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.

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.

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.

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.

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• 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.

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• 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.

Triticum aestivum L., commonly known as wheat, has long been considered one of the most important crops worldwide. Over the past 20 years, there has been a notable increase in domestic demand for wheat in South Korea, raising interest in locally grown varieties. In recent years, an expansion in reclaimed land areas has prompted extensive research into crop breeding and varietal improvement for salt tolerance. As part of this research effort, salt-tolerant mutant individuals selected through gamma radiation mutation were used as experimental materials to study the temporal gene expression profiles related to salt response in "Urimil" varieties following salt treatment. In this study, physiological analyses were conducted by measuring the changes in the Na⁺ and K⁺ contents, as well as the K⁺/Na⁺ ratios, in plant leaves as indicators of salt response. RNA-Seq was used to analyze gene expression patterns post-salt treatment across different time points. Furthermore, gene ontology compartmentalized the genes into biological processes, molecular functions, and cellular components. Finally, the wheat reference genome was compared with the experimental and control groups to identify non-synonymous SNPs that could induce changes in protein expression. This analysis aimed to investigate the mechanisms of salt tolerance in wheat and to identify candidate genes for further research.

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.

Quantitative trait locus (QTL) analysis is a powerful approach for identifying variants associated with the phenotypic variation of complex traits. However, selecting optimal methods and pre-processing steps require considerable time and effort. In this study, we demonstrated applicability and replicability of machine learning (ML) models in QTL analysis by evaluating their performance in comparison with conventional QTL analysis methods using 142 recombinant inbred lines derived from two japonica rice cultivars, Koshihikari and Baegilmi. Random forest and gradient boosting models showed the highest predictive accuracy, and consistently identified three QTLs associated with heading date: qDTH3, qDTH6, and qDTH7. Moreover, ML-based QTL analysis detected minor-effect qDTH10, where Koshihikari allele promoted heading date when combined with Koshihikari alleles of qDTH6 and qDTH7. These results demonstrate the applicability of ML models in QTL analysis on bi-parental mapping population in rice.

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• Machine Learning Method to Select Single Nucleotide Polymorphism Markers for Protein Content, Grain Filling Rate, Height, and Panicle Length in Korean Rice
  Jeong-Gu Kim, Minwoo Kim, Gyu-Hwang Park, Jinhyun Kim, Jinho Jung, Tae-Ho Lee
  Korean Journal of Breeding Science.2025; 57(4): 403.     CrossRef

Rice blast, caused by the pathogenic fungus Magnaporthe oryzae, is a highly destructive disease of rice that leads to significant reductions in crop yield each year and poses a serious threat to rice production worldwide. Utilizing R genes to develop resistant varieties continues to be the most cost-effective and efficient approach for managing rice blast. Molecular screening of important blast resistance genes of rice and their allelic diversity were assessed in forty eight wild and local rice genotypes of Bangladesh using ten previously synthesized gene-based SSR markers. A varying range between 18.7% to 87.5% was seen in the genetic frequencies of ten key blast resistance genes. Fourteen genotypes possessed maximum eight blast resistance genes while, nine of the genotypes had seven blast resistance genes. Nine genotypes contained six blast resistance genes and five genotypes had a minimum of two blast resistance genes. At least five positive pieces of the predicted product size were occupied by thirty-five genotypes, among total forty eight genotypes. These findings are important for identifying and incorporating functional resistance genes from Bangladeshi local germplasms into the elite cultivars by using marker-assisted selection and providing better resistance to blast. Marker analysis of resistant and susceptible genotypes using ten RAPD showed that, markers OPA 5, OPF 9 and OPH 18 clearly differentiate resistant genotypes BAU dhan-3 from susceptible genotypes BRRI dhan 28 and BRRI dhan 29 indicating the potentiality of these markers to identify blast resistant rice genotypes and use in marker assisted breeding (MAB) to develop blast resistant high yielding rice varieties in Bangladesh.

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• Genetic diversity and identification of blast resistance genes through SSR markers in Bangladeshi aromatic rice (Oryza sativa L.) landraces
  Sumi Saha, Md Mamunur Rashid, Rabeya Khatun, Md Sams-Al Safin, Sohana Jui, Mst Tanjina Shahanaj Turin, Md Mamunur Rashid, Md Arifuzzaman
  Ecological Genetics and Genomics.2026; 39: 100481.     CrossRef

The storage proteins in wheat, particularly the high molecular weight glutenin subunits (HMW-GS), play crucial roles in the processing of flour and the quality of bread made from common wheat. These subunits are encoded by the Glu-A1, Glu-B1, and Glu-D1 loci. This study aimed to determine the composition of high molecular weight glutenin subunits in 89 Mongolian cultivars of spring wheat using KASP markers and sodium dodecyl-sulfate polyacrylamide gel electrophoresis (SDS-PAGE). The result showed the presence of the 5+10 allele at the Glu-D1 locus in Mongolian-developed varieties was confirmed through SDS-PAGE, providing evidence for the synthesis of high molecular weight glutenin subunits. The uniform presence of high molecular weight glutenin subunit alleles across the tested cultivars contributes valuable insights into the bread-making quality of Mongolian wheat varieties.

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• Comparative Transcriptomic Analysis of High- and Low-Protein Wheat Lines Reveals Differential Nitrogen Responses at the Seedling Stage
  Min Jeong Hong, Chul Soo Park, Dae Yeon Kim
  Agronomy.2026; 16(6): 628.     CrossRef
• Recent Advances in Nitrogen Use Efficiency (NUE) Research in Wheat
  Min Jeong Hong, Dae Yeon Kim
  Korean Journal of Breeding Science.2025; 57(3): 251.     CrossRef
• Latest Research Trends in Reducing the Immunogenicity of Wheat
  Sora Lee, Jong-Yeol Lee, Sichul Lee, Jae-Ryeong Sim, Sewon Kim, Woo-Suk Cho
  Korean Journal of Breeding Science.2025; 57(2): 65.     CrossRef

Black rot, a disease of significance affecting vegetable Brassica crops, is primarily caused by the bacterium Xanthomonas campestris pv. campestris (Xcc). When the disease spreads extensively in the field, it can lead to substantial yield losses, particularly under favorable environmental conditions. Controlling the spread of this disease is challenging, and the primary approach involves utilizing resistant cultivars or disease-free seeds. Among the various methods available for identifying different Xcc races, Polymerase Chain Reaction (PCR)-based molecular markers have proven to be highly reliable. To date, the PCR method has successfully identified Xcc races 1 to 7. In this study, molecular markers were developed for races 4 and 9 through the sequencing and alignment of the whole genome sequences of Xcc races, closely related Xanthomonas campestris (Xc) pathovars, and two Xanthomonas species. These designed markers were subsequently validated by PCR with bacterial genomic DNA samples from Xcc races and 7 other bacteria. The results indicated successful amplification only for race 4 and race 9, yielding amplicon sizes of 1080 bp and 830 bp, respectively, while the other strains failed to amplify. Furthermore, the amplicons from races 4 and 9 were cloned and sequenced, confirming that both races exhibited matching sequences after alignment. Consequently, the molecular marker method offers a rapid and efficient means of differentiating between Xcc races 4 and 9 within a few hours, presenting itself as a viable alternative to conventional methods that rely on the use of differential cultivars of Brassicaceae for identifying Xcc races.

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• Development of molecular markers for the detection of Paracidovorax citrulli strains causing bacterial fruit blotch in watermelon
  San Ha Choe, Nihar Sahu, Ijaz Yaseen, Se Hyeon Jeong, Gyoung Hee Kim, Jong In Park, Hoy Taek Kim
  Canadian Journal of Plant Pathology.2026; 48(3): 220.     CrossRef
• An update to the molecular identification of Xanthomonas campestris disease causing pathogens in crucifers – A mini review
  Nihar Sahu, Masao Watanabe, Jong-In Park
  Physiological and Molecular Plant Pathology.2026; 142: 103102.     CrossRef
• Molecular marker development for specific amplification of Xanthomonas campestris pv. campestris race 8 causing black rot disease in Brassica crops
  Sopheap Mao, Yeo-Hyeon Kim, Nihar Sahu, Su-Won Kim, Hoy-Taek Kim, Masao Watanabe, Jong-In Park
  Journal of General Plant Pathology.2025; 91(1): 31.     CrossRef

Foxglove aphid (FA), Aulacorthum solani Kaltenbach, is a notable economic pest of soybean plants causing deformation of leaves, the transmission of viruses, and significant yield losses. Host plant resistance is considered the most environment-friendly and economic approach to insect-pest management. However, studies on the activities, biology, and management of FA are still limited. This review article will focus on current knowledge on the prospect of utilizing host plant resistance in the management of FA based on molecular and genetic studies. The soybean plant’s resistance against FA is conferred by the presence of the resistance to Aulacorthum solani gene (Raso). Currently, two Raso genes with NB-ARC domain and leucine-rich repeat-containing gene (NBS-LRR) were proposed to confer resistance against FA biotypes in Japan and Korea. The use of soybean Williams 82 sequence assembly in these studies showed the chromosome position of identified QTL/genes where they were fine-mapped. In exploring this existing knowledge, we suggest identifying more resistant soybean cultivars and new Raso genes and then combining the R genes in resistant cultivars to produce plants with active defense responses across different biotypes of FA. Furthermore, we recommend an aphid whole-genome sequence study to understand FA adaptation to soybean and biotype.

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• Courtship and Mating Behavior of the Aphid Parasitoid Praon volucre: Effects of Host Association and Behavioral Lateralization
  Maria C. Boukouvala, Demeter Lorentha S. Gidari, Nickolas G. Kavallieratos
  Insects.2026; 17(2): 192.     CrossRef

The development of rice seedlings stressed by drought and salt is shown by different morphometric and colorimetric traits. These distinctions can be used to understand the response of plants to challenging conditions. Therefore, this study aimed to assess the efficacy of image-based phenotyping in the early testing of rice plants and observe how the plants respond to both drought and salinity. A stress tolerance index with multivariate analysis was used for the selection of the most important traits. The experiment consisted of 2 factors, namely the degree of environmental stress and rice genotype. Furthermore, the degree of environmental stress comprised normal (NaCl and PEG 0%), drought (10% PEG), salinity (60 mM NaCl), as well as a combination of moderate drought and salinity (5% PEG + 30 mM NaCl). The results showed that both morphometric (area, convex hull, bounding area, perimeter, centermassy) and colorimetric (CIVE, VARI, RGBVI, MGRVI, NDI, GLI, NGRDI) can be used as selection characters.

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• Geometric image-based phenotyping and physiological analysis for validation of rice salinity tolerance screening under artificial pot conditions
  Muhammad Fuad Anshori, Bambang Sapta Purwoko, Iswari Saraswati Dewi, Willy Bayuardi Suwarno, Sintho Wahyuning Ardie, Nono Carsono, Abd Haris Bahrun, Suharman Hamzah, Achmad Kautsar Baharuddin, Purnama Isti Khaerani, Bernadetta Rina Hastilestari, Zeeshan A
  BMC Plant Biology.2026;[Epub]     CrossRef
• Yield assessment of F6 generation tomato lines under irrigated and drought environments based on stress tolerance index
  Nirwansyah Amier, Muh Farid, Muhammad Fuad Anshori, Rahmansyah Dermawan, Adnan, Jekvy Hendra
  Reproduction and Breeding.2025; 5(4): 214.     CrossRef
• Yield and vegetation index of different maize varieties and nitrogen doses under normal irrigation
  Rusnadi Padjung, Muh. Farid, Yunus Musa, Nasaruddin Nasaruddin, Nurfaida Nurfaida, Muhammad Fuad Anshori, Mahmud Achmad, Abdul Rahman Arinong, Nirwansyah Amier
  Open Agriculture.2025;[Epub]     CrossRef
• Integration of gamma irradiation breeding from doubled haploid and systematic screening to develop adapted rice mutants under salinity stress
  Muhammad Fuad Anshori, Bambang Sapta Purwoko, Nono Carsono, Iswari Saraswati Dewi, Abd Haris Bahrun, Achmad Kautsar Baharuddin, Reskiana Rahman, Wijaya Murti Indriatama, Majed Alotaibi, Nawab Ali, Mahmoud F. Seleiman
  BMC Plant Biology.2025;[Epub]     CrossRef
• Optimizing hydroponic salinity screening: a novel approach using image-based phenotyping for double haploid rice selection
  Muhammad Fuad Anshori, Bambang Sapta Purwoko, Nono Carsono, Iswari Saraswati Dewi, Willy Bayuardi Suwarno, Sintho Wahyuning Ardie, Abd Haris Bahrun, Achmad Kautsar Baharuddin, Purnama Isti Khaerani, Zeeshan Ali, Majed Alotaibi, Nawab Ali, Mahmoud F. Selei
  Frontiers in Sustainable Food Systems.2025;[Epub]     CrossRef

To determine the lethal dose (LD) and growth-reducing dose (GR), the exposures were from gamma activity rates such as low activity rate by multipurpose panoramic 70 Ci and high activity rate by Gamma Cell 3 kCi. The study material was sourced by Cobalt-60 (⁶⁰Co) with variant doses, i.e., 10Gy, 20Gy, 30Gy, 40Gy, 50Gy, and 60Gy for each gamma activity rate. The study was performed at the Center for Isotope and Radiation Application, National Nuclear Energy Agency of Indonesia (CIRA-NNEA). Data were analyzed using non-parametric tests and analysis of variance. The lethal dose (LD₅₀) and growth reduction (GR₅₀) were identified based on regression analysis. The analysis of variance revealed that highly significant differences among irradiation treatments in number of leaves, survival rate, and plant height. A linear regression model was developed to determine the mean LD₅₀ and GR₅₀ of Super Napier grass. The highest variability of mutants was observed in gamma-ray irradiated mutants with lethal doses (LD₅₀). LD₅₀, 35.82Gy-55.71Gy, at a low activity rate (Multipurpose panoramic irradiator 70 Ci) is higher than the high activity rate (Gamma Cell 3 kCi), 28.98-28.99. In general, the survival rate of Super Napier grass decreased along with increasing irradiation dose. The generated LD₅₀ and GR₅₀ were identified as optimal dosages for the radiosensitivity of Super Napier grass. This study becomes preliminary mutagenesis breeding to generate genetic diversity of grass, specifically in Super Napier grass.

Hops are dioecious, with only female plants cultivated for resin production and primarily used in brewing. Therefore, early sex identification at the seedling stage is crucial for breeding and cultivation. Molecular marker-assisted selection facilitates rapid and reliable sex identification of hops. We developed molecular male markers by leveraging sequence information from male-specific regions in a designated public database. To assess the accuracy of sex identification using the newly generated markers, we performed PCR analysis on four cultivars of hops with known sexes. Seventy-eight percent of the tested PCR primers correlated with the male sex phenotype. Following optimization, four primer pairs were successfully converted into male-specific PCR markers.

Rice domestication has led to cultivated rice with no or short awns. Discovery of novel genes associated to awn length is of paramount importance for understanding the molecular mechanisms for the transformation of wild rice long awns to awnless cultivated rice. In this study, we employed Next-Generation Sequencing based QTL-seq approach to identify genomic regions associated with awn length using mapping population derived from a cross between awnless Tun Sart and awned Sobaekmangsudo. QTL-seq analysis identified two awn length QTLs viz. qAwn-4 (12.8-20.3 Mb) and qAwn-8 (22.3-27.2 Mb) on chromosome 4 and 8, respectively. Based on the sequence comparison between the two parents, Os04g0350700 (bHLH transcription factor) was postulated to be the candidate of Awn-4 gene. Further discovery of the novel genes in qAwn-8 interval will provide insights into the genetic architecture of awn length.

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• Genetic variability, heritability and genetic advance in Iranian local rice genotypes for yield, and some agronomic traits
  Mostafa Modarresi
  Reproduction and Breeding.2026; 6(1): 9.     CrossRef
• QTLs associated with sex inheritance in Pistacia atlantica
  S. Kafkas
  Acta Horticulturae.2025; (1439): 425.     CrossRef
• OsLRR-RLP2 Gene Regulates Immunity to Magnaporthe oryzae in Japonica Rice
  Hyo-Jeong Kim, Jeong Woo Jang, Thuy Pham, Van Tuyet, Ji-Hyun Kim, Chan Woo Park, Yun-Shil Gho, Eui-Jung Kim, Soon-Wook Kwon, Jong-Seong Jeon, Sun Tae Kim, Ki-Hong Jung, Yu-Jin Kim
  International Journal of Molecular Sciences.2024; 25(4): 2216.     CrossRef

Soybean [Glycine max (L.) Merrill] seed has poor storability under high temperature and high humidity. It loses viability in a relatively short time. Seed aging of stored soybeans leads to poor germination and a decrease in yield. The accelerated aging vigor test, which provides useful information for determining seed storability as well as field emergence potential, is a rapid aging experiment and could be used to determine soybean seed quality. This study was conducted to determine the seed viability of Korean soybean cultivars and soybean lines with altered fatty acid compositions under accelerated aging conditions. Results demonstrated that Songhagkong, a Korean soybean cultivar, was the most stable at 3, 4, and 5 days of accelerated aging conditions. Furthermore, two soybean lines with high stearic acid content exhibited >70.0% reduction rate, whereas three soybean lines with high oleic acid content exhibited 7.4%-11.8% reduction rates. Soybean lines with mid-oleic acid and elevated linolenic acid contents exhibited various reduction rates depending on genotypes. Therefore, these soybean lines can be used as breeding material for developing a new soybean cultivar with strong seed vigor and better storability under unfavorable conditions. Therefore, a genetic study on this soybean cultivar is warranted.

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• Non-Destructive Detection of Soybean Storage Quality Using Hyperspectral Imaging Technology
  Yurong Zhang, Wenliang Wu, Xianqing Zhou, Jun-Hu Cheng
  Molecules.2025; 30(6): 1357.     CrossRef
• Measures to Revitalize Seed Processing to Improve Added Value in Crop Breeding
  Jin-heon Kim, Dong-gyu Kim, Ki-Taek Kim, Chanju Yu
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• Prediction of Seed Viability in Wheat (Triticum aestivum L.) Using Near-Infrared Reflectance Spectroscopy
  Hee-Jong Woo, Kyung-Soon Kim, So Yeon Hong, Hyemyeong Yoon, Nayoung Ro, Gyu Taek Cho, Ho-Cheol Ko, Dong Su Yu
  Korean Journal of Breeding Science.2024; 56(4): 461.     CrossRef

Gene introgression that involves the transfer of favorable allelic diversity for broadening the genetic base of breeding materials is a powerful 'toolkit' for creating novel allelic combinations during plant sexual reproduction. It is a key factor playing an important role in plant breeding schemes by reintroducing genetic variation at selective sweeps or introgression of desirable traits required for the development of new varieties. Meiosis is a specialized cell division not only enables sexually reproducing organisms to reduce their genomic constituent by half, also provides indefinitely novel combinations of allelic diversity by reshuffling the parental genetic makeup. Crossing over that takes place during prophase-I facilitates the meiotically exchange of genetic materials between homolog pairs as well as their accurate segregations. It is tightly modulated and many intrinsic factors and extrinsic agents are associated with regulation of the process, however, the modulation of meiosis is possible. Although, advanced approaches such as CRIPR/Cas and Virus-Induced gene Silencing (VIGS) have opened new horizons for manipulation of meiotic recombination, distant hybridization could effectively influence the frequency and distribution of homologous (HR) and particularly homoeologous recombination (HeR). In this review, we provide a brief overview of the recent advances in the plant mechanisms for manipulation of HR and HeR employing distant hybridization.

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• Validation of SNP Markers for Diversity Analysis, Quality Control, and Trait Selection in a Biofortified Cassava Population
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  South African Journal of Botany.2024; 171: 315.     CrossRef

Watermelon [Citrullus lanatus (Thunb.) Matsum and Nakai] is one of the economically most important fruit crops of the Cucurbitaceae family. Among different watermelon traits, disease resistance and fruit quality are the important traits for growers and consumers. The single nucleotide polymorphism (SNP) markers similar to those traits can potentially and cost-effectively distinguish the genetic variations among these traits. Consequently, we developed 33 SNP makers linked to different watermelon traits associated with fruit quality and disease resistance, and validated in the genetic resources of watermelon and F1 breeding lines using ‘Fluidigm SNP Genotyping’ assay. Most of the SNP markers distinguished the alleles into three different types such as reference allele, alternative allele and heterozygous from watermelon genotypes for various traits. The SNP markers ‘ZymFL-T81P’ (ZYMV- resistance), ‘FON1-U161’ and ‘FON1-S075’ (Fusarium wilt-resistance), ‘Pmr21-Cla831’ (PM-resistance), and ‘ClGBS-J168’ and ‘GBS-GC230’ (GSB-resistance) can successfully differentiate resistant (R), susceptible (S) and heterozygous watermelon genotypes. Similarly, the SNP marker associated with sugar content, citrulline content, arginine content, rind hardness, flesh firmness, fruit shape, rind strip pattern of watermelon fruit and seed coat colour can successfully distinguished the watermelon genetic resources and F1 breeding lines as reference allele (A) type, alternative allele (B) type and heterozygous (H). These SNP markers could be utilized for marker assisted selection as well as screening of a large number of watermelon germplasm for fruit quality and disease resistance. However, further validation like artificial inoculation of pathogens for the traits related to disease resistance is required in watermelon crops.

Amylose content is a key factor affecting the eating and cooking qualities of rice. In our previous study, protein disulfide isomerase like 1-1 (PDIL1-1) on chromosome 11 was a candidate gene for amylose content (AC) trait. Based on whole genome sequencing, polymorphisms were identified between Dodamssal and Hwayeong on PDIL1-1. In this study, the association of PDIL1-1 on AC was characterized. Haplotype analysis of 79 KNU accessions highlighted the presence of allelic patterns identifiable by the sequence variants between Dodamssal and Hwayeong. Identified SNPs and InDel were used to develop gene-based molecular markers for PDIL1-1. The 29 F₂ plants and 160 Korean japonica cultivars were classified into two and three groups, respectively, based on the G/A SNP at position -4973180 and ATTCG/G at position -4974161. Our findings revealed that the G/A SNP at position -4973180 of PDIL1-1 plays a role in regulating the AC in japonica rice. This suggested that PDIL1-1 would be useful for fine-tuning the rice AC. To our knowledge, no studies of the allelic variation of the PDIL1-1 gene regulating AC have been reported worldwide. Furthermore, no research had reported the development of PDIL1-1 gene-based molecular markers.

The conventional soybean breeding program by single seed descent method required around 8 to 9 years to develop a cultivar. Through the advancement of breeding techniques, such as marker-assisted selection, required resources could be significantly saved, but the generation advancement step still slows down the entire soybean breeding program time course. In this study, 28 soybean varieties were tested to find the optimal speed breeding conditions for soybeans that could rapidly advance one generation with 2 light sources, 3 light conditions, and 2 planting densities. Plants were kept under short-day conditions (9 hours light/15 hours dark). We optimized the growth conditions for shortening the period of soybean generation progression based on speed breeding. The optimizing conditions are as follows. (1) Irradiation using LED light source for 9 hours, (2) 506 mmol/(m²∙s) of PPFD at 30 cm from the ground, (3) Planting density of 5 cm × 5 cm, (4) temperature of 25℃ ± 2℃ and (5) humidity of 50% ± 10%. If this condition is used, soybeans can be advanced by one generation within an average of 73 days. It is possible to advance five generations a year using only indoor speed-breeding system. Furthermore, if it includes the development of lines in the field, four generation per year, which is advance three generations using indoor speed-breeding system and one generation in the field, is allowed to increase soybean breeding speed with minimum input.

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• Eight Fusion Events of TIFY-Transcription Factor Family Genes in Eudicots
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  Tropical Plant Biology.2026;[Epub]     CrossRef
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  Frontiers in Plant Science.2025;[Epub]     CrossRef
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  Physiologia Plantarum.2025;[Epub]     CrossRef
• Impact of light quality on accelerating soybean speed breeding efficiency using LED-based systems
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  Discover Plants.2025;[Epub]     CrossRef
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  Marina Ćeran, Dragana Miladinović, Vuk Đorđević, Dragana Trkulja, Aleksandra Radanović, Svetlana Glogovac, Ankica Kondić-Špika
  Frontiers in Sustainable Food Systems.2024;[Epub]     CrossRef

Submergence damage to rice was reported as one of the major problems in rainfed lowland areas where the water remains. This study assessed the submergence tolerance of core collection during the seedling stage of the rice using dry seeds. Also, genome-wide association study (GWAS) combined with principal component analysis (PCA) and kinship matrix analysis was performed to identify quantitative trait loci (QTL) for submergence tolerance. Through this GWAS analysis, nine lead SNPs were confirmed to be associated with submergence tolerance, and a linkage disequilibrium (LD) decay analysis identified the 230 kb exploratory range for the detection of QTLs and candidate genes. Nine QTL were detected, on chromosomes 3 (qSUB3), 4 (qSUB4), 6 (qSUB6-1 and qSUB6-2), 11 (qSUB11-1, qSUB11-2 and qSUB11-3), and 12 (qSUB12-1 and qSUB12-2). Two candidate genes (Os03g0679300 and Os11g0517800) in the two QTL regions associated with submergence tolerance were detected. The results of this study provide associated SNPs in candidate genes for submergence condition and strategies for developing submergence condition in breeding programs.

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• Comprehensive Evaluation of Cold and Anaerobic Tolerance in Rice Oryza sativa L. and Screening of Multistress‐Resistant Germplasm
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  Plant Breeding.2026; 145(3): 425.     CrossRef
• Identification of Candidate Genes for Hypoxia Tolerance in Rice by Genome-Wide Association Analysis and Transcriptome Sequencing
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  Rice.2025;[Epub]     CrossRef
• Unraveling the genetic enigma of rice submergence tolerance: Shedding light on the role of ethylene response factor-encoding gene SUB1A-1
  Md Ibrahim Khalil, Md Mahmudul Hassan, Swadesh Chandra Samanta, Abul Kashem Chowdhury, Md Zahid Hassan, Nasar Uddin Ahmed, Uzzal Somaddar, Sharmistha Ghosal, Arif Hasan Khan Robin, Ujjal Kumar Nath, Mohammad Golam Mostofa, David J. Burritt, Chien Van Ha,
  Plant Physiology and Biochemistry.2024; 206: 108224.     CrossRef
• Biocuration of a Transcription Factors Network Involved in Submergence Tolerance during Seed Germination and Coleoptile Elongation in Rice (Oryza sativa)
  Sushma Naithani, Bijayalaxmi Mohanty, Justin Elser, Peter D’Eustachio, Pankaj Jaiswal
  Plants.2023; 12(11): 2146.     CrossRef

Cold stress is one of the serious abiotic stresses for stable rice production especially in high-latitude temperate region and high-altitude tropical area. Improving cold tolerance at seedling stage led stable seedling growth with yield stability. In this study, QTLs for cold tolerance at seedling stage were identified using the 96 introgression lines (ILs) derived from an inter-specific cross between Hwaseong (Oryza sativa) and Oryza rufipogon. Three QTLs were detected and the O. rufipogon alleles at two QTL (qCTS1 and qCTS12) improved cold tolerance in the Hwaseong genetic background whereas the O. rufipogon allele at qCTS10 on chromosome 10 decreased cold tolerance. Among these three QTLs, a major QTL qCTS12 explained 27.5% of phenotypic variation. Fine-mapping indicated that qCTS12 was different from those QTL reported in previous studies based on the map location suggesting that qCTS12 might be a new allele and is not associated with deleterious genes such fertility reduction. Among the 96 introgression lines, two lines, CR60 and CR61 were selected based on enhanced cold tolerance at seedling stage. qCTS12, therefore, provides a valuable allele for breeding rice with improved cold tolerance.

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• Stage-specific screening reveals differential resilience response to cold stress in rice
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  PLOS One.2026; 21(4): e0338290.     CrossRef
• Genome-wide Association Study for Cold Tolerance at Seedling Stage Using a Core Collection of Korean Rice
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  Korean Journal of Breeding Science.2024; 56(3): 225.     CrossRef

Drought tolerance is derived from complex quantitative traits that are associated with different shoot and root morphological characters. This study assessed the genetic and phenotypic variation of 12 maize inbred lines and performed association analysis of 11 drought-related traits using 360 simple sequence repeats (SSRs), detecting 1,604 alleles, with an average of 4.4 alleles per locus. The average values of gene diversity (GD) and polymorphism information content (PIC) were 0.648 and 0.598, respectively. In principal component analysis (PCA), shoot fresh weight (SFW), shoot dry weight (SDW), stem weight (SW), leaf weight (LW), root fresh weight (RFW), root dry weight (RDW), and leaf area (LA) traits contributed greatly to the PCA. Association analysis was performed using a general linear model with a Q-matrix (Q GLM) and a mixed linear model with Q and K-matrices (Q + K MLM). Twelve SSR markers for drought tolerance trait were detected by Q GLM, and all maize inbred lines were clearly divided into two groups in accordance with their drought tolerance. Duplicated significant marker-trait associations (SMTAs) between Q GLM and Q + K MLM identified eight marker-trait associations involving four SSR markers that were associated with the traits of SW, SFW, RFW, and RDW with a significant level of P < 0.05. The umc1175 and umc2092 were associated with SW and SFW; umc1503 was associated with RFW, SFW, and SW; and umc2341 was associated with RDW. The detection of loci associated with drought-related traits in this study may provide better opportunities to improve maize drought tolerance by marker-assisted selection (MAS).

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• Association Mapping for Evaluation of Population Structure, Genetic Diversity, and Physiochemical Traits in Drought-Stressed Maize Germplasm Using SSR Markers
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Plant Growth Promoting Rhizobacteria (PGPR) were used in many previous studies for increasing plant growth and productivity. Some mechanisms were used to enhance the soil productivity such as mineral phosphate solubilization, siderophore production, biological nitrogen fixation, induced systemic resistance and indole acetic acid (IAA) production. Some of the related researches adopted the phosphate solubilization in organisms which was repressed in the presence of succinate resembling the phenomenon of catabolite repression. In addition, the sugar utilization pattern (monosaccharide, disaccharide, and trisaccharide), organisms showed the characteristics like slow and fast-growing rhizobia respectively. Whole-genome sequencing has been used for identifying unique genes in Fast-growing Rhizobia. Existing literature in PGPR studies has been considered and mechanisms for increasing plant growth and productivity have been identified. The review tries to analyse the mechanism of phosphate solubilization and sugar utilization in fast growing Rhizobia. On the contrary, repression due to various carbon sources such as succinate has been reported, leading to succinate mediated catabolite repression.

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