Search Results (4,243)

Wild orchid populations are declining with intensified habitat fragmentation posing severe challenges to germplasm conservation. As an important ornamental Orchidaceae species, Cymbidium ensifolium has abundant germplasm resources and frequent natural and artificial hybridization. Long-term natural evolution and anthropogenic disturbance have led to complex genetic backgrounds and ambiguous phylogenetic relationships hindering accurate germplasm identification, elite resource excavation, and selective breeding. As a distinctive variety, Cymbidium ensifolium var. susin has great breeding potential. Clarifying its phenotypic and genetic characteristics is crucial for accelerating breeding progress. In this study, phenotypic determination, Hyper-seq reduced-representation genome sequencing, SNP/InDel genotyping, genetic diversity analysis, and core collection construction were used to evaluate the genetic diversity, population differentiation, and core germplasm screening of 13 Cymbidium ensifolium var. susin accessions. The results showed significant phenotypic differences and rich genetic variation among tested materials. Based on highly weighted floral traits, accessions were divided into three major phenotypic groups. At the molecular level, 963,239 SNP and 182,399 InDel loci were identified and mainly distributed in intergenic regions, followed by introns and exons. A phylogenetic tree was constructed from SNP loci combined with principal component and phenotypic clustering analyses. This study preliminarily clarified the genetic structure of pure-heart Cymbidium ensifolium var. susin, showing a distinct geographical pattern: “high consistency in Fujian and Guangdong; strong differentiation in Southwest China; and a transitional gradient in Central China”. Meanwhile, six core germplasm accessions were screened in this study, which provides a solid theoretical basis and material support for the conservation of pure-heart Cymbidium ensifolium var. susin accessions, variety improvement, hybrid parent selection, and molecular marker-assisted breeding. This is of great significance for promoting the innovation of Chinese orchid germplasm resources and the high-quality development of the industry. Full article

Potato early blight (EB), caused by Alternaria, is an economically devastating fungal disease affecting global potato production. Using a hybrid population derived from distantly related varieties, we combined resistance evaluation, histological analysis, Bulked Segregant Analysis sequencing, RNA sequencing and molecular dynamics simulation, which successfully identified key candidate resistance genes. Genetic mapping localized three major resistance-associated regions on chromosome 8 spanning positions 25.07–29.20 Mb, 38.05–38.80 Mb, and 39.40–40.78 Mb. Through candidate gene analysis, we identified CND41, encoding an aspartic protease, as the prime candidate. This gene exhibited significantly higher basal expression levels and stronger pathogen-induced upregulation in resistant genotypes. Molecular dynamics simulations further identified six crucial non-synonymous mutations in the TAXI-N domain that likely contribute to enhanced resistance by destabilizing the susceptibility-associated protein conformation. Transient overexpression of CND41 provided functional evidence supporting its likely involvement in early blight resistance (EBR). These findings contribute valuable genetic resources and a strong candidate gene for molecular breeding toward EBR potato varieties. Full article

This study presents a genetic characterization and population structure analysis of an ancient Algerian collection of Citrus fruits, dating back to the colonial period of the early 1900s. Genetic diversity was assessed using eight Simple Sequence Repeat (SSR) markers, with the objective of accurately identifying their varieties and elucidating their genetic relationships, particularly in the absence of passport data and documented origins. A total of 96 accessions were analyzed. Instances of homonymy, synonymy, and labeling errors were detected. Observed heterozygosity ranged from 0.451 to 0.715, with a mean value of 0.54, while polymorphic information content (PIC) values varied between 0.225 (CCSM18) and 0.635 (TAA41). The genetic relationship patterns among the different Citrus groups were consistent with their botanical classification. Structureanalysis suggested differentiation between the pomelo–orange cluster and the lemon group, as well as between the mandarin and clementine groups. These results suggest thatAlgerian Citrus germplasm may represent a valuable and relatively underexplored resource for breeding programs, highlighting the importance of its proper characterization and conservation to prevent genetic erosion. Full article

Husk tomato (Physalis ixocarpa Brot.) is a crop of major economic, cultural, and nutritional importance in Mexico and exhibits substantial genetic and morphological diversity. Characterizing this variability is essential for both germplasm conservation and breeding programs. During the spring–summer 2024 growing season, 28 husk tomato populations were evaluated at the Bajío Experimental Station (INIFAP), Guanajuato, Mexico, using a completely randomized design with 12 replications. Forty-one traits were assessed following UPOV and IPGRI descriptors. Cluster analysis, canonical discriminant analysis, and the ESIM selection index were applied. A total of 77 morphotypes were identified, exhibiting variation in 33 of the 41 evaluated traits, mainly related to growth habit, leaf morphology, fruit traits, and calyx attributes. Correspondence analysis revealed a close relationship between vegetative growth and fruit size. Cluster analysis clustered the morphotypes into six clusters with no clear geographic structure, suggesting extensive gene flow. Canonical discriminant analysis explained 94.65% of the total variation, identifying seed size, leaf dimensions, and number of anthers as key discriminant traits. The ESIM index highlighted six morphotypes with favorable agronomic and morphological combinations. These results provide a practical basis for the selection of parental materials in husk tomato breeding programs under diverse agroecological conditions. Full article

GDSL esterase/lipase (GELP) proteins constitute an evolutionarily conserved yet functionally diversified hydrolase family in land plants. They participate in cuticle and secondary cell wall biosynthesis, seed lipid remobilization, reproductive development, and hormone-mediated responses to biotic and abiotic stresses. Despite extensive genome-wide and comparative genomic studies that have categorized large GELPs across numerous crops and model species, only a fraction of members have been functionally characterized in plants, and their catalytic mechanisms and regulatory architectures remain poorly understood. Recent population genomics and cross-species orthogroup analyses in 46 angiosperms have uncovered substantial natural variation within GELP coding sequences and regulatory regions, providing a powerful framework to link allelic diversity to evolutionary trajectories and physiological functions. This review synthesizes current knowledge on GELP evolution, biochemical properties, and roles in development and stress adaptation, and critically evaluates how these insights can be translated into biotechnology and molecular breeding strategies. It highlights emerging resources and concepts from orthogroup-based classification and multi-species datasets that enable systematic discovery of GELP alleles affecting agronomic traits. It further outlines research exploiting GELPs in crop improvement, emphasizing the integration of reverse and forward genetics with multi-omics profiling, biochemical and structural characterization, and gene regulatory network reconstruction. Systematic assessment of the phenotypic impacts of single and combinatorial GELP perturbations on yield, quality, and stress resilience is proposed as a key step toward translating basic insights into breeding and engineering strategies. Full article

Modern cattle comprise two major evolutionary lineages: intensively selected commercial breeds and locally adapted native populations. To investigate their genomic divergence, we performed a comparative population genomic analysis by integrating whole-genome resequencing (WGS) data from multiple representative native breeds and major European commercial breeds. Population genetic analyses showed clear phylogenetic separation between the two groups, with distinct patterns of genetic diversity. Chinese native cattle exhibited generally higher nucleotide diversity (π), lower inbreeding levels, and geographically structured admixed ancestry. Comparative analyses of selection signatures identified 886 candidate selected genes in European commercial breeds, which were primarily enriched in pathways related to production traits, including protein turnover, reproductive regulation, lipid metabolism, and neuro-regulation. In contrast, 50 candidate selected genes in Chinese native cattle were significantly enriched in nervous system functions, particularly ligand-gated ion channel activity and chloride transport (e.g., GRID2, GLRA2/4, GABRD), suggesting neural/ionic regulation may contribute to local adaptation alongside other polygenic mechanisms. Additionally, the two groups also differed in patterns of deleterious mutation load. These findings indicate partially distinct evolutionary trajectories between “production-optimized” and “environment-adapted” cattle and highlight the value of conserving the genetic diversity and adaptive alleles of Chinese native cattle. Full article

Despite the productivity and economic limitations imposed by environmental and climatic conditions, livestock systems play a fundamental role in preserving habitats and high-conservation-value species, while delivering a broad spectrum of ecosystem services to rural populations. Breeders need timely information to produce safe, inexpensive, environmentally, and welfare-friendly food products. Information on feeding and nutrition is of particular importance since it represents a significant percentage of animal breeding costs. Automating the collection, analysis, and use of production-related information on livestock feeding systems represents one of the central challenges facing the sector. Precision feeding systems (PFSs) have deeply changed farm management by providing new information on the health status of animals, their welfare, and nutritional requirements. PFSs encompass modern electronic and ICT-related (information and communication technologies) technologies that facilitate the electronic measurement of critical components, ensuring optimum efficiency of both resource use and animal productivity. This review analyzes the current state and potential applications of precision feeding systems for sustainable livestock production. The implementation and feasibility of PFSs have been investigated across the major animal production species and contexts. Based on the available literature, real-time monitoring and control systems can improve the production efficiency of livestock farms. However, further research is needed, as several components of PFSs are still at different stages of development and commercial readiness. Full article

In urban areas, green spaces have become the main refuge for biodiversity, providing essential habitat and resources for urban-adapted species. However, scientific evidence on the fitness consequences of urban green space management for urban populations remains scarce, limiting our ability to design successful conservation and management strategies. Here, we assess the fitness consequences of different levels of management practices in green spaces (i.e., high for areas with continuous intervention such as regular mowing and irrigation, and low for areas with minimal, sporadic maintenance) based on a 19-year long-term monitoring of the Eurasian Tree Sparrow (Passer montanus), a species with high behavioural plasticity in response to human-altered habitats. We formulated a unistate capture–mark–recapture model to estimate age-dependent survival while accounting for uncertainty in recapture probability. Furthermore, by means of GLMMs, we tested if the level of management influences reproductive parameters (i.e., breeding failure, number of eggs, nestlings, fledglings, brood number from the same year, breeding success). We found that high urban green space management caused a decline in adult survival, but we found no effect on juvenile survival. We also found lower breeding failure, a greater number of eggs, and larger brood numbers in the low management areas, but no differences were found in the number of nestlings and fledglings. Consequently, we found no differences in overall breeding success. Our results highlight the reduction in survival in a near-threatened passerine species due to routine green urban space management, in addition to differences in reproductive parameters depending on the degree of green urban space management. Overall, we confirm that the same species show several reproductive strategies with different breeding effort to reach similar breeding success, whatever the human context is. However, birds pay the cost in adult survival, and probably in shortening life span. Therefore, the management of urban green spaces has a negative impact on biodiversity in cities. It is necessary to review the management practices of these urban areas and promote practices that are friendly to biodiversity. Full article

White clover (Trifolium repens L.) is a major legume in Mediterranean agroecosystems. This study systematically evaluates 15 autochthonous white clover populations from the Trikala region of Greece, focusing on chemical composition and derived nutritional indices relevant for germplasm characterization and breeding. Fifteen local populations were evaluated under controlled pot cultivation over two consecutive years. Clonal plants were harvested at the early flowering stage. Key traits—crude protein (CP), Ash, Fat, crude fibre (FIBRE), acid detergent fibre (ADF), neutral detergent fibre (NDF), digestible dry matter (DDM), dry matter intake (DMI), and relative feed value (RFV)—were measured. Combined ANOVA revealed significant differences among populations for all traits (p ≤ 0.001), while genotype × year interactions were present but generally minor compared to genotypic effects. Broad-sense heritability was high across most traits (H² = 90.8–99.4%), demonstrating strong genetic control. CP showed positive correlations with DDM, DMI, and RFV, whereas ADF and NDF were negatively correlated with intake and digestibility. Canonical and discriminant analyses showed that a reduced set of traits (CP, Ash, FIBRE, RFV) contributed strongly to differentiation among populations. Hierarchical clustering (heatmap) confirmed these groupings based on fibre and digestibility-related traits. Populations such as Dendrochori and Gorgogyri consistently showed favorable chemical and nutritional profiles, while Fiki and Dendrochori showed the highest stability across years. The present study highlights substantial genetic variability among local white clover populations and identifies trait structures of relevance for germplasm characterization. These findings enhance the characterization of genetic diversity in Trifolium repens and support its potential use in future breeding research under Mediterranean environments. Full article

Sunflower downy mildew, caused by Plasmopara halstedii, remains one of the most destructive diseases worldwide. The genetic diversity of P. halstedii populations continues to challenge resistance breeding efforts. This study evaluates the effectiveness of key resistance genes against P. halstedii isolates collected in Hungary. Eight isolates were tested using the sunflower differential lines HA-335, RHA-419, and RHA-340, with the resistance genes Pl6, Pl_Arg, and Pl8, respectively. Disease development was assessed by observing sporulation and symptoms including stunting, chlorosis, damping-off, and abnormal development at three time points after inoculation. Plant height was also measured to evaluate growth responses. The Pl6 resistance gene (HA-335) did not provide effective protection against any of the tested isolates, indicating that Pl6 does not confer reliable resistance against the Hungarian isolates examined in this study. The resistance conferred by Pl8 was not uniformly effective against the Hungarian isolates tested. This study provides the first report of Pl8-virulent P. halstedii isolates identified in both Hungary and Central Europe. The resistance gene Pl_Arg (RHA-419) conferred resistance to all tested P. halstedii isolates. These findings highlight the changing virulence profiles of P. halstedii populations in Hungary, emphasizing the need for ongoing pathogen monitoring and strategic use of resistance genes. Full article

Powdery mildew, caused by Blumeria graminis f. sp. tritici, is a devastating disease threatening global wheat production. Thinopyrum intermedium, a wild relative of wheat, harbors valuable resistance genes for wheat improvement. In this study, we characterized a wheat-Th. intermedium double disomic substitution line X482 (4St-J^S (4D) + 6St (6D)) and wheat-Th. intermedium partial amphiploid TA8034 using ND-FISH and Oligo-FISH painting. Importantly, a unique type of translocation between chromosomes 1B and 6B was identified in line X482. Subsequent immunostaining assays revealed the distinct DNA methylation maintained on Thinopyrum and wheat B-genome chromosomes in X482 and TA8034. Genetic analysis combined with ND-FISH of line X482-derived populations demonstrated that chromosome 6St confers adult-stage powdery mildew resistance. Through ⁶⁰Co-γ irradiation of a 6St monosomic addition line, we developed seven homozygous 6St translocation lines with various breakpoints. Physical mapping using 56 6St-specific molecular markers delineated the resistance locus to bin 6StL-3, corresponding to 358.03–398.21 Mb in the Th. intermedium reference genome v2.1. Notably, the wheat-6St translocation line exhibited powdery mildew resistance without significant negative effects on agronomic traits. These results indicated that the distal region of homologous group 6 chromosomes harbors novel powdery mildew resistance genes, and the developed translocation lines provide valuable germplasm for wheat breeding programs. Full article

As global food security challenges intensify, edible crickets are recognized as sustainable protein alternatives; however, genomic resources for commercially important species remain limited, restricting evolutionary inference and the development of robust tools for farm management. We sequenced and assembled the complete mitochondrial genomes of Gryllus bimaculatus and provided the first report for Teleogryllus mitratus, both derived from commercial farms in Thailand, using high-throughput Illumina sequencing, achieving high coverage depths of 32,391× and 63,258×, respectively. The circular mitochondrial genomes were 15,955 bp and 16,046 bp and exhibited the typical insect mitochondrial gene complement of 37 genes, with a strong AT bias. Selective pressure analyses indicated pervasive purifying selection across all protein-coding genes (PCGs) (ω < 1), while episodic diversifying selection was detected in cox1, cox3, cytb, and nad5; additionally, atp8 displayed a comparatively elevated ω. Codon usage analyses revealed a strong preference for AT-ending codons, with leucine codons showing the highest bias. Phylogenetic analyses using concatenated protein-coding and ribosomal RNA genes recovered well-supported relationships within Gryllidae. These farm-derived mitogenomes provide practical foundations for molecular species authentication, population monitoring, and comparative analyses relevant to breeding and traceability. Furthermore, they provide candidate loci for future investigations into mitochondrial evolutionary dynamics and the potential development of molecular markers for commercial breeding management. Full article

The first female flower node (FFFN) is a crucial trait affecting earliness and yield in bitter gourd (Momordica charantia L.). To identify the genetic locus and candidate gene controlling FFFN, we performed phenotypic and genetic analyses using two parental lines, ‘M144’ (average FFFN: 6.3 ± 2.0) and ‘K55’ (average FFFN: 22.0 ± 4.5), along with their F₁ hybrid and an F₂ population consisting of 317 individuals. The results show that the low FFFN trait was incompletely dominant over the high FFFN trait. Using BSA-seq, we mapped a FFFN locus to an interval of 18.8–22.5 Mb on chromosome 4. Fine mapping with KASP markers narrowed the McFFFN4.1 to a 73.05 kb interval between markers 25QP334 and 26QP20, which contained seven predicted genes. Transcriptome analysis revealed that only Moc04g29650, which is annotated as cytochrome b-c1 complex subunit Rieske, was differentially expressed between the parents within this mapping interval. Sequence comparison identified a single SNP (C > A) in the promoter region of Moc04g29650, which was located within a putative YAB1/FIL-binding motif. Given the known role of FILAMENTOUS FLOWER (FIL) in regulating floral transition in Arabidopsis thaliana, Moc04g29650 is proposed as the most likely candidate gene for McFFFN4.1. The KASP marker 26QP20, located near Moc04g29650, showed the strongest association with FFFN in the F₂ population, with a maximum LOD score of 5.45, and thus represents a valuable tool for marker-assisted selection (MAS) breeding in bitter gourd. This study lays a foundation for cloning McFFFN4.1 and genetically improving early maturity in bitter gourd. Full article

Cucumber (Cucumis sativus L.) is a globally significant vegetable crop, and its fruit quality remains a major focus of research. The hollow-heart trait, characterized by internal cracks or cavities, severely compromises both the commercial value and edible quality of cucumber fruit. In this study, a six-generation segregating population (P₁, P₂, F₁, F₂, BC₁P₁, BC₁P₂) was developed from the parental lines “JZ6-1-2” and “D0432-3-4”. BSA-seq was employed to map candidate genomic regions associated with the hollow-heart trait to chromosomes 2, 3, and 7. Subsequently, a major QTL for the trait was delineated on chromosome 7, spanning a region containing 98 genes. Comparative RNA-seq between the parental lines identified 2141 differentially expressed genes. The integration of QTL mapping and RNA-seq data revealed 11 candidate genes residing within the key QTL interval. Through further validation via qRT-PCR, gene sequence comparison, and gene annotation, Csa7G039280 was identified as a promising candidate gene regulating hollow-heart formation, potentially via the lignin biosynthesis pathway. The identification of these candidate regions and genes provides critical information for molecular breeding aimed at developing non-hollow-heart cucumber varieties, thereby enhancing the understanding of the genetic regulatory mechanisms underlying this economically important trait. Full article

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