Template-Type: ReDIF-Article 1.0 Author-Name: Samuel Goitom Misginna Author-Workplace-Name: Department of Genetics and Biotechnology, Faculty of Agriculture and Technology, University of South Bohemia, České Budějovice, Czech Republic Author-Name: Petra Röszlerová Author-Workplace-Name: Department of Genetics and Biotechnology, Faculty of Agriculture and Technology, University of South Bohemia, České Budějovice, Czech Republic Author-Workplace-Name: Institute of Laboratory Diagnostics and Public Health, Faculty of Health and Social Sciences, University of South Bohemia, České Budějovice, Czech Republic Author-Name: Omar Gaoua Author-Workplace-Name: Department of Genetics and Biotechnology, Faculty of Agriculture and Technology, University of South Bohemia, České Budějovice, Czech Republic Author-Name: Patrick Kamulegeya Author-Workplace-Name: Department of Genetics and Biotechnology, Faculty of Agriculture and Technology, University of South Bohemia, České Budějovice, Czech Republic Author-Name: Marie Pichová Author-Workplace-Name: Department of Genetics and Biotechnology, Faculty of Agriculture and Technology, University of South Bohemia, České Budějovice, Czech Republic Author-Name: Eva Jozová Author-Workplace-Name: Department of Genetics and Biotechnology, Faculty of Agriculture and Technology, University of South Bohemia, České Budějovice, Czech Republic Author-Name: Vladislav Čurn Title: Molecular markers and genomic resources in caraway (Carum carvi L.): Current status, research gaps, and strategic directions for breeding Abstract: Caraway (Carum carvi L.) is an economically important spice and medicinal crop valued for its essential oil composition, particularly its high content of carvone and limonene. Despite its commercial relevance, compared with that of other Apiaceae species, the development of genomic resources remains limited. Molecular research has progressed from early dominant marker systems, including random amplified polymorphic DNA (RAPD) and inter simple sequence repeat (ISSR), to more recent SNP-based genotyping approaches that clarify population structure and flowering-type differentiation. However, key genomic resources, such as simple sequence repeat (SSR) markers, a high-quality reference genome, quantitative trait locus (QTL) mapping, genome-wide association studies (GWAS), and transcriptomic datasets, are still lacking. This review synthesises current knowledge on molecular marker applications in caraway and identifies major gaps limiting breeding progress. Evidence from related Apiaceae species indicates that systematic SSR development and integration of genome-based tools can substantially enhance breeding efficiency. Particular emphasis is placed on a phased strategy for SSR development in caraway, positioned as complementary to single-nucleotide polymorphism (SNP)-based approaches within a progressive genome-enabled breeding framework. Strengthening the molecular infrastructure of caraway will support precision breeding aimed at improving yield stability, essential oil quality, and environmental adaptability. Keywords: Apiaceae, germplasm characterisation, microsatellites, single nucleotide polymorphism (SNP) genotyping, transcriptomics Journal: Czech Journal of Genetics and Plant Breeding Pages: 121-134 Volume: 62 Issue: 3 Year: 2026 DOI: 10.17221/16/2026-CJGPB File-URL: http://cjgpb.agriculturejournals.cz/doi/10.17221/16/2026-CJGPB.html File-Format: text/html File-URL: http://cjgpb.agriculturejournals.cz/doi/10.17221/16/2026-CJGPB.pdf File-Format: Application/pdf X-File-Ref: http://agriculturejournals.cz/RePEc/caa/references/cjg-202603-0001.txt Handle: RePEc:caa:jnlcjg:v:62:y:2026:i:3:id:16-2026-CJGPB Template-Type: ReDIF-Article 1.0 Author-Name: Berna Sarman Author-Workplace-Name: Agricultural Biotechnology, Faculty of Agriculture, Van Yüzüncü Yil University, Van, Türkiye Author-Name: Metin Koçak Title: Assessment of genetic diversity and population structure of almond germplasm in Van Province, Türkiye, using iPBS-retrotransposon-based markers Abstract: The genetic characterisation of naturally occurring almond genotypes can guide the selection of genetic resources to be used in the breeding programme. Therefore, this study aims to assess the genetic diversity and population structure of almond germplasm comprising 50 accessions naturally occurring in Van, Türkiye, along with two commercial varieties (Pabuç and Dokuzoğuz). Thirteen inter-primer binding site (iPBS) retrotransposon markers generated a total of 102 bands, of which 95 were polymorphic. The average polymorphic band number per marker was 7.3, with a range of 5 to 13. A formula yielding a maximum of 0.5 resulted in polymorphic information content (PIC) values between 0.27 and 0.43, with a mean value of 0.36. Unweighted pair group method algorithm (UPGMA), principal coordinate analysis (PCoA), and STRUCTURE analysis, based on Bayesian clustering analysis, yielded consistent results, indicating that local populations (Akdamar and Çarpanak) were distinctly grouped, while commercial accessions were clustered with Çarpanak accessions. The diversity metrics and classification analysis utilising 13 iPBS-retrotransposon markers demonstrated that the iPBS-retrotransposon marker system possesses significant promise for evaluating the genetic variety and population structure of almonds. Keywords: almond, genetic resources, genetic variation, iPBS-retrotransposon markers, molecular characterisation Journal: Czech Journal of Genetics and Plant Breeding Pages: 135-145 Volume: 62 Issue: 3 Year: 2026 DOI: 10.17221/12/2026-CJGPB File-URL: http://cjgpb.agriculturejournals.cz/doi/10.17221/12/2026-CJGPB.html File-Format: text/html File-URL: http://cjgpb.agriculturejournals.cz/doi/10.17221/12/2026-CJGPB.pdf File-Format: Application/pdf X-File-Ref: http://agriculturejournals.cz/RePEc/caa/references/cjg-202603-0002.txt Handle: RePEc:caa:jnlcjg:v:62:y:2026:i:3:id:12-2026-CJGPB Template-Type: ReDIF-Article 1.0 Author-Name: Shahril Ab Razak Author-Name: Alny Marlynni Abd Majid Author-Workplace-Name: Agri-omic and Bioinformatic Programme, Biotechnology & Nanotechnology Research Centre, MARDI Headquarters, Serdang, Malaysia Author-Name: Rahiniza Kamaruzaman Author-Workplace-Name: Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Malaysia Author-Name: Norliza Abu Bakar Author-Workplace-Name: Agri-omic and Bioinformatic Programme, Biotechnology & Nanotechnology Research Centre, MARDI Headquarters, Serdang, Malaysia Author-Name: Rabiatul Adawiah Zainal Abidin Author-Workplace-Name: Agri-omic and Bioinformatic Programme, Biotechnology & Nanotechnology Research Centre, MARDI Headquarters, Serdang, Malaysia Author-Name: Yun Shin Sew Author-Workplace-Name: Agri-omic and Bioinformatic Programme, Biotechnology & Nanotechnology Research Centre, MARDI Headquarters, Serdang, Malaysia Author-Name: Norfarhan Mohd-Assaad Author-Workplace-Name: Department of Applied Physics, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Malaysia Author-Workplace-Name: Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, Bangi, Malaysia Author-Name: Asmuni Mohd Ikmal Author-Workplace-Name: Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Malaysia Author-Name: Noraziyah Abd Aziz Shamsudin Author-Workplace-Name: Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Malaysia Title: Genetic diversity of selected Malaysian rice accessions using microsatellite markers Abstract: Genetic diversity of plant genetic resources provides the foundation for breeding programmes aimed at developing high-yielding rice varieties with tolerance to biotic and abiotic stresses. Given the abundance of available genetic resources, efficient approaches for their characterisation are essential. In this study, 182 Malaysian rice accessions representing different maturity groups were characterised using 20 polymorphic simple sequence repeat (SSR) markers. The analysis identified 183 alleles, ranging from two (RM507) to 22 (RM154), with an average of 9.15 alleles per locus. Observed and expected heterozygosity ranged from 0.000 to 0.506 and 0.319 to 0.864, respectively. Polymorphism information content (PIC) values ranged from 0.2744 (RM495) to 0.8475 (RM154), with an average of 0.6216 per locus. Unweighted pair group method with arithmetic mean (UPGMA) analysis revealed two major groups. In general, the accessions were clustered according to their adaptive ecosystem type, with most lowland varieties, including lowland breeding lines (92.4%), assigned to Group I, whereas most upland varieties (86.7%) belonged to Group II. This grouping pattern was supported by STRUCTURE analysis, which identified K = 2 as the optimal number of clusters, indicating that the studied accessions were structured into two major genetic groups. Principal coordinate analysis (PCoA) further supported this grouping pattern, with the first three axes explaining 39.63% of the total variation. Analysis of molecular variance (AMOVA) showed that 31% of the total variation occurred among populations, 63% among accessions, and 6% within accessions. The results also indicated the possible presence of duplicate accessions within the collection. This study provides valuable insights for future breeding programmes aimed at developing high-yielding rice varieties with a broad genetic base and supports the effective management and conservation of rice genetic resources. Keywords: genetic variability, population structure, SSR marker, traditional rice Journal: Czech Journal of Genetics and Plant Breeding Pages: 146-156 Volume: 62 Issue: 3 Year: 2026 DOI: 10.17221/133/2025-CJGPB File-URL: http://cjgpb.agriculturejournals.cz/doi/10.17221/133/2025-CJGPB.html File-Format: text/html File-URL: http://cjgpb.agriculturejournals.cz/doi/10.17221/133/2025-CJGPB.pdf File-Format: Application/pdf X-File-Ref: http://agriculturejournals.cz/RePEc/caa/references/cjg-202603-0003.txt Handle: RePEc:caa:jnlcjg:v:62:y:2026:i:3:id:133-2025-CJGPB Template-Type: ReDIF-Article 1.0 Author-Name: Tri Joko Santoso Author-Workplace-Name: Research Center for Horticultural Crops, Research Organization for Agriculture and Food, National Research and Innovation Agency, Cibinong, Indonesia Author-Name: Reflinur Reflinur Author-Workplace-Name: Research Center for Applied Botany, Research Organization for Life Sciences and Environment, National Research and Innovation Agency, Cibinong, Indonesia Author-Name: Zeeshan Ali Author-Name: Tri Handayani Author-Workplace-Name: Research Center for Horticultural Crops, Research Organization for Agriculture and Food, National Research and Innovation Agency, Cibinong, Indonesia Author-Name: Alberta Dinar Ambarwati Author-Workplace-Name: Research Center for Horticultural Crops, Research Organization for Agriculture and Food, National Research and Innovation Agency, Cibinong, Indonesia Author-Name: Chotimatul Azmi Author-Workplace-Name: Research Center for Horticultural Crops, Research Organization for Agriculture and Food, National Research and Innovation Agency, Cibinong, Indonesia Author-Name: Atmitri Sisharmini Author-Workplace-Name: Research Center for Food Crops, Research Organization for Agriculture and Food, National Research and Innovation Agency, Cibinong, Indonesia Author-Name: Aniversari Apriana Author-Workplace-Name: Research Center for Food Crops, Research Organization for Agriculture and Food, National Research and Innovation Agency, Cibinong, Indonesia Author-Name: Dwinita Wikan Utami Author-Workplace-Name: Research Center for Horticultural Crops, Research Organization for Agriculture and Food, National Research and Innovation Agency, Cibinong, Indonesia Author-Name: Kristianto Nugroho Author-Workplace-Name: Research Center for Horticultural Crops, Research Organization for Agriculture and Food, National Research and Innovation Agency, Cibinong, Indonesia Title: Transcriptomic profiling of shallots (Allium cepa var. aggregatum) reveals differential gene expression patterns under nitrogen deficiency Abstract: Nitrogen (N) is essential for crop productivity, yet excessive fertilisation decreases the nitrogen use efficiency and increases the environmental risks. Despite the economic and medicinal importance of the shallot, its molecular response to N deficiency remains unclear. We performed transcriptome profiling of two cultivars (Bima-0 and Bima 1) under N deficient and N-sufficient conditions. The RNA sequencing identified 438 differentially expressed genes (DEGs). The gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed significant modulation of the nitrogen metabolism, amino acid biosynthesis, glutathione metabolism, and stress responses pathways, indicating coordinated metabolic reprogramming under N limitation. The cultivar-specific expression patterns suggested differential adaptive strategies. The quantitative real-time polymerase chain reaction (qRT-PCR) validation of fifteen DEGs confirmed the reliability of the RNA-Seq results. The nitrogen deficiency predominantly repressed the photosynthetic and growth-linked genes while activating the stress-responsive pathways. These findings provide the first transcriptome-level insights into the N deficiency responses in shallots and identify candidate genes and pathways for improving the nitrogen use efficiency (NUE) and developing the sustainable fertiliser management of Allium crops. Keywords: DEGs, gene enrichment, gene expression, metabolic pathways, nitrogen use efficiency Journal: Czech Journal of Genetics and Plant Breeding Pages: 157-169 Volume: 62 Issue: 3 Year: 2026 DOI: 10.17221/25/2026-CJGPB File-URL: http://cjgpb.agriculturejournals.cz/doi/10.17221/25/2026-CJGPB.html File-Format: text/html File-URL: http://cjgpb.agriculturejournals.cz/doi/10.17221/25/2026-CJGPB.pdf File-Format: Application/pdf X-File-Ref: http://agriculturejournals.cz/RePEc/caa/references/cjg-202603-0004.txt Handle: RePEc:caa:jnlcjg:v:62:y:2026:i:3:id:25-2026-CJGPB Template-Type: ReDIF-Article 1.0 Author-Name: Samuel Goitom Misginna Author-Workplace-Name: Department of Genetics and Biotechnology, Faculty of Agriculture and Technology, University of South Bohemia, České Budějovice, Czech Republic Author-Name: Omar Gaoua Author-Workplace-Name: Department of Genetics and Biotechnology, Faculty of Agriculture and Technology, University of South Bohemia, České Budějovice, Czech Republic Author-Name: Petra Röszlerová Author-Workplace-Name: Department of Genetics and Biotechnology, Faculty of Agriculture and Technology, University of South Bohemia, České Budějovice, Czech Republic Author-Workplace-Name: Institute of Laboratory Diagnostics and Public Health, Faculty of Health and Social Sciences, University of South Bohemia, Czech Republic Author-Name: Musab A Isak Author-Workplace-Name: Department of Agricultural Sciences and Technology, Faculty of Graduate School of Natural and Applied Sciences, Erciyes University, Kayseri, Türkiye Author-Name: Ondrej Hejna Author-Workplace-Name: Department of Genetics and Biotechnology, Faculty of Agriculture and Technology, University of South Bohemia, České Budějovice, Czech Republic Author-Name: Patrick Kamulegeya Author-Workplace-Name: Department of Genetics and Biotechnology, Faculty of Agriculture and Technology, University of South Bohemia, České Budějovice, Czech Republic Author-Name: Eva Jozová Author-Workplace-Name: Department of Genetics and Biotechnology, Faculty of Agriculture and Technology, University of South Bohemia, České Budějovice, Czech Republic Author-Name: Vladislav Čurn Title: Quantum-inspired machine learning for screening PEG-induced drought stress responses in caraway (Carum carvi L.) Abstract: Drought is a significant factor limiting the growth and early establishment of caraway (Carum carvi L.), a valuable medicinal and aromatic plant. In this study, polyethylene glycol (PEG-6000)-induced osmotic stress assays were combined with statistical and machine learning (ML) approaches to assess early drought responses in five caraway cultivars and breeding materials. Seeds were subjected to four PEG concentrations (0, 5, 10 and 15 %), and key germination and seedling traits, including germination percentage (GP), root length (RL), root fresh weight (RFW), root dry weight (RDW), shoot height (SH), shoot fresh weight (SFW), and shoot dry weight (SDW), were measured. Higher PEG levels caused a sharp, accession-dependent decline in all traits, with germination dropping by 68 % at a 15 % PEG. Cultivars Aprim and H1b2/12 consistently showed better germination, shoot height, and biomass retention across stress levels, while Aklei exhibited lower germination but relatively stronger root growth, suggesting a differential adaptive response under osmotic stress. A linear model (LM) incorporating PEG concentration, accession, and their interaction served as the primary interpretable framework, explaining a large proportion of trait variation (R2 = 0.81-0.94). Principal component analysis (PCA) and correlation analyses further revealed coordinated responses among biomass-related traits and differentiation in early-stage stress responses among accessions. Traditional ML models (MLP and SVR) were compared with quantum-inspired architectures (QiMLP and QiSVR); the quantum-inspired models showed comparable predictive performance in this dataset for certain traits, with QiMLP achieving the highest overall accuracy (R2 = 0.88-0.94). This study presents an integrated phenotyping framework combining controlled stress assays with interpretable statistical modelling to evaluate early growth responses to PEG-induced drought stress in caraway. Overall, the results highlight accession-specific differences in early drought response and provide a useful basis for phenotyping and early-stage screening in caraway breeding. Keywords: medicinal, aromatic and spice plants, neural networks, osmotic stress, predictive phenotyping, seedling traits Journal: Czech Journal of Genetics and Plant Breeding Pages: 170-189 Volume: 62 Issue: 3 Year: 2026 DOI: 10.17221/18/2026-CJGPB File-URL: http://cjgpb.agriculturejournals.cz/doi/10.17221/18/2026-CJGPB.html File-Format: text/html File-URL: http://cjgpb.agriculturejournals.cz/doi/10.17221/18/2026-CJGPB.pdf File-Format: Application/pdf X-File-Ref: http://agriculturejournals.cz/RePEc/caa/references/cjg-202603-0005.txt Handle: RePEc:caa:jnlcjg:v:62:y:2026:i:3:id:18-2026-CJGPB Template-Type: ReDIF-Article 1.0 Author-Name: Bingjie Tu Author-Workplace-Name: Key Laboratory of Heilongjiang Province for Cold-Regions Wetlands Ecology and Environment Research, Harbin University, Harbin, P.R. China Author-Name: Changkai Liu Author-Name: Qiuying Zhang Author-Workplace-Name: State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, P.R. China Author-Name: Xiaobing Liu Author-Workplace-Name: State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, P.R. China Author-Name: Nan Xu Author-Workplace-Name: Key Laboratory of Heilongjiang Province for Cold-Regions Wetlands Ecology and Environment Research, Harbin University, Harbin, P.R. China Title: Synergistic effects of low IAA and GA concentrations promote dehiscence-zone separation in vegetable soybean Abstract: Pod dehiscence, also known as pod shattering, is the process by which mature pods open and release their seeds at physiological maturity. In vegetable soybean (Glycine max L.), premature seed release from mature pods is a major cause of yield loss during seed production. As pod dehiscence occurs within the dehiscence zone, understanding the physiological mechanisms governing its formation and degradation is essential. To investigate these mechanisms, we compared the activities of pectinase, polygalacturonase (PG), cellulase, indole-3-acetic acid (IAA), gibberellin (GA), abscisic acid (ABA) and zeatin (ZA) in the pod ventral sutures of dehiscent vegetable soybean and indehiscent grain soybeans. The ventral sutures of dehiscent vegetable soybean exhibited significantly higher activities of pectinase, polygalacturonase, and cellulase, but lower concentrations of IAA and GA than those of indehiscent grain soybean. Reduced levels of IAA and GA in the dehiscence zone were associated with increased activities of cellulase, pectinase, and polygalacturonase activities, which may accelerate cell wall degradation and promote lignification, thereby promoting pod dehiscence. Keywords: dehiscent, enzymes, hormones, pod valves, soybean Journal: Czech Journal of Genetics and Plant Breeding Pages: 190-199 Volume: 62 Issue: 3 Year: 2026 DOI: 10.17221/37/2026-CJGPB File-URL: http://cjgpb.agriculturejournals.cz/doi/10.17221/37/2026-CJGPB.html File-Format: text/html File-URL: http://cjgpb.agriculturejournals.cz/doi/10.17221/37/2026-CJGPB.pdf File-Format: Application/pdf X-File-Ref: http://agriculturejournals.cz/RePEc/caa/references/cjg-202603-0006.txt Handle: RePEc:caa:jnlcjg:v:62:y:2026:i:3:id:37-2026-CJGPB