The concerned study sought to determine the variations based on the DNA fingerprint in two important medicinal plants, sage (Salvia officinalis L.) and thyme (Thymus vulgaris L.), belonging to the family Labiatae, using three different types of DNA markers—random amplified polymorphic DNA (RAPD), inter-simple sequence repeats (ISSR), and start codon targeted (SCoT). The comparison of these three types of markers revealed the recording of the highest molecular size of amplified bands (988 bp) was with SCoT markers, while the lowest molecular size (156 bp) resulted in RAPD markers. By comparing the RAPD and SCoT markers, the latter produced the highest main, amplified, monomorphic, and discriminatory values. The SCoT markers also gave the most polymorphic bands. The ISSR markers outperformed the other markers in polymorphism, efficiency, and the number of unique fingerprints.

Keywords: Sage (S. officinalis L.), thyme (T. vulgaris L.), RAPD, ISSR, SCoT, DNA fingerprints

Key findings: The SCoT, RAPD, and ISSR markers considerably distinguished the two species of medicinal plants, sage (S. officinalis L.) and thyme (T. vulgaris L.), besides variations in their phytochemical content.

Cotton (Gossypium hirsutum L.) is a major global fiber crop. Early-maturing cotton offers the advantage of avoiding stresses by shortening the growth period. This study evaluated the heterotic potential and correlation of morphological and biochemical traits for earliness in upland cotton. The crossing of eight parental genotypes used a half-diallel mating design; the resultant F₁, along with parents, underwent evaluation for earliness. The cross VH-327 × CRIS-613 (-19.55% and -19.98%) displayed a maximum significant negative heterobeltiosis for days to flowering and squaring. SAS-2 × Coker Wild (53.11%) exhibited the higher heterotic response for superoxide dismutase activity, whereas Ghauri-2 × Coker Carolina Queen showed the maximum significant positive heterobeltiosis of 21.39% for peroxidase activity. For catalase, Cyto-124 × SAS-2 (6.58%), Cyto-124 × CRIS-613 (7.59%), and Ghauri-2 × Coker Wild (9.84%) demonstrated a significant positive heterobeltiosis. The correlation results revealed a significant positive association between days to squaring and flowering, while superoxide dismutase had a negative correlation with days to flowering at the phenotypic level. Overall, VH-327 × CRIS-613 and Ghauri-2 × Coker Wild had desirable results for earliness and yield-related traits and can be favorable for the breeding of early-maturing and high-yielding cotton genotypes.

Keywords: Upland cotton (G. hirsutum L.), heterobeltiosis, antioxidant enzymes, early maturity, diallel, correlation

Key findings: In upland cotton (G. hirsutum L.), the cross combination VH-327 × CRIS-613 exhibited desirable heterosis for earliness-related traits, while Ghauri-2 × Coker Carolina Queen and Ghauri-2 × Coker Wild provided valuable resources for targeted breeding programs, particularly for antioxidant enzymes and yield-related traits.

This research describes positive effects of the combined use of stimulant + insecticide + fungicide in improving phytosanitary conditions of the cotton field. The upland cotton (Gossypium hirsutum L.) crop acquired proper nourishment with robust stems, numerous leaves, and enhanced photosynthesis productivity and resulted in the highest seed cotton yield with better fiber quality. By analyzing the cotton leaf surface area, fine fiber cultivar Marvarid provided 4,375,200 cm²/ha, followed by medium fiber cultivar Bukhara-8 with 4,262,700 cm²/ha, using the combination of stimulant + insecticide + fungicide. By analyzing the seed cotton yield, the fine-fiber cultivar Marvarid resulted in 11.3 t/ha (35.0%) higher than the standard variant, followed by the medium-fiber cultivar Bukhara-8 with 10.6 t/ha (33.7%).

Keywords: Upland cotton (G. hirsutum L.), cultivars, diseases, pests, convolution neural network, fungicides, insecticides, seed cotton yield

Key findings: The use of stimulant + insecticide + fungicide in cotton (G. hirsutum L.) improved the phytosanitary conditions of the cotton field, with the crop properly nourished, having strong stems, numerous leaves, and photosynthesis productivity.

The plants’ recovery from the clonal rootstock of apple tree 62-396 from the Apple (Malus domestica BORKH) chlorotic leaf spot virus (ACLSV) and Apple stem grooving virus (ASGV) succeeded in using antiviral drugs (AVD), ribavirin (standard), salicylic, and jasmonic acids, at air temperatures of +20 °C and +38 °C. Magnetic pulse processing (MPР) application used a device with a frequency of 200 Hz. With the temperature of +20 °C, the possibility of using AVDs for 90 days was definitive. The combination of temperature (+38 °C) and MPР (without AVD) and temperature (+38 °C) and salicylic acid (81.3%) provided the highest survival rate. The increased temperature (+38 °C) also inhibited shoot proliferation, leading to a decrease in shoot number by 2.9 times in the control and by 1.1–1.5 times in the variants with AVD. MPР reduced the inhibitory effects of high temperature in the control. The explants’ yield of the clonal rootstock of apple tree 62-396 was free from latent viruses in vitro using various methods of rehabilitation, which was 50%–100%. A low virus infection index (1.2) was notable during complex therapy with the use of AVD (salicylic acid + jasmonic acid), thermotherapy, and MPР.

Keywords: Apple (M. domestica BORKH) viruses’ elimination, in vitro thermotherapy, in vitro chemotherapy, in vitro magnetic pulse processing, apple clonal rootstock

Key findings: In breeding programs and planting mother trees, it is crucial to use the clonal apple (M. domestica BORKH) rootstocks that have already received treatments against viruses using in vitro chemotherapy (salicylic acid 30 mg/l + jasmonic acid 2.5 mg/l), thermotherapy (+38 °C), and magnetic pulse processing (200 Hz).

Siam orange (Citrus nobilis Lour.) is a major horticultural commodity with wide distribution and the largest share in Citrus production in Indonesia. The information on genetic relationships among C. nobilis populations from major production centers remains limited in Indonesia. This study evaluated the genetic diversity, haplotype structure, and phylogenetic relationships of C. nobilis populations from four major production centers in Sumatra (Gunung Omeh, Pasaman, Bangkinang, and Berastagi) using ITS markers. Forty DNA samples were amplified using ITS1 and ITS4 primers, generating ITS (internal transcribed spacer) fragments of 603–666 bp. The resulting sequences incurred analysis for nucleotide composition, genetic diversity, haplotype structure, and phylogenetic relationships. The results revealed eight polymorphic nucleotide sites and a high GC content (65.24%). Eight haplotypes identified had the Hap_1, representing 65% of all samples and occurring across all populations. Haplotype diversity was the highest in Gunung Omeh and lowest in Berastagi. The haplotype network positioned Hap_1 as the central node, while other haplotypes differed by one to three nucleotide substitutions. This study provides the first ITS-based assessment of genetic relationships among major C. nobilis populations in Sumatra and complements previous random amplified polymorphic DNA (RAPD)-based findings with sequence-level evidence. The genetic information obtained may support germplasm selection, conservation efforts, and future breeding programs for the Siam orange in Indonesia.

Keywords: Siam orange (Citrus nobilis), genetic variation, ITS marker, haplotype diversity, phylogenetic analysis, Sumatra

Key findings: The analysis of C. nobilis from four production centers using ITS markers revealed eight haplotypes with low nucleotide diversity. The shared and region-specific haplotypes disclosed an extensive exchange of planting materials among the production centers. Phylogenetic analysis placed all accessions within a single monophyletic clade, reflecting a close genetic relationship.

Cowpea (Vigna unguiculata L. Walp.), being a leguminous plant, has the second highest vegetable protein content after soybean. Cowpea development considerably supports food diversification and plays a vital role as a highly nutritious food source. The concerned study aimed to determine the variations in morphological traits and the morphological diversity among 18 local cowpea accessions. The collection of seed cowpea accessions came from four different Regencies, i.e., Sumenep (KT1, KT2, KT3, and KT4), Pamekasan (KT5, KT6, KT7, and KT8), Sampang (KT9, KT10, KT11, KT12, and KT13), and Bangkalan (KT14, KT15, KT16, KT17, and KT18), carrying out respective exploration activities per regency. The phenetic analysis, as executed in NTSys ver. 2.1, used simple matching similarity index and the unweighted pair group method with arithmetic average (UPGMA) method. The results revealed that accessions of 18 cowpeas showed variation for 12 morphological traits, including plant pigmentation, terminal leaflet shape, pod attachment, pod curvature, seed shape and color, and flower, eye, and pod colors. Based on the phenetic analysis of Madura cowpea accessions’ morphology, the cowpea accessions showed similarity coefficients from 0.30 to 0.83, which further underwent division into two large groups. Accession KT11 displayed a separation from other accessions because of its significantly different traits of testa texture, pod eye color, and distinctive flower color.

Keywords: Cowpea (V. unguiculata L.), Madura local accessions, morphological diversity, leaf and pod traits, similarity coefficient, Leguminaceae

Key findings: Madura cowpea (V. unguiculata L.) accessions revealed significant differences for 12 morphological traits, including plant pigmentation, terminal leaflet shape, pod attachment, pod curvature, seed shape and color, and flower, eye, and pod colors.

Tissue culture-somaclonal variation can generate desirable phenotypes in clonally propagated crops. In our previous study, inducing two horn banana (Musa spp.) mutants (Torpedo 1/TM1 and Torpedo 2/TM2) used benzyl aminopurine (BAP) that produced substantially enhanced fruit weight compared with their parental wild-type cultivars (Agung Semeru/PAS and Local Bogor/PLB). In this study, the employment of RAPD and SCoT markers with the sequencing of polymorphic amplicons sought to determine the genetic distinctiveness of these two mutants. RAPD analysis produced 68 loci up to 83% polymorphism, while SCoT markers generated 39 alleles with lower polymorphism (8%–14%). Sequencing of the 750 bp OPC-07 RAPD and SCoT-2 revealed SNPs and indels with extensive nucleotide variations. Although OPC-07 had a nearly identical band size, a mutation hotspot at positions 116–123 uniquely distinguished TM2 from others. Similarly, sequencing of SCoT-2 amplicons revealed numerous A–T, C–G, and A–G substitutions, several triallelic polymorphic sites, and small indels. The TM2 mutants were notable with point mutations, which revealed somaclonal variations, differentiating mutants from their wild types. The results disclosed RAPD and SCoT markers effectively distinguish the improved banana genotypes. Further characterization of these genetic differences will help in planning more precise and targeted banana breeding programs.

Keywords: Banana (Musa spp.), induced mutation, benzyl aminopurine (BAP), genetic characterization, plant tissue culture, mutants, Torpedo bananas

Key findings: RAPD and SCoT markers distinguished the superior banana (Musa spp.) mutants Torpedo 1 and 2 from their wild type. Beyond detecting polymorphic bands, sequencing of selected amplicons revealed nucleotide variations in genes associated with organ formation and growth. Cluster analysis supported these findings by clearly separating the mutants Torpedo 1 and 2 from the wild type.

Limited arable and productive soil is the primary hindrance to increasing maize production, requiring appropriate selection of genotypes and planting density combinations. The present study aimed to evaluate maize hybrids’ responses under normal and high planting densities, genetic parameters, and trait correlations, as well as identify the adaptive hybrids. The two separate experiments comprised normal (53.333 plants ha⁻¹) and high (83.333 plants ha⁻¹) planting densities, carried out during 2023–2024. Each experiment layout was in an augmented randomized complete block design, involving 23 maize genotypes comprising 19 hybrids and four check cultivars replicated three times. The results showed the high planting density produced 1.46 t ha-1 higher yield than the normal planting density, with G8 and G4 as the high-yielding candidate hybrids across both densities. Leaf angle and grain yield exhibited the highest genotypic and phenotypic coefficients of variation and broad-sense heritability. Anthesis-silking interval, leaf angle, and shelling percentage showed significant correlations with grain yield under normal planting density. The MGIDI (multi-trait genotype-ideotype distance index) selected hybrids G4, G8, and G15 under normal planting density; G11, G2, and G9 under high planting density; and G20 and G23 under both densities. Identifying maize hybrids suitable for higher planting densities may support breeding efforts to develop efficient and high-yielding genotypes.

Keywords: Maize hybrids, genetic parameters, correlation, MGIDI, adaptability, planting density

Key findings: Maize (Z. mays L.) traits, such as anthesis-silking interval, leaf angle, and shelling percentage, showed a significant correlation with grain yield under normal planting density. MGIDI-based multivariate selection identified five maize hybrids as potential candidates for improving productivity under normal and high planting densities.

Gyrinops versteegii (Gilg.) Domke, an endangered agarwood-producing tree, faces threats from overexploitation and genetic erosion in Indonesia. This study sought to evaluate the intraspecific genetic diversity and molecular markers for conservation via sequencing and assembling of the chloroplast genomes of six G. versteegii genotypes from four regions using Oxford Nanopore Technology (ONT). The assemblies ranged from 32,442 to 138,782 bp, and the genotype CLD2 produced the largest and most complete chloroplast draft assembly among the six genotypes (138,782 bp; 126 genes). Comparative analysis of nine chloroplast genes revealed notable variations, particularly in the atpA (Pi = 0.09178). The highest genetic distance emerged between genotypes NTB2 (from Nusa Tenggara) and CLD1 (from West Java). The phylogenetic analysis suggested clustering of G. versteegii genotypes into three subclusters, separated from other species of the family Thymelaeaceae. Additionally, 235 chloroplast simple sequence repeats (cpSSRs) entailed identification, predominantly A/T motifs, including several novel loci not reported in the reference genomes. These cpSSRs provided valuable resources for species authentication, population monitoring, and conservation breeding. The results revealed intraspecific variation among G. versteegii genotypes and demonstrated the utility of ONT sequencing for developing molecular markers in tropical tree species. The genomic insights will support effective conservation strategies and sustainable management of agarwood-producing tree resources.

Keywords: G. versteegii, chloroplast genomes, genetic distance, genetic diversity, conservation, intraspecific variation, microsatellites, nucleotide diversity

Key findings: This study explored the crucial intraspecific variations in G. versteegii genotypes as the endangered agarwood-producing tree, offering insights essential for developing effective conservation strategies for this endangered species.

Flax (Linum usitatissimum L.) is a strategic fiber crop with increasing importance for sustainable agriculture and textile industries. With crop diversification and development of domestic fiber resources, the renewed interest has emerged in fiber flax cultivation in Uzbekistan. However, the genetic improvement of fiber-related traits—such as fiber yield, length, strength, and fineness—remains challenging because of their quantitative inheritance and robust environmental sensitivity. The present review summarized recent research advancements in flax fiber, particularly focusing on germplasm diversity, conventional and molecular breeding strategies, and the application of DNA marker technology. The local landraces, advanced lines, and introduced accessions have expanded the genetic base for fiber improvement. Modern approaches, including quantitative trait loci (QTL) mapping, genome-wide association studies (GWAS), and marker-assisted selection (MAS), have also enabled the identification of genomic regions and candidate genes involved in the development of fiber quality. This review also discussed future perspectives for flax breeding under Uzbekistan’s agro-climatic conditions, emphasizing integrated phenotypic, molecular, and genomic approaches to develop high-yielding, better-quality, and stress-resilient fiber flax cultivars. The results provide a scientific framework to accelerate breeding efficiency and support the sustainable expansion of flax production in Central Asia.

Keywords: Flax (Linum usitatissimum L.), fiber traits, breeding, germplasm resources, fiber quality, DNA markers, QTL mapping, marker-assisted selection

Key findings: This review provides a comprehensive overview of the current status and future prospects of flax (Linum usitatissimum L.) fiber traits improvement research in Uzbekistan. The findings highlighted the importance of combining traditional breeding with molecular and genomic approaches to improve fiber yield and quality.