Search Results (9,326)

In recent years, genomic selection (GS) has been widely adopted in plant breeding; however, its practical application is constrained by the high cost of genotyping large segregating populations. To address this issue, this study employed a Quantitative Trait Nucleotide (QTN)-assisted GS strategy to evaluate its efficiency in reducing genotyping costs for soybean seed oil content (OC) and protein content (PC). Based on six multi-parent F₄ populations (n = 4404) derived from seven elite soybean cultivars, which were genotyped using a 20K SNP chip, we identified 83 and 110 QTNs that were significantly associated with OC and PC, respectively. Among these loci, 37 and 62 QTNs were specific to OC and PC, respectively. Genomic prediction accuracies were evaluated across different training population (TP) sizes using three marker panels: genome-wide SNPs, all detected QTNs, and trait-specific QTNs. The panel consisting of all detected QTNs exhibited significantly higher prediction accuracy than the other two panels, except for PC when using 90% of the population as the training set. Phenotypic verification of the selected individuals showed that the PC-specific QTN panel yielded higher PC values and increased OC + PC values compared with the other marker panels. These results demonstrate that a small set of QTNs provides a cost-effective approach for genomic selection in practical soybean breeding programs. Full article

The rapid accumulation of genome-scale data has transformed plant biology from descriptive genetics to predictive and increasingly mechanistic genomics. Longan (Dimocarpus longan Lour.) is an economically important subtropical fruit tree in China and Southeast Asia, but compared with model plants and major temperate fruit crops, its genomic resources and functional studies have developed relatively late. Here, we review recent progress in longan genomics with emphasis on three interrelated areas: genome assembly and annotation, transcriptomic resources, and representative gene family studies associated with flowering, somatic embryogenesis, and transporter-mediated stress tolerance. The progression from the first draft genome of ‘Honghezi’ to the chromosome-scale assemblies of ‘Jidanben’ and ‘Shixia’ has substantially improved contiguity and gene annotation, thereby enabling population-genomic analysis, genome-wide gene family identification, and candidate-gene discovery. Available transcriptomic datasets further support studies of reproductive development, stress responses, and embryogenic competence, although cross-study integration remains limited. We also summarize how gene family analyses have advanced the current understanding of floral induction, continuous flowering, somatic embryogenesis, mineral transport, and sugar transport in longan. Importantly, the field is still dominated by cataloguing and expression-based inference, whereas causal validation, pan-genomic analysis, and multi-omics integration remain insufficient. We therefore argue that future progress in longan molecular breeding will depend on integrating high-quality genomic resources with functional validation, standardized comparative annotation, and improved transformation or regeneration systems. Full article

The fig tree (Ficus carica L.) is one of the oldest cultivated fruit trees in the Mediterranean region and represents an important genetic resource for both traditional and emerging production systems. Despite its agronomic and economic relevance, modern fig breeding remains limited, and large-scale phenotypic evaluations across Mediterranean germplasms are still scarce. The objective of this study was to assess phenotypic diversity and identify key agronomic traits relevant for fig breeding. A total of 257 female fig genotypes conserved in germplasm banks located in Spain, Turkey, and Tunisia were used. Over two consecutive seasons (2021 and 2022), a total of 27 morphological, phenological, and pomological traits were assessed according to the International Union for the Protection of New Varieties of Plants (UPOV) descriptors for fig (TG265/1), with 23 phenotypic traits retained for statistical analyses. Linear mixed models were used to estimate marginal means and to partition genetic and environmental variance, while multivariate analyses and trait correlations were employed to explore the structure of phenotypic diversity. The germplasm exhibits remarkable variation in productive type, reproductive behaviour, harvesting date, and fruit quality traits. Harvesting date spans nearly three months. Fruit weight ranges from 11.7 to 134.5 g, total soluble solids from 9 to 39 °Brix, and maturation index values reached high levels, indicating pronounced sweetness during fruit ripening. Most genotypes showed high skin scratch resistance, absence of cracking at maturity, and medium or small ostiole size, highlighting the presence of ideotypes specifically suited for fresh market production. Heritability estimates indicate strong genetic control of key traits, such as fruit weight, fruit size, and total soluble solids, highlighting their suitability for selection in breeding programs. Stakeholder prioritisation further confirmed the relevance of fruit size, sweetness, firmness, and ostiole characteristics, helping to identify best genotypes for breeding and agronomic purposes. Overall, this study demonstrates the value of Mediterranean fig germplasm as a reservoir of valuable agronomic and commercial traits and provides a robust phenotypic framework to support future breeding, conservation, and cultivar selection strategies. Full article

Shoot branching, as an important architectural trait, influences the number of flower heads and the pattern of flowering in sunflowers (Helianthus annuus L.). However, the main genetic factors leading to extensive branching throughout the plant were not clearly understood. In this study, we analyzed branching inheritance and identified a significant locus using an F₂ population (n = 660) from a cross between the non-branched line 150A and the highly branched line PT326. The branching phenotypes varied from having no branches to complete plant branching, with segregation fitting a 3:1 ratio (χ² = 2.916, p > 0.05), suggesting that a single major gene controls this trait, with the non-branched phenotype being dominant. Using bulked segregant analysis (BSA) and whole-genome resequencing, a strong and consistent signal was identified on chromosome 10 across three separate statistical analyses, pinpointing a primary candidate interval of approximately 3.40 Mb, named qBr10. Through the use of 10 developed Kompetitive Allele-Specific PCR (KASP) markers and recombinant screening, qBr10 was restricted to a 388.5 kb (Chr10:13,422,378–13,780,875). Analysis of this interval identified 21 genes, among which WRKY21 and MTB3 were prioritized as candidate genes for further functional validation. Our findings identified qBr10 as a strong candidate for cloning and offer closely associated markers to aid in marker-assisted improvement of branching and capitulum number in sunflower breeding. Full article

Lodging is a major constraint limiting grain yield in dry direct seeding rice (DDSR), yet the key traits and phenotypic relationships governing lodging resistance in japonica varieties adapted to this system remain poorly understood. This study evaluated 79 japonica accessions over two years in Shenyang, Northeast China, to dissect phenotypic variation in lodging index and identify ideotypes for breeding. Based on hierarchical clustering, varieties were classified into strong lodging resistance (SLR), medium lodging resistance (MLR), and weak lodging resistance (WLR) types, with SLR varieties achieving lodging indices 27.4–31.8% lower than those of MLR and 63.2–83.8% lower than those of WLR varieties. SLR varieties reduced lodging risk by coordinately balancing whole-plant bending moment and stem breaking resistance: plant height and center-of-gravity height were 5.2–10.7% lower, while basal internode bending stress was 27.9–81.9% higher than in other types. Structural equation modeling identified culm dry weight, inner diameter, and culm phenotype index as primary determinants of lodging variation. Notably, despite 11.0–13.7% fewer spikelets per panicle, SLR varieties maintained grain yields comparable to those of WLR varieties through compensatory increases in grain-filling rate (6.7–7.3%) and 1000-grain weight (8.1–8.7%). These findings demonstrate that optimizing basal internode structure and enhancing culm tissue density can simultaneously improve lodging resistance and preserve yield potential, providing a practical framework for breeding lodging-resistant, high-yielding japonica varieties for DDSR systems in Northeast China. Full article

Diaporthe spp. are among the most serious pathogens of soybean. Many different Diaporthe species can infect soybean plants. The species differ in their aggressiveness or virulence and in the severity of the damage they cause. Resistance breeding in soybean has been performed for only two Diaporthe species, so far. It would be very advantageous to identify soybean cultivars with resistance against other Diaporthe species as well, both as sources of resistance for breeding and to inform farmers which cultivars should be planted when a given Diaporthe species shows high incidence. We performed greenhouse experiments to differentiate levels of resistance using the Stem Cut and Stem Wound methods for inoculation of the plants with Diaporthe. Symptom severity was rated visually, and at 5 dpi the level of lipid peroxidation (LP), activity of superoxide dismutase (SOD), total phenolics and total flavonoids were measured. Among the four Diaporthe species tested, D. caulivora was most aggressive, followed by D. longicolla. Of the cultivars evaluated, Magnolia exhibited the highest level of resistance with no significant differences observed among the other cultivars. Although biochemical responses could be observed, it was impossible to determine the specific response responsible for elevated resistance in Magnolia. Full article

Nicotiana tabacum is a classic model for studying pollination on wet stigma. Reactive oxygen species (ROS) and nitric oxide (NO) production are closely related to stigma fertility and depend on the activity of redox enzymes. This study is devoted to the comparison of two tobacco lines differing in physiological parameters and reproductive success. Samsun is a tobacco variety that is widely used in research due to its low demands; however, the reproductive potential of the variety is quite low. Based on this variety, a new line was obtained, called “Fortune”; the plants are externally similar to the Samsun plants, but are more successful in reproduction. The total production of ROS + NO on the stigmas of the Fortune plants is lower than the Samsun plants, but their ROS production is higher, and the main decrease occurs due to NO. Superoxide dismutase activity differs between the two lines at all stages of stigma development except the fertile stage, while ascorbate peroxidase activity is higher in “Fortune” at all stages. Additional isoforms of ascorbate peroxidase are detected in developing stigmas of the Fortune variety. Presumably due to differences in redox metabolism, Fortune plants produce more seeds, their fruit are larger, and their leaves and flowers are also larger compared to the Samsun plants. In this study, we investigated both redox homeostasis parameters and plant productivity using tobacco as the model plant and suggested that there is a correlation between these groups of parameters, which may be important for breeding highly productive plants. Full article

Sweet peppers (Capsicum annuum L.) are an important dietary source of antioxidants. Optimizing fruit antioxidant quality under reduced inputs is essential to valorize sustainable pepper production. Here, we evaluated seven Spanish genotypes (traditional/local, derived experimental hybrids and commercial hybrids) across six treatments combining two fertilization (100% and 50%) and irrigation (100% and 75%) regimes, with plant growth-promoting rhizobacteria (PGPR) applied under reduced fertilization treatments. Vitamin C and flavonoids were quantified by HPLC at the green-ripe and fully ripe stages, and carotenoids were determined spectrophotometrically at the fully ripe stage. Several genotypes largely maintained antioxidant content under stress treatments, whereas specific genotype × ripening stage combinations showed maximum increases in vitamin C (+102%), flavonoids (+86% for kaempferol) and carotenoids (+67% for yellow-orange carotenoids) under certain low-input treatments compared to the control. The PGPR effects on vitamin C and carotenoids were generally small, with occasional reductions. However, the PGPR increased total and some individual flavonoids by up to 96% (luteolin) in green-ripe Piquillo and 128% (quercetin) in fully ripe Isabel F1 fruits compared to the corresponding non-inoculated treatments. This multi-genotype, two ripening-stage evaluation identifies Spanish traditional germplasm and derived hybrids with stable or improved antioxidant profiles under low-input conditions and provides insight into PGPR effects. These results support the use of traditional genotypes in breeding for sustainable production. Full article

CCCH zinc-finger proteins constitute a unique class of transcription factors that play vital roles in mediating plant tolerance to biotic and abiotic stresses and regulating various physiological and developmental processes. This study systematically identified and characterized the apple (Malus domestica) CCCH (MdC3H) gene family, aiming to elucidate its evolutionary patterns, functional characteristics, and regulatory mechanisms under drought stress. Genome-wide analysis revealed 85 MdC3H genes, which were unevenly distributed across chromosomes and exhibited significant differences in physiochemical properties, suggesting functional divergence. Phylogenetic analysis classified these genes into 9 subfamilies with distinct conservation. Collinearity analysis indicated a close evolutionary relationship between apple and Malus sieversii, with 150 collinear gene pairs identified, highlighting the conservation of the C3H gene family during speciation. Cis-acting element prediction in promoter regions uncovered abundant stress-responsive elements (e.g., ABRE, DRE, MYB), implying the potential of MdC3H genes in coordinating environmental signals. Functional verification demonstrated that MdC3H49, a key member of the family, is localized in the nucleus and possesses transcriptional activation activity. Overexpression of MdC3H49 in Arabidopsis and apple calli significantly enhanced drought tolerance, characterized by reduced malondialdehyde (MDA) content, relative electrical conductivity, and increased proline accumulation. Mechanistic studies revealed that MdC3H49 directly regulates the expression of MdP5CS, a core gene in proline biosynthesis, thereby strengthening the cellular antioxidant capacity and mitigating drought-induced damage. Collectively, this study establishes MdC3H49 as a critical regulator in apple drought stress response, providing valuable insights into the molecular mechanisms underlying abiotic stress tolerance in perennial plants and laying a foundation for genetic improvement of drought resistance in apple breeding. Full article

Salt stress is a major abiotic factor that significantly limits crop yields worldwide. Late embryogenesis abundant (LEA) proteins, which are widely present across diverse organisms, play critical and multifaceted roles in plant responses to abiotic stress. However, only a few salt tolerance-related HvLEA genes have been identified in barley. In this study, we characterized 107 HvLEA proteins in barley, which were classified into eight groups and found to be distributed across all seven chromosomes. RNA-Seq analysis of root and leaf tissues from the cultivar “Golden Promise” at 12, 48, and 120 h after salt stress treatment identified 69 differentially expressed HvLEA genes across both tissues. Among these, 41 HvLEA genes were commonly differentially expressed in leaves and roots. Six genes (HvDHN2, HvDHN5, HvDHN10, HvLEA1.1, HvLEA1.6, and HvSMP2) were extremely up-regulated after salt stress in both roots and leaves, with log2FC values exceeding 10, indicating their potential key roles in salt stress response. qPCR validation of selected genes confirmed expression trends consistent with the RNA-Seq data. Database predictions and co-expression network analysis suggested that, in addition to potential protein interactions within the same family, these genes may interact with partners such as cysteine-rich receptor kinases, zinc finger proteins, calcium-binding EF-hand family proteins, NAC domain-containing proteins, and glycosyltransferases. This study identified key HvLEA genes involved in salt stress response and provided valuable genetic resources for improving barley tolerance through molecular breeding. Full article

Background: Differentiating plant species is complex, complicated by morphological similarities that confound species’ delineation. For hundreds of years, researchers have used herbarium specimens to study plant morphology, and over the last forty years, these samples have also served as material for molecular phylogenetic research. Taxonomists have alternately split and combined morphotypes of Pediomelum tenuiflorum for two centuries. With samples of P. tenuiflorum from across its distribution, this research aimed to (1) infer a robust phylogeny using molecular data, i.e., gene sequences from chloroplast and nuclear genomes; (2) assess genetic diversity using molecular markers, specifically Inter Simple Sequence Repeats (ISSRs); (3) provide evidence to support the taxonomic placement and possible splitting of P. tenuiflorum; and (4) identify consistent morphological characteristics using a correlation matrix to distinguish among the morphotypes. Results: Striking morphological differences among the individuals of P. tenuiflorum from across the species’ distribution resulted in more than two morphotypes. Phylogenetic data suggest hybridization is occurring among genetically and morphologically distinct members of P. tenuiflorum and with other species in the genus Pediomelum, whereas ISSR results indicate detectable genetic variation but do not resolve discrete clusters. This study reports the first ISSR markers used to assess genetic diversity in Pediomelum species. Conclusions: Morphological and genetic variation exist across individuals of P. tenuiflorum but not in monophyletic groups that support splitting the morphotypes into multiple species. Future investigations into chromosome numbers might reveal polyploidization in the lineage, and phylogenies estimated from low-copy nuclear genes could elucidate hybridization pathways. Full article

The MADS-box family is a multifunctional family of transcription factors characterized by the presence of a unique MADS domain, which plays an important part in regulating essential biological processes, including metabolic synthesis and the stress response. In this review, we analyze the structural features and classification of MADS-box proteins, then summarize the functions of the MADS-box family in the stress response. The MADS-box family can directly regulate downstream functional genes by binding to the CArG-box in the promoters of target genes, thereby influencing growth, development, and stress responses. Also, MADS-box transcription factors can form protein complexes with both MADS-box proteins and other types of transcription factors and chromatin regulatory proteins to modulate the chromatin state or transcriptional activation. Furthermore, they can regulate plant physiological responses by facilitating the synthesis of essential signaling molecules, including hormones and non-coding RNA. Finally, we discuss the potential of the MADS-box family in crop molecular breeding, offering a novel approach for developing high-yield and stress-resistant cultivars for solving global food security and climate change challenges. Full article

The genus Passiflora includes species important for fruit production, ornamental value, and breeding programs. Conventional methods, such as seed propagation and vegetative cuttings, face challenges like genetic heterogeneity, pathogen transmission, and long juvenile phases, limiting large-scale cultivation and breeding efficiency. In vitro culture technologies are essential for clonal propagation, germplasm conservation, and improving Passiflora species using biotechnology. This review critically evaluates current progress in micropropagation and regeneration systems in Passiflora spp. and examines the prospects of haploid and doubled haploid technologies as future breeding tools. Unlike previous reviews, which primarily focus on summarizing tissue culture protocols, this study integrates regeneration biology, developmental constraints, and emerging biotechnological approaches to provide a broader framework for research. Additionally, this review offers a comparative analysis of various regeneration systems across Passiflora species and highlights the challenges of genotype-dependent methods. By synthesizing recent advancements in haploid technology, it provides new insights into the potential for accelerating breeding programs in Passiflora, a field where robust protocols are still lacking. Full article

The perennial grass timothy (Phleum pratense) is an important forage crop in cold temperate regions. It forms three types of tillers: vegetative (VEG), generative (GEN), and non-flowering elongated (ELONG). To understand the influence of plant development and tiller formation on biomass production and the diversity in these traits, a total of 246 wild and domesticated accessions of timothy and the related species, P. nodosum and P. alpinum, were investigated. The length of different plant developmental stages and the formation of different tiller types were studied to test the hypotheses: (1) the proportion (%) of different tiller types affects biomass and is influenced by the lengths of the different plant developmental stages, (2) domestication and breeding have affected the length of developmental stages and proportions of tiller types. While timothy cultivars did not differ significantly from wild accessions in biomass, wild accessions had higher VEG%, which increased with latitude of accession origin. P. nodosum cultivars produced the highest number of ELONG of all accessions and species, and the ELONG% showed a strong positive correlation with biomass. Timothy cultivars showed later emergence and tillering, and reached stem elongation and heading earlier than wild accessions, suggesting that delayed tillering, but an overall faster development, has been favoured during breeding. The time between tillering and stem elongation showed a positive correlation with VEG%. This study reveals large diversity in developmental and tiller traits among accessions, reflecting differences in their domestication and breeding history, and highlighting the importance of considering early developmental traits and ELONG formation for yield and quality in further pre-breeding research. Full article

Hordeum brevisubulatum ‘Mengnong No. 2’ is a new forage variety developed using traditional group selection breeding techniques. It features notable advantages in plant height, tillering capacity, and overall biomass yield. However, key molecular breeding techniques such as molecular marker identification and genetic manipulation have yet to be established for this variety, limiting improvements in important traits. Consequently, we assessed the biomass of ‘Mengnong No. 2’ against ‘Mengnong No. 1’, the most widely cultivated variety in the central and western regions of Inner Mongolia, China. We report that fresh forage, dry forage, and seed yields of ‘Mengnong No. 2’ increased by 20.6%, 31.78%, and 34.35%, respectively, compared with the control variety, indicating broad prospects for its application and promotion. To enable rapid identification of ‘Mengnong No. 2’ during its promotion and to prevent production losses caused by variety admixture, we used three screened SSR primer pairs (GST25, GST37, GST127) to construct a DNA fingerprint for five H. brevisubulatum varieties, including ‘Mengnong No. 2’. With the percentage of polymorphic bands exceeding 95%, these profiles enabled precise identification of the ‘Mengnong No. 2’ variety. Furthermore, callus regeneration in H. brevisubulatum represents a bottleneck for directed molecular breeding techniques such as genetic transformation and gene editing. Accordingly, we selected the inflorescences of ‘Mengnong No. 2’ as explants and investigated the callus induction and regeneration capacity of inflorescences at different developmental stages. We found that explants at the spikelet primordia differentiation stage exhibited the highest callus induction and regeneration efficiencies, reaching 62.7% and 72.8%, respectively. The resulting embryogenic callus lines can serve as recipients for Agrobacterium-mediated transformation or gene gun bombardment, facilitating the development of subsequent high-efficiency genetic transformation and gene-editing systems. The SSR-based variety identification system and the highly efficient regeneration technology using inflorescence-derived callus established in this study lay a solid foundation for the development of a molecular breeding system for ‘Mengnong No. 2’. Full article