistance. In the third section, we reviewed SA-responsive genes and enzymes associated with cotton plant growth and development. The scientific data regarding SA-linked cotton fiber development have been discussed in the last section. In summary, we discussed SA-responsive genes, proteins, and metabolites that could be used to develop genotypes with enhanced traits.

Citations

Citations to this article as recorded by  

• Genome-Wide Identification and Characterization of the Key Genes for Salicylic Acid Biosynthesis in Four Cotton Species
  Jiaqi Lin, Xin Zhou, Shandang Shi, Xin Li, Manhong Wang, Fei Wang, Liping Zhu, Hongbin Li
  International Journal of Molecular Sciences.2026; 27(9): 3936.     CrossRef

Black sapote (Diospyros digyna Jacq.) is a fruit that is rich in benefits and has high economic value. However, the sex of this plant is difficult to determine early, and data on the plant is still very limited. This qualitative quantitative research was conducted to identify the genetic diversity of black sapote based on RAPD marker to determine the sex of black sapote plants. The sample used consisted of seven black sapote accessions with sample codes including P, M1, M2, M3, F1, F2, and F3. This research consists of several stages, namely DNA extraction and PCR amplification using six RAPD primers (OPA 02, OPA 05, OPA 08, OPA 09, OPC 09, and OPD 15), including electrophoresis to visualize amplified DNA. Data were analyzed using NTSYS 2.02 software and dendogram were obtained using the UPGMA method in the SAHN function. The results of the analysis showed that the polymorphism resulting from the seven black sapote accessions ranged from 50–80%, with PIC (Polymorphic Information Content) values ranging from 0.28–0.50. The closest related accessions are M1 with F2, while accession P with F2 has the highest genetic diversity. The OPA 02 primer with a band measuring 380 bp can be used as a putative marker in the determination of the female sex and hermaphrodite of black sapote plants.

Everbearing strawberry cultivars provide fruit during the summer–fall period when June-bearing strawberries are unavailable, but their breeding progress has been constrained by complex trait interactions. To characterize segregation patterns and evaluate phenotypic diversity, we developed an F₁ population from a cross between two everbearing cultivars, ‘Charlotte’ and ‘Flamenco’. Twenty selected progenies were evaluated for 30 quantitative traits encompassing vegetative vigor, inflorescence structure, fruit morphology, firmness, and biochemical composition. Substantial variation was observed among lines, with several individuals exceeding parental performance for key traits such as fruit size, soluble solids content, and sucrose accumulation. Principal component analysis revealed three major axes of variation: fruit composition (sugars and acids), vegetative vigor, and fruit size and morphology. K-means clustering grouped the progeny into three phenotypic classes, representing high-sugar, large-fruited, or vigorous growth types. Notably, some lines combined favorable attributes across classes, such as high sweetness and large fruit, indicating the potential to overcome typical trade-offs between yield and quality. These findings provide a practical framework for breeding selection and highlight superior progeny as immediate candidates for clonal advancement or as parents in future crossing. The results also establish a foundation for integrating phenotypic classifications with molecular tools to accelerate the development of high-value everbearing strawberries.

CRISPR (clustered regularly interspaced short palindromic repeats) gene-edited (GEd) crops have demonstrated significant potential to enhance global food security in the face of escalating climate challenges and rapid population growth. Since 2019, for regulatory purposes, the United States (U.S.) and several other countries have recognized transgene-free, genome-edited lines as equivalent to conventionally bred varieties. Notably, the first genome-edited food product, Calyno™ soybean oil, was commercialized in the U.S. and marketed as a non-genetically modified organism (GMO) item. Recently, regulatory frameworks, such as the enactment of the Precision Breeding Law in the United Kingdom, the European Union’s New Genomic Techniques (NGT) legislation, and the repeal of the SECURE Rule in the United States, have further established guidelines permitting the use of genome-edited lines in agriculture similar to with conventionally bred crops, provided that these lines are free of transgenic elements. In Korea, researchers and policymakers are actively engaging in discussions to establish a preliminary review committee for GEd crops to align regulatory practices with international trade standards. Thus, this study aimed to evaluate two gene-edited rice lines for generational stability in terms of molecular characteristics, focusing on edited nucleotide sequences, gene expression, target phenotypes, the presence of transgene elements, and potential off-target effects across multiple generations. Additionally, several technical challenges in nucleotide editing tracing emerged during the evaluation process that warrant further attention. The findings presented in this study are expected to offer valuable insights for shaping the regulatory framework in Korea for CRISPR-based gene-edited crops.

Citations

Citations to this article as recorded by  

• CRISPR/Cas9 Mediated Genome Editing for Enhancing Abiotic Stress Tolerance in Rice: An Omics Guided Perspective
  Mahavir Joshi, Pari Panwar, Smile Sharma, Bharat Sagar, Sukhminderjit Kaur, Manikant Tripathi
  Molecular Biotechnology.2026;[Epub]     CrossRef

Milk thistle (Silybum marianum (L.) Gaertn.), a valuable medicinal plant with economic importance, serves as a source of both therapeutic compounds and vegetable oil for human use. Genome editing techniques have been widely applied to improve key agronomic traits in various species. Therefore, this study aims to develop an efficient method for seed sterilization and protoplast isolation in milk thistle. For seed sterilization, seed treated with hydrogen peroxide for either 4 hours or 7 hours with ethanol and detergent showed more sufficient to sterilize seed of milk thistle for in vitro growth than ethanol, sodium hypochlorite, and chlorine gas. For protoplast isolation in milk thistle, high-yielding, viable protoplasts were successfully isolated from the leaves of 21-day-old plants using a 2 hours enzymatic treatment containing 2% Viscozyme^® L, 1% Celluclast^® 1.5 L, and 1% Pectinex^® Ultra SP-L. Additionally, transient expression of green fluorescent protein was observed following polyethylene glycol-mediated transfection. Therefore, the seed sterilization and protoplast isolation methods developed in this study can facilitate in vitro culture, gene function analysis, and genome editing aimed at improving agronomic traits in milk thistle.

This research attempted to validate novel molecular markers linked to high antioxidant traits using an F₂ population and a local Thai rice population. We performed total flavonoid content, total phenolic content (TPC), and ferric reducing antioxidant power (FRAP) assays to assess the antioxidant capacities of rice populations. In the F₂ (“Pathum Thani 1”דHawm Mali Daeng”) population, these traits exhibited a quantitative distribution with high heritability (82.7%–98.3%) and high genetic advance (66%–94%). In validation using 10 molecular markers, OsRc and In1-Rc displayed polymorphism in parent cultivars and in bulked segregant analysis. However, only OsRc had strong associations with TPC (R² = 52.2%, p < 0.001) and FRAP (R² = 43.0%, p < 0.001), whereas In1-Rc featured no significant associations (R² ≤ 0.1%). When verified in Thai rice cultivars, OsRc could discriminate red pericarp rice cultivars with high antioxidant properties from white pericarp cultivars with low antioxidant activity, confirming its efficiency in selecting antioxidant traits in rice. These findings indicate that OsRc is a functional marker for selecting rice lines with high antioxidant activity, thereby facilitating early-stage genotyping in rice breeding programs.

Citations

Citations to this article as recorded by  

• Genome-wide association study of antioxidant compounds and antioxidant activity in a panel of Thai rice cultivars
  Saranyu Thaworn, Phanomsak Tomjai, Teerapong Buaboocha, Supachitra Chadchawan, Monnat Pongpanich, Chanita Paliyavuth, Waraluk Kasettranan
  Euphytica.2026;[Epub]     CrossRef

Genetic diversity among 20 Azerbaijani grape (Vitis vinifera L.) accessions was assessed using 10 Inter-Simple Sequence Repeat (ISSR) markers to elucidate relationships among samples and identify a convenient marker for determining genetic diversity. Based on the polymorphic information parameters such as PIC, EMR, MI, and RP were critically analyzed for utilizing these ISSR primers for genetic variability and 4 ISSR (UBC 811, UBC 812, UBC 815, UBC 857) markers were selected for future germplasm management. The total number of identified bands varied between 2-5. The maximum PIC value was observed in UBC 857 (0.478). Among genotypes, Ag oval kishmish and Yumru kishmish cultivars had the closest genetic similarity index (0.913), while Ag oval kishmish and Marandi, Yerli Muskat and Yabani uzum 1, Yerli Muskat and Yumru kishmish cultivars had the most distant genetic similarity index (0.406). These findings highlight both the complexity of grapevine genetic structure and the value of ISSR markers for detecting non-obvious relationships.

Adzuki bean (Vigna angularis [Willd.] Ohwi & Ohashi) has recently become widely cultivated in Asia. Generally, it is sensitive to flooding stress. Wild relatives of adzuki bean have shown higher tolerances to abiotic stressors than cultivars, but their responses to flooding are not well understood. In this study, the waterlogging tolerance levels of 202 accessions from two cultivated Vigna species including V. angularis var. angularis (cultivated adzuki bean), V. umbellata (rice bean), and two wild ones consisting of V. angularis var. nipponensis (wild adzuki bean), and V. nakashimae, were evaluated at the early vegetative stage using a foliar damage score. Additionally, the responses of 119 accessions from V. angularis var. nipponesis bean and V. nakashimae to submergence at the germination stage were evaluated using germination-related traits. Among the tested species, cultivated adzuki bean showed the lowest tolerance to waterlogging, while V. nakashimae showed the greatest. At the germination stage, seeds of V. nakashimae were more tolerant of submergence than seeds of V. angularis var. nipponesis, exhibiting significantly higher normal seedling indexes. There was no significant correlation between the early vegetative-stage index and either germination-stage index for both V. angularis var. nipponensis and V. nakashimae, suggesting that the genetic bases regulating flooding stress responses at the two growth stages differ. However, we identified four V. nakashimae accessions that exhibited tolerant or very tolerant responses to flooding at both stages, suggesting their potential for use in breeding flood-tolerant adzuki bean varieties.

Perilla frutescens is a traditionally cultivated crop in East Asia that exhibits significant morphological variation between its two main variants: var. frutescens and var. crispa. To investigate the genetic basis of trait variation and segregation, we developed an F₂ population from a cross between weedy accessions of the two variants of Perilla and analyzed 107 individuals. Four qualitative and nine quantitative traits were evaluated, including leaf color, stem color, flower color, days to flowering, plant height, and leaf area. The F₂ population showed wide phenotypic variation. In the chi-square test for four qualitative traits, two traits (color of leaf reverse side, color of flower) followed a Mendelian segregation ratio of 1:2:1. Heritability analysis revealed high values for days to flowering and leaf width. In contrast, traits such as number of florets and leaf length exhibited lower heritability, indicating a more substantial influence of environmental factors. Hierarchical clustering analysis grouped the parental lines into distinct clusters, revealing a diverse distribution of F₂ individuals across multiple groups. Some individuals closely resembled one of the parents, while others formed novel clusters, reflecting recombination and the emergence of new trait combinations. These findings underscore the genetic complexity underlying morphological traits in Perilla and highlight the potential of weedy accessions as valuable resources for breeding. The foundation established by this study will aid in developing new cultivars with desirable traits.

Polyploid plants, such as hexaploid Solanum nigrum, present new challenges and opportunities for trait improvement due to their complex genome structures and homoeologous gene interactions. Gene editing of homoeologs provides a powerful tool to investigate the inheritance and phenotypic effects of mutations in polyploid systems. Here, we investigated the inheritance and phenotypic traits of homoeolog-edited triple and double mutants in hexaploid S. nigrum. Triple mutant genotypes (sns and snsp) were used for analyzing inheritance patterns through backcrossing and self-pollination, revealing independent segregation of homoeologous variants and consistent genotypic ratios across generations. Yield and related traits were evaluated in fixed double mutants (sns1 sns2, sns1 sns3, sns2 sns3) under greenhouse and open-field conditions. Open-field cultivation significantly enhanced yield, primarily through increased fruit weight per inflorescence, whereas greenhouse cultivation showed more modest improvements. Other traits such as plant weight and Brix values remained largely unchanged. Yield improvements were stable across F3 to F5 generations, with minimal genotype-specific variability. These findings highlight the potential of homoeolog-targeted editing in polyploid plants to achieve stable and environment-specific yield enhancements.

Citations

Citations to this article as recorded by  

• Genetic mapping of tomato mutants using InDel markers between S. pimpinellifolium and two S. lycopersicum cultivars
  Smita Mirsyad Warsadiharja, Shandra Amarillis, Jung Heo, Seunghye Park, Hye-yeong Kang, Yong Jun Kim, Junwoo Lee, Kang Il Cha, Eun Song Lee, Ji In Jang, A-ra Joh, Keunhwa Kim, Young Koung Lee, Jong Chan Hong, Soon Ju Park
  Plant Biotechnology Reports.2025; 19(6): 839.     CrossRef

The GeBP gene family, known for its GLABROUS1 enhancer-binding proteins, represents a standard transcription factor characterized by an unconventional leucine-zipper motif. The constituents of this family possess a core DNA-affinity domain. This protein is crucial for controlling plant growth and development. GeBP genes have been analyzed and defined only in some Gramineae crops, Arabidopsis, rice and soybean. However, a comprehensive examination of the role of the GeBP genes in Brassica rapa has yet to be conducted. This study used genome-wide characterization to identify twenty BrGeBP genes and accessible RNA sequencing data to evaluate each gene's expression. Based on phylogenetic research, we grouped 114 GeBP proteins from five different plant species into six groups. Generally, groupings of BrGeBP genes with comparable motifs and exon-intron distribution were conserved. The twenty BrGeBP genes were found on six of the ten B. rapa chromosomes, and one paralog showed segmental duplication. The varied protein motifs and gene structures showed that the GeBP genes had various roles in plants. The functions of BrGeBP genes are numerous and include expressions responsive to specific tissues, stress, and hormones according to cis-elements analysis. Furthermore, expression analysis using RNA sequencing revealed that the genes BrGeBP3, BrGeBP9, and BrGeBP20 showed substantially increased expression in different organs. These findings will aid in elucidating the possible roles and traits of BrGeBP genes in the B. rapa biological cycle and related species.

This study evaluates the phenolic content, antioxidant, and antibacterial properties of hydro-ethanolic extracts from six medicinal and aromatic plants in Morocco: Eucalyptus torquata, Thymus broussonetii, Lavandula angustifolia, Rosmarinus officinalis, Ziziphus lotus, and Acacia raddiana. Sonication was employed for extraction. Total phenolic content, total flavonoid content, and condensed tannin content were quantified using the Folin-Ciocalteu, aluminum chloride, and hydrochloric acid assays, respectively. Antioxidant capacity was assessed via DPPH, total antioxidant capacity, ferric reducing antioxidant power, and ABTS assays. Antibacterial activity was measured by the microdilution method. Phytochemical analysis revealed that E. torquata and Z. lotus had the highest total phenolic content, with 86.75 and 87.58 mg GAE/g of dry matter, respectively. T. broussonetii and R. officinalis had the highest flavonoid and condensed tannin content, at 297.12 mg QE/g of dry matter and 5.10 g/L, respectively. E. torquata exhibited the strongest antioxidant activity, with DPPH and ABTS values of 0.048 and 0.11 mg/mL, and a ferric reducing antioxidant power value of 209.375 mg/g. R. officinalis showed the highest total antioxidant capacity at 1.03 mg AAE/g of dry matter. All extracts displayed bactericidal effects. R. officinalis demonstrated the most potent antibacterial activity, with minimum inhibitory concentrations ranging from 0.625 to 5 mg/mL and minimum bactericidal concentrations from 1.25 to 10 mg/mL. High phenolic content and significant antioxidant activity were noted in E. torquata and R. officinalis. Additionally, all extracts showed substantial antibacterial activity against four bacterial strains, with R. officinalis being the most effective.

The genetic control of rice resistance has been extensively studied, but how the resistance mechanism is genetically controlled has received less attention. This study revealed that the rice resistance mechanism toward brown planthopper was genetically controlled by several genes with several mendelian patterns. The tolerance mechanism is controlled by three complementary genes; this is confirmed by QTL analysis, whereas the Antibiosis is controlled by three separate loci on chromosomes 2, 8, and 11. The antixenosis was controlled by polygenic, but detected locus only on chromosome 3, with minor effects.

Citations

Citations to this article as recorded by  

• ‘Drimi9ho’, A Lodging Tolerance with Mid-late Maturing, Improved White-backed Planthopper (Sogatella furcifera) and Cultivation Stability
  Jae-Ryoung Park, Eun-Gyeong Kim, Yoon-Hee Jang, Kyung-Min Kim
  Korean Journal of Breeding Science.2025; 57(4): 493.     CrossRef

Bread wheat (Triticum aestivum L.) is a fundamental crop worldwide, playing a crucial role in ensuring food security for human beings. Understanding the genetic diversity of wheat cultivars and developing genetic passports through DNA fingerprinting is essential for preventing varietal duplication enhancing breeding diversity and protecting breeders' rights globally. This study investigated the genetic diversity, phylogenetic relationships, and allelic frequencies of 32 Uzbekistan bread wheat cultivars using 66 polymorphic simple sequence repeat (SSR) markers. Unique marker alleles were identified and used to develop genetic passports for the cultivars. The results showed that the primers Barc181, Wmc522, Wmc407, Wms18, Cfa2201, Wms294, Cfd76, Wmc73, Wmc486, Cfa220, Wmc314, And Wms495 are reliable SSR markers for assessing genetic polymorphism in Uzbek wheat cultivars.

Citations

Citations to this article as recorded by  

• Genetic analysis of fusarium wilt resistance in Upland cotton germplasm ( Gossypium hirsutum L.)
  Naim N. Khusenov, Jurabek K. Norbekov, Umid A. Boykobilov, Zebo S. Yuldosheva, Ilyos S. Normamatov, Abdusalom Kh. Makamov, Mirzakamol S. Ayubov, Mukhtor M. Darmanov, Akmal M. Asrorov, Zabardast T. Buriev, Maftuna U. Makhmudova, Ozod S. Turaev, John Z. Yu,
  Journal of Plant Interactions.2025;[Epub]     CrossRef

Black soybeans are valued for their rich nutritional content and potential health benefits, attributed to their functional components that enhance antioxidant activity. In this study, we evaluate and compare the isoflavone and anthocyanin content, as well as the antioxidant potential, of seven Korean black soybean genotypes. Isoflavone content ranged from 2,032.8 to 3,536.8 µg/g, with Soman displaying the highest levels of both aglycones and glucosides, indicating notable bioactive potential. In terms of anthocyanins, Danheuk had the highest total content (24,080.6 µg/g), while Soman excelled in Pelargonidin-3- glucoside (Pg3glc). Soman also showed superior antioxidant activity across all measures, including total polyphenol, flavonoid content, as well as radical scavenging abilities (ABTS and DPPH). Strong correlations were found between total flavonoid content, total polyphenol content, genistin, total isoflavone content and antioxidant activity, while correlations with total anthocyanins were relatively weaker. These findings reveal significant genetic variability in isoflavone and anthocyanin content among soybean genotypes, with Soman showing particularly high antioxidant potential, suggesting its value for health-related applications and soybean breeding programs.

Citations

Citations to this article as recorded by  

• Health benefits of Cyanidin-3-O-glucoside and other supporting natural compounds in black soybean (Glycine max (L.) Merrill): A narrative review
  Chiew Erh Jacqueline Moey, Wai Kwan Lau
  Journal of Functional Foods.2026; 140: 107285.     CrossRef
• Enhanced Antitumor Activity of Korean Black Soybean Cultivar ‘Soman’ by Targeting STAT-Mediated Aerobic Glycolysis
  Su Hwan Park, Jeong Hyun Seo, Min Young Kim, Hye Jin Yun, Beom Kyu Kang, Jun Hoi Kim, Su Vin Heo, Yeong Hoon Lee, Hye Rang Park, Man Soo Choi, Jong-Ho Lee
  Antioxidants.2025; 14(2): 228.     CrossRef

Elaeis guineensis is a tropical oil plant with the highest oil yield per unit area in the world. The Tenera hybrid is the most valuable variety for cultivation compared to the parent varieties Dura and Pisifera. It is difficult to select for the morphological characteristics of the oil palm cultivar in oil palm seedlings at the nursery stage; thus, the development of a molecular marker is necessary. In the present study, a sequence characterized amplified region (SCAR) marker was developed that yields 159-bp and 195-bp fragments specific for female and male parents, respectively. Sequence alignment revealed that the 159-bp fragment has a 36-bp deletion. Molecular characterization of the fragments reveals that the sequence is identical to the ALBINO3-like protein 2 (EgALB3.2) and is localized on chromosome 16 of the E. guineensis genome with expression noted in the kernel/endosperm of Tenera fruits only. These markers help in the selection of oil palm hybrids codominantly expressing both fragments; thus, heterozygous individuals can be distinguished from homozygous individuals. The SCAR-specific marker could therefore be used to distinguish oil palm hybrids from their parents by PCR. Moreover, these specific SCAR primers can be used directly to identify the oil palm hybrids without the need for postprocessing steps, and the specific fragments can be detected using an automated sequencer and real-time PCR. This marker-assisted selection is sensitive and suitable for the identification of oil palms in breeding programs.