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Despite all the complications that arise with root research, such as slow, laborious, and unclear genetics, roots are a promising object of interest for breeders because many root traits are compatible with high yield potential. It is a great challenge for further research that there is a wide demand for information on the “hidden half of plant metabolism” from many research fields. We have summarized the main obstacles in root system research and sketched a solution for breeding in field conditions so that the result was more meaningful to the farmer. (i) The most important challenge in root research is linking the functional identification of root system properties with the aboveground parts. (ii) Field breeding is irreplaceable, and methods allowing the evaluation of roots under field conditions are indispensable. (iii) Low heritability of root system trait discourages breeders. However, root properties show broad genotypic variability, allowing the efficient use of these traits as selection criteria. (iv) The root traits are variable, and many fluctuate under the influence of environmental factors, which complicates efforts to define ideotypes and explains the different conclusions obtained by researchers from different environments. The breeding programs targeting the root system are sporadic even in a global context. This is a great reserve for breeding progress in the era of climate change, water scarcity, a possible shift to extensive farming systems, and in the era of environmental programs.

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.

The need of vernalisation, controlled by the gene VRN-1, impacts wheat adaptation and yield stability, yet field evidence on the plasticity of VRN-1 homoeologs expression is limited. We quantified VRN-1 homoeolog dynamics across two sites and two seasons in seven cultivars, by sampling their apex and leaf. VRN-A1 varied with genotype (P < 0.001***), tissue (apex > leaf; P < 0.001***), apex development (P < 0.001***), day length (P < 0.001***), and to a lesser extent, on short-term freezing exposure, quantified as a 5-day freezing-degree sum (FDS; P = 0.019*). Photoperiod class (Ppd-D1a vs Ppd-D1b) added an additional effect (P = 0.001***). VRN-B1 showed strong genotype effects (P < 0.001***), a modest effect of site on its expression (P = 0.025*), and pronounced associations with microclimate variables (day length, thermal sums, freezing exposure; all P < 0.001***). Directionally, Ppd-D1a backgrounds tended to advance the development while showing earlier apex VRN-A1 peaks. Overall, VRN-A1 expression mainly reflected developmental stage and seasonal forcing, whereas VRN-B1 might be more microclimate-responsive, indicating complementary roles for timing and stress-response plasticity. To isolate causal effects and to further explain these dynamics, targeted sequencing and tests in near-isogenic lines will be needed in future work.

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.

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.

Biofortification provides a sustainable, pragmatic strategy to address the lack of vitamin A and the associated health complications. The objectives of the study encompassed the quantification of the carotenoid content of 147 maize inbred lines, the identification of variable regions within the ZEP1 gene, the correlation of these observed variances in the presence of this gene with carotenoid content, and the identification of lines harbouring the favourable alleles of the crtRB1 gene. The observed correlations among the carotenoids synthesised by distinct branches of the biosynthetic process were both significant and positive. Utilising gel-based genotyping, 24 lines with contrasting carotenoid profiles were selected, evaluated and sequenced. Analysis of the variation in the sequence classified these lines based on their similarities to give 8 allele groups. The findings highlight that inbred lines both group 1 and group 8 exhibited significant associations with the carotenoid content of the lines. Specifically, ZEP1_7852, a discernible variation belonging to group 8, was found to be significantly associated with zeaxanthin content and total carotenoid content. Furthermore, 25 lines were found to have provitamin A content above 15 μg/g, harbouring the favourable alleles of the crtRB1 gene using KASP SNP zm0016. These lines can serve as parents for source populations and hybrids, leading to the further enhancement of provitamin A in maize.

With climate change, plants face numerous stresses, notably drought for rice cultivation. Improving rice drought tolerance is vital for sustainable production in water-scarce regions. Identification of drought tolerant genotypes at the seedling stage of the crop contributes to build a climate resilient genotype during the period of water scarcity and under challenging environmental conditions. Hence, polyethylene glycol-6000 (PEG-6000) induced drought conditions could be used for testing the drought tolerance in rice at an earlier stage of the crop. Optimization of PEG-6000 concentration for screening index at -6 bar was done using three drought-tolerant and two drought-susceptible check varieties based on probit analysis. Subsequently, 100 rice landraces underwent PEG-6000 induced drought screening at –6 bar and a total of 32 genotypes were selected as tolerant. After 14 days of treatment, the nine observations viz. germination %, root length (cm), shoot length (cm), number of secondary roots, fresh weight (g), dry weight (g), shoot/root ratio, root/shoot ratio and vigour index were recorded. Variance analysis, revealing significant genetic variation among genotypes for all studied traits, indicating genetic variability. Post hoc analysis confirmed notable variation among treatments. Principal component analysis revealed three components, with the first three accounting for 88.89% of total variability. With respect to the biplot, the ten genotypes viz., IRGC109, IRGC403, IRGC448, IRGC461, IRGC466, IRGC486, IRGC508, IRGC518, IRGC527 and IRGC535 are the seedling stage drought tolerant genotypes based on shoot length, number of secondary roots and vigour index. Population structure classified the accessions into two subpopulations, reflecting diversity. The allele frequency divergence is 0.095 which is a measure of fixation index revealing that the moderate divergence is not extremely pronounced. Genetic diversity, assessed through 26 SSR markers selected from drought tolerant QTLs and markers related to vigour index, exhibited 100% polymorphism with 115 alleles and an average PIC value of 0.61 per primer. Shannon index varied between 0.34 (RM212) and 1.96 (RM252), averaging 1.18. Six SSR markers viz., RM246, RM302, RM252, RM219, RM251, and RM486 were associated with the six key traits viz., shoot length, root length, number of secondary roots, dry weight, shoot/root ratio, and root/shoot ratio respectively offering valuable resources for selecting drought-tolerant accessions as it provides the first step in the selection of genotypes based on the key traits.

Wheat Fusarium head blight (FHB) leads to losses of grain yield and quality. Ingestion of diseased grain is detrimental to human health due to the mycotoxins present in the grain. Developing resistant cultivars for environments where FHB is prevalent is therefore an important breeding objective. One of the most effective wheat genes conferring type II resistance to FHB is Fhb1, originally discovered in the Chinese cultivar (cv) Sumai 3. Another excellent FHB resistance gene is Fhb7 located on the long arm of Lophopyrum elongatum chromosome 7E. Several alleles of Fhb7 have been identified. Allele Fhb7^The2 was found in disomic substitution lines 7E(7A), 7E(7B) and 7E(7D) derived from amphiploid AgCS. The amphiploid was produced from a hybrid Triticum aestivum cv Chinese Spring × L. elongatum. To find if combining Fhb7^The2 with Fhb1 confers higher resistance in wheat than single genes, an introgression line derived from AgCS and possessing Fhb7^The2 was recurrently backcrossed to bread wheat cv Rollag and MN-Washburn possessing Fhb1. Experimental lines possessing both Fhb7^The2 and Fhb1 were developed and validated cytogenetically and with the L. elongatum genome-wide Sequenom SNP MassARRAY. Spikes of these lines, parental cv Rollag and MN-Washburn, and those of disomic addition line 7E possessing Fhb7^The2 plus controls were inoculated with Fusarium in a twice-replicated trial in controlled greenhouse environmental conditions. FHB infection rates were significantly lower in lines combining Fhb7^The2 with Fhb1 than in materials with Fhb7^The2 or Fhb1 alone.

Tomato is a major global crop, extensively cultivated in China. However, the molecular mechanisms underlying its responses to high-temperature stress remain poorly understood. This study investigates these mechanisms by examining a heat-resistant tomato variety, Hm 2-2 (R), and a heat-sensitive variety, BY 1-2 (S), under high temperature (40 °C). Total RNA was extracted from samples taken at 0 and 24 h post-treatment, followed by RNA-sequencing (RNA-seq). Differentially expressed genes (DEGs) were screened based on the criteria of |log₂ fold change| ≥ 2 and false discovery rate ≤ 0.05. Gene ontology (GO) function annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathway enrichment analysis were performed to explore the biological significance of these DEGs. The results revealed 6 038 upregulated and 2 866 downregulated DEGs in the R-0 (Hm 2-2 plants treated at 40 °C for 0 h) vs. R-24 (Hm 2-2 plants treated at 40 °C for 24 h) group and 5 297 upregulated and 3 920 downregulated DEGs in the S-0 (BY 1-2 plants treated at 40 °C for 0 h) vs. S-24 (BY 1-2 plants treated at 40 °C for 24 h) group, respectively. GO enrichment analysis indicated that the majority of DEGs were associated with biological processes, followed by cellular components and molecular functions. KEGG pathway analysis identified 130, 131, 89, and 115 regulatory (or altered) pathways in the R-0 vs. R-24, S-0 vs. S-24, S-0 vs. R-0, and S-24 vs. R-24 group comparisons, respectively. Notably, pathways related to protein processing in the endoplasmic reticulum and plant hormone signal transduction were significantly enriched, suggesting their critical roles in the tomato’s response to heat stress. Moreover, 156 transcription factors (TFs) implicated in heat stress response were identified, spanning various TF families such as MYB, AP2-EREBP, b-ZIP, bHLH, NAC, and WRKY. Quantitative RT-PCR analysis of 14 randomly selected DEGs validated the RNA-seq results confirming the reliability of the data. In summary, this study provides valuable insights into the molecular mechanisms of tomato’s responses to high-temperature stress, laying a crucial foundation for future research in this area.

Diagnostic morphological traits distinguishing Tilia cordata and T. platyphyllos are not always apparent. Precise species identification is crucial for conservation management and for establishing genetic resources of forest reproductive material. In this study, we employed fifteen microsatellite (SSR) markers to identify diagnostic loci for reliable species discrimination between T. cordata and T. platyphyllos species and to evaluate the genetic diversity. A total of 250 trees were sampled from eight natural autochthonous populations of T. cordata and T. platyphyllos in the Czech Republic, and additional ten individuals of T. tomentosa were included for comparison. Markers Tc8 and Tc918 were identified as diagnostic, exhibiting species-specific alleles for T. cordata and T. platyphyllos. Contrary to the previously published results, we obtained PCR amplicons at locus Tc918 with an allele size of 226 bp in T. cordata. An analysis of the fifteen SSR loci revealed a high level of genetic variability in both the T. cordata and T. platyphyllos populations. No clonally identical genotypes were detected across the eight study sites. The genetic differentiation (Fst) was higher between T. platyphyllos and T. tomentosa (0.316) than between T. platyphyllos and T. cordata (0.205). Bayesian clustering further revealed distinct genetic structures for T. cordata, T. platyphyllos, and T. tomentosa.

The genus Solanum comprises numerous wild and cultivated species that are important for potato breeding. This pilot-scale study aimed to evaluate the genetic diversity in 44 accessions from Solanum sect. Petota, comprising wild species, Andean landraces, and modern cultivars, obtained from the Potato Research Institute Havlíčkův Brod, Ltd. and the Department of Crop Sciences and Agroforestry at the Faculty of Tropical AgriSciences, Czech University of Life Sciences Prague. Nuclear microsatellite markers (SSR, 29 loci) were applied via five multiplex PCR reactions and analysed using capillary electrophoresis. Binary data matrices were analysed using DARwin software to generate dendrograms reflecting allelic polymorphism. The SSR panel effectively differentiated cultivated accessions from wild types, consistent with the current taxonomy of the genus Solanum, with particularly clear clustering of Andean landraces and modern varieties. However, resolution among wild accessions was limited, likely due to their high genetic complexity and interspecific overlap. These results support the suitability of the SSR panel for analysing diversity in cultivated potatoes. while also highlighting the challenges in resolving wild Solanum taxa. This study contributes to germplasm characterisation and provides a molecular basis for future breeding programmes.

Leaf rust is an important wheat disease that considerably reduces the wheat production in most wheat growing regions worldwide. This study aimed to identify leaf rust resistance genes in 42 wheat varieties to find genetic sources with the broadest spectrum of resistance against leaf rust pathotypes, to enable effective breeding for disease resistance. In this study, 42 wheat cultivars were inoculated with 18 pathotypes of Puccinia triticina Eriks. at the seedling stage to postulate the Lr genes in the cultivars. Resistance to leaf rust at the adult stage was then tested in field trials under natural infection during the 2019 to 2020 cropping seasons at Baoding, Hebei Province. Gene postulation together with molecular marker detection identified ten Lr genes (Lr1, Lr10, Lr14a, Lr26, Lr2a, Lr17, Lr20, Lr34, Lr37, and Lr46) among the 42 accessions.  Lr1 was present in 16 accessions, Lr14a in three accessions, Lr17 in five accessions, Lr2a in five accessions, Lr34 in one accession, Lr10 in two accessions, Lr37 in two accessions and Lr46 in 29 accessions. Additionally, 15 wheat accessions displayed adult-plant resistance or other unknown genes. These results suggest that a high level of leaf rust resistance can be achieved by combining known resistance genes and adult-plant resistance genes in wheat cultivars.

Ascochyta blight, caused by a complex of pathogenic fungi including Didymella pinodes, Ascochyta pisi, and Phoma pinodella, is a major disease of field pea (Pisum sativum), causing severe losses through lesions on leaves, stems, and pods. Mutation breeding using gamma irradiation is a non-GMO strategy to induce genetic variation and accelerate the development of improved genotypes. In this study, the M₂ generation of the forage pea cultivar Dodoni (Pisum sativum L. var. arvense), derived from M₀ seeds irradiated with 100 Gy, was evaluated for tolerance to D. pinodes (CBS 251.47) using a detached-leaf assay under controlled greenhouse conditions. Disease progression was quantified via image-based analysis on the 3^rd and 5^th days post-infection, calculating diseased area and disease severity index. Extensive phenotypic evaluation was also conducted on 16 families in the greenhouse and 100 families under field conditions, using an augmented incomplete block design. Screening revealed several M₂ families with significantly improved tolerance compared to non-irradiated controls. Among these, some individuals combined enhanced resistance with improved yield-related traits, such as higher pod number and biomass, while others exhibited reduced agronomic performance. These findings highlight the phenotypic diversity induced by gamma irradiation and demonstrate the potential to generate dual-purpose pea genotypes with both disease resistance and enhanced productivity, providing valuable material for future breeding of resilient cultivars.

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.

Foxtail millet (Setaria italica) is a resilient yet underutilised C₄ cereal valued for its adaptability to abiotic stress and high nutritional content. While panicle traits have been linked to yield in many cereals, the spatial arrangement of foxtail millet panicles remained unexplored, especially among locally adapted genotypes. This study aimed to characterise spatial panicle architecture traits and to analyse the DUF-640, a gene controlling primary branch number, among Indonesian foxtail millet genotypes. Results revealed substantial variation in panicle architecture, including primary branch number, grain number, and grain density in eight Indonesian foxtail millet genotypes, suggesting potentially greater diversity across broader germplasm. In contrast to the substantial panicle trait variations, phylogenetic and structural analyses showed that DUF-640 genes were highly conserved across Setaria species. Although previously associated with primary branch development, the coding sequence of DUF-640 was not associated with branching variation in this study. However, its high sequence conservation across Setaria species suggests a vital and possibly conserved regulatory function. This study enhances the understanding of the morphological and genetic diversity of foxtail millet, particularly among Indonesian foxtail millet genotypes. Future research should focus on the functional characterisation of DUF-640 and the identification of regulatory sequences governing its gene expression.

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.

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.

High-throughput molecular technology DArTseq generates markers for potential use in molecular breeding of crops. Using DArTseq, we analysed a comprehensive set of 333 European potato varieties reflecting the outcomes of long-term breeding history and representing a potential germplasm for future breeding of potatoes in the Central European region. The varieties were classified according to four factors: region of origin, breeder, earliness and utilisation mode, that may potentially reflect their genetic structure, and for which complete data were publicly available. The DArTseq analysis was performed by the service centre, the Diversity Array Technology (University of Canberra), which generated approximately 38 000 silicoDArT and 64 000 SNP (single nucleotide polymorphism) polymorphic markers. The discriminatory ability of the markers in relation to the factors was confirmed using neighbour-joining and principal coordinate analysis (PCoA), while the informativeness was assessed using the discriminant analysis of principal components (DAPC). The analyses identified the 50 SNPs most strongly associated with each factor, along with their highly probable chromosomal localisation. Herein presented research contributes to the evaluation of potato genetic resources by adding the novel molecular data of active germplasm and implies their future utilisation in genome wide association studies and marker assisted selection.

Tea (Camellia sinensis (L.) Kuntze) is a globally important crop valued for its flavour diversity and health benefits. Whole-genome sequencing (WGS) was performed to compare genomic variation and functional potential between clone Yabukita and locally adapted clone I.1.93. Using next-generation sequencing, approximately 10× genome coverage was achieved for both clones, with high mapping efficiency (98.24% for Yabukita and 97.88% for clone I.1.93), ensuring reliable downstream analyses. Single nucleotide polymorphism (SNP) analysis revealed distinct genomic patterns, with Yabukita showing a more uniform chromosomal SNP distribution, while clone I.1.93 exhibited higher SNP densities on specific chromosomes, particularly chromosomes 5 and 13. Silent mutations predominated in Yabukita (48.21%), whereas missense mutations were more frequent in clone I.1.93 (57.97%), suggesting greater functional divergence. Most SNPs occurred in non-coding regions, indicating potential regulatory roles. GO and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses revealed highly similar shared pathways, including photosynthesis and protein interactions, alongside clone-specific enrichment related to photosynthesis in Yabukita and stress responses in clone I.1.93. miRNA profiling identified distinct regulatory patterns, including the clone-specific miR530 in clone I.1.93. Biosynthetic gene cluster analysis further predicted secondary metabolite pathways associated with terpenoid, polyketide, and saccharide biosynthesis. These findings provide valuable genomic insights for tea improvement and breeding programs.

Soil salinity is a major environmental constraint that limits the growth and productivity of peanut (Arachis hypogaea L.), a legume adapted to mildly acidic soils but highly sensitive to saline–alkaline conditions. Dehydration-Responsive Element Binding (DREB) transcription factors are key regulators of plant responses to abiotic stresses. In this study, the AhDREB gene from peanut was introduced into tobacco (Nicotiana tabacum) to examine its functional role under salt stress. The transgenic lines (L32.2 and L37.2) exhibited strong induction of AhDREB expression upon exposure to 150 and 250 mM NaCl, with transcript levels increasing up to 2.34-fold compared with untreated controls (P < 0.001). Quantitative RT-PCR analysis revealed that AhDREB enhanced the transcription of two osmolyte-related genes, NtP5CS and NtSUSY. Under saline conditions, the expression of these genes was 1.20–1.89-fold higher in transgenic lines than in wild-type (WT) plants and 4.74–7.66-fold higher than in non-stress conditions (P < 0.001). Consistently, both lines accumulated greater amounts of proline and soluble sugars, showing 2.09–2.30-fold and 2.40–4.70-fold increases, respectively, compared with the WT. Relative to non-stress conditions, proline and sugar contents increased by 3.59–5.47 fold and 3.75–7.65-fold, respectively. Line L37.2 accumulated higher proline levels, whereas L32.2 exhibited greater sugar content, indicating distinct osmolyte regulation patterns. Overall, the AhDREB gene enhances salt tolerance in tobacco by transcriptionally activating osmolyte biosynthetic pathways and improving cellular osmotic adjustment, providing molecular evidence for its potential application in developing stress-tolerant peanut cultivars.

Assessing of genetic diversity is essential for identifying useful alleles for crop improvement. This study evaluated genetic diversity among two cassava breeding populations for total carotenoid content (TCC), dry matter content (DMC), and hydrogen cyanide (HCN) concentration using trait-linked single nucleotide polymorphism (SNP) markers. A total of 360 genotypes were analysed, including 261 from the IITA breeding programme (Population 1), 23 progenitor lines, and 76 from the University of Ibadan Cassava (UIC) breeding programme (Population 2). Minor allele frequency (MAF), gene diversity (GD), observed heterozygosity (H_e), and polymorphic information content (PIC) were computed. Principal component analysis (PCA) and hierarchical clustering were performed to examine genetic variation and population structure. Call rates were high (96–100%). MAF ranged from 0.00 to 0.50, with mean values of 0.28, 0.28, and 0.29 for Population 1, Population 2, and progenitors, respectively. GD averaged 0.36, 0.36, and 0.35 across these groups. Observed heterozygosity was 0.42, 0.41, and 0.43, while PIC values averaged 0.29, 0.27, and 0.27 for Population 1, Population 2, and progenitors, respectively. PCA and clustering analyses grouped the genotypes into three clusters containing 257, 88, and 15 genotypes. The first two principal components explained 39.1% of the total genetic variation. The results indicate substantial genetic diversity among the studied genotypes, suggesting strong potential for allele pyramiding and highlighting the informativeness of the SNP markers used.

Iris × germanica L. (bearded iris) is a popular ornamental plant with numerous commercially important cultivars; however, little is known about the genetic diversity and population structure of the species, as limited DNA markers have been explored. In this study, 34 722 expressed sequence tag (EST)-simple sequence repeat (SSR) loci were identified from RNA sequencing data. The most abundant SSR motifs belonged to the tri-nucleotide type, of which the most common were AGG/CCT followed by AAG/CTT. Overall, 50 primer pairs derived from these EST-SSRs were randomly selected and synthesized, and 22 primer pairs with good polymorphism effects were used for the following experiment. Correlation analysis of nine floral traits showed that most floral traits had significant correlations with each other. Association analysis between SSR molecular markers and nine floral traits showed that 11 EST-SSR markers were associated with 3–6 floral traits. The cluster tree constructed by using the unweighted pair group method demonstrated that the cultivars that had the same parents or similar colour were clustered together. The genotypic relations of most cultivars were consistent with their pedigree-based relationships. The EST-SSR loci identified in this study will facilitate the exploitation of genetic resources and molecular breeding of I. × germanica.

Food insecurity which has been a global threat, forces researchers to develop crops with increased productivity even under varying climatic conditions. Rice, being a significant staple and strategic crop, helps ensure economic stability, food, and nutritional security globally. It meets 20% of the calorie requirement of people residing all over the world. Lately, rice cultivation and research have been facing hitherto unprecedented difficulties in the context of climate-induced water scarcity and dwindling resources of manpower, arable land, etc. In this regard, direct seeded rice (DSR) as a resource conservation technique is gaining popularity as a potential alternative to conventional transplanting with reduced input requirement, reduced methane and CO₂ emission, increased adaptability to climate change, and increased economic returns. The weed menace in DSR prevents it from reaching its fruitful attainment to a significant level. DSR highly depends on herbicide for weed control as manual weeding and other cultural practices are labour intensive which again meets a setback of crop injury (non-selective herbicide) and resistant weeds (selective herbicides). Herbicide-tolerant (HT) rice could be an effective and long-term solution for weed management in DSR. Three HT rice systems, viz., imidazolinones, glyphosate, and glufosinate, have already been developed in this context. This review gives an insight into the need for HT rice in DSR, its production system, limitations, and stewardship guidelines for proper weed management in rice.

Pod dehiscence or pod shattering from mature soybean (Glycine max L.) is one of the most outstanding disadvantages in domesticated cultivars. Pod shattering in relation to 16 quantitative traits and 3 qualitative traits among 140 cultivars of vegetable soybeans, grain soybeans and small-grain soybeans was evaluated over two years. We found the pod shattering percentage is positively correlated with the number of productive branches, pod width, pod length, pod area, 100-seed weight, 1-seeded-pod percentage, 2-seeded-pod percentage and seed protein content, but negatively correlated with the plant height, pod height at the bottom, number of nodes on the main stem, 3-seeded-pod percentage, 4-seeded-pod percentage and seed oil content. The pod shattering percentage in vegetable soybeans is remarkably high, reaching up to 93%, 7.8 times higher than that of grain soybeans. A schematic model of the characteristics for shatter-susceptible and shatter-resistant soybean cultivars is proposed. The pod shattering in vegetable soybeans is related to the “umbrella-shaped” architecture and pod size. It is suggested to select lines with more 2-seeded and 3-seeded pods for vegetable soybeans, but a higher seed oil content and greater node number on the main stem for grain soybeans and small-grain soybeans, to avoid pod shattering in future breeding programmes.

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Strigolactones (SLs) are a comparatively novel class of phytohormones that are involved in the maintenance of plant architecture with key regulation of lateral branching. They are also reported to play an important role in regulating plant responses to various abiotic stresses. The potential of SLs to improve crop resilience and productivity needs to be effectively translated into agriculture. Therefore, both the endogenous biosynthesis of SLs and their exogenous application need to be thoroughly investigated to understand and exploit the mechanism underlying the alleviation of abiotic stress responses. Although several reviews have emphasised the biosynthesis of SLs in plants under abiotic stress, the mechanism underlying the alleviation of stress responses upon exogenous application has been less explored. Accordingly, in this review, although we have briefly discussed the beneficial effects of endogenous production of SLs in different sections, our main focus is to summarise the influence of exogenous SLs on the growth and development of different plant species grown under various abiotic stresses, including drought, nutrient, heavy metal, and salinity stress. Apart from providing an overview of the transcriptomic studies conducted to observe the alleviating effects of SLs on abiotic stress responses, the research gaps in this field were briefly discussed. The review provides insight for researchers to conduct further research on SLs and fill the gap so that they can be effectively used for sustainable agriculture.

Aloe vera and A. arborescens are succulent plants widely used in cosmetics, pharmaceuticals, and food supplements. The objective of this study was to perform interspecific crosses and agronomically characterise three genotypes cultivated in a Venezuelan highland region (altitude 1 727 m, 13–17.9 °C). Successful hybridisation was achieved only when A. arborescens pollen (P1) was used on A. vera pistils (P2), whereas the reciprocal cross was largely unsuccessful. Hybrid seed germination reached 11.86%, and adult hybrids exhibited significant vegetative superiority over P1, particularly in leaf volume, leaf weight, and flower number. The progeny outperformed both parents in leaf base width and lateral tooth size, thereby enhancing its ornamental value. The expected 2n = 2x = 14 karyotype was confirmed in the root meristems of hybrids. The analysis of leaf pulp processing indicated that the hybrid was promising for juice production (39.8% yield, 1 203 ppm acemannan), thus highlighting its potential for agro-industrial applications in tropical highlands or comparable temperate regions. Other agronomic traits, including number, thickness, colour, and shape of leaves; sprouting of stem branches and basal suckers, flowering period, inflorescence, eggs/ovary, and details of the colour and dimensions of bracts, perianth, pedicel, and ovary, were also evaluated.

The testing and evaluation of native populations of perennial ryegrasses (Lolium perenne L.) collected from the Republic of Srpska, Bosnia and Herzegovina were conducted from 2020 to 2022 at experimental fields and laboratories of the Institute for Genetic Resources and the Agricultural Institute of the Republic of Srpska in Banja Luka. Six native populations (labelled G1–G6) and two cultivars, Esquire and Tivoli (labelled G7 and G8), were analysed in this study. The following traits were examined: the plant height (cm), number of generative stems per plant, inflorescence length (cm), number of spikes per inflorescence, seed mass per inflorescence (g), and seed yield per plant (g). The results showed that all the native populations exhibited higher average plant heights compared to the Esquire standard (G7). Population G2 had the highest average number of spikes per inflorescence (26.8), while population G4 achieved the greatest average inflorescence length (27.7 cm). Statistically significant differences in the inflorescence length were observed between populations G2, G3, G4, and G6, compared to the standards G7 and G8 (Esquire and Tivoli). The genotype and year had a significant impact on the seed yield per plant. The average yield ranged from 32.4 g (G7) to 53.4 g (G4). The seed yield per plant showed a strong positive correlation with the number of generative stems per plant, the inflorescence length, and the number of spikes per inflorescence. The native populations G4 and G5 achieved significantly higher seed yields per plant compared to the other populations and may serve as highly valuable material for breeding programmes.

Sunflower (Helianthus annuus L.), a globally significant oilseed crop, faces substantial yield losses due to drought stress, a major environmental constraint. In this study, the effects of nitric oxide (NO) to increase drought tolerance in four sunflower genotypes (resistant Irtysh, RAR 56 and sensitive Zarya, RAR 133) showing different stress responses were investigated. Conducted in a controlled hydroponic system, the experiment applied 100 µM NO under 12% polyethylene glycol (PEG)-induced drought, assessing growth, physiological, and biochemical parameters. PEG alone reduced shoot and root growth, relative water content (RWC), and ion levels (K, Ca, Mg, Na), while increasing oxidative stress markers (malondialdehyde (MDA), H₂O₂, •OH) and electrolyte leakage, particularly in sensitive genotypes. NO application, both alone and with PEG, significantly mitigated these effects, enhancing root fresh weight, RWC, and antioxidant enzyme activities (superoxide dismutase (SOD), peroxidase (POX), catalase (CAT) and glutathione reductase (GR)), while reducing reactive oxygen species (ROS) and lipid peroxidation. Resistant genotypes (Irtysh, RAR 56) exhibited superior stress amelioration. These findings highlight NO’s role as a signalling molecule in augmenting drought resilience through genotype-specific mechanisms. The differential responses among genotypes suggest opportunities for identifying genetic markers associated with NO-mediated drought tolerance, which could guide marker-assisted breeding programs. Additionally, integrating these insights with genomic editing techniques may accelerate the development of drought-resistant sunflower cultivars tailored for water-scarce regions. Future research should optimise NO delivery methods and evaluate field-scale efficacy to advance sustainable sunflower production in water-limited environments.