Search Results (4,236)

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

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

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

The evaluation of biomechanical parameters in four-beat gaited horses remains limited by the subjectiveness and complexity of current standard methods. Through a deep learning approach, we aimed to infer dissociation % using only acoustic signals. A total of 268 audio samples were extracted from publicly available videos featuring three Brazilian horse breeds (Mangalarga Marchador, Campolina, and Piquira) performing marcha batida and marcha picada. Acoustic features, including root mean square energy (RMS), zero-crossing rate (ZCR), and 13 Mel-frequency cepstral coefficients (MFCCs), were extracted and used to train a long short-term memory (LSTM) neural network. The model accurately predicted the time intervals between successive hoof–ground contacts (R² = 0.98; MAE = 0.0071), enabling the calculation of the dissociation %. While no significant differences were found between gait types and dissociation %, breed-related differences in both mean hoof–ground contact interval and dissociation were observed, with 8 acoustic features demonstrating discriminative power. Our results suggest that hoof–ground contact patterns can be quantified objectively from audio alone, offering a practical and non-invasive method for gait analysis. The approach holds potential for applications in breed standardization, selection, and digital locomotion phenotyping of horse populations. Full article

The objectives of this paper were to assess the genetic diversity, population structure, genetic differentiation, and phylogenetic relationships among seven duck populations using 14 microsatellite (MS) markers. This paper included 176 individuals representing seven duck populations of Bangladesh: indigenous duck (BLD), Nageswari (NAG), Rupali (RUP), Jinding (JIN), Pekin (PEK), BAU Black and White (BWC), and BAU White (WHC). A total of 133 alleles were observed with a mean of 9.50 alleles per locus. Genetic diversity was evaluated using measures such as allele frequency, observed and expected heterozygosity, and Shannon’s information index with average values of 5.44 ± 0.31, 0.59 ± 0.02, 0.64 ± 0.02, and 1.28 ± 0.05, respectively. Population differentiation and inbreeding analysis (F-statistics) indicated moderate genetic diversity and a slight degree of inbreeding across populations. Analysis of molecular variance indicated that 75% of the total genetic diversity was attributable to the within-population variation, whereas 9% and 16% were attributed to the variation among individuals and population differentiation, respectively. Indigenous duck populations (BLD, NAG, and RUP) had a close genetic relationship with JIN ducks and an intermediate relationship with two crossbreds (BWC and WHC), and the highest genetic distance was observed with PEK ducks. Neighbor-joining phylogenetic analysis revealed that the Bangladeshi indigenous duck populations formed a single cluster, while the two crossbreds (BWC and WHC) and PEK exhibited their distinct genetic identities in separate clusters. Furthermore, structure analysis at K = 2 to 5 confirmed the distinct genetic architecture (ΔK = 4.00) of the studied duck populations. This paper provides important insights into genetic diversity measures and population differentiation that will be helpful in future genetic improvement, conservation initiatives, and the design of appropriate breeding programs. Full article

Cymbidium eburneum Lindl. is a valuable ornamental orchid and breeding parent, but its genetic background remains unclear due to habitat destruction and germplasm mixing. This study developed specific SSR markers to evaluate the genetic diversity and structure of 96 C. eburneum Lindl. accessions from China and Vietnam. Transcriptome analysis identified 47,248 SSR loci. Sixteen polymorphic core primer pairs detected 150 alleles (mean Na = 9.375) with an average Polymorphism Information Content (PIC) of 0.444. Observed heterozygosity (Ho = 0.290) was noticeably lower than expected (He = 0.478), indicating heterozygote deficiency. UPGMA clustering identified eight groups strongly correlated with geography. Principal Coordinate Analysis (PCoA) revealed a clear geographical differentiation pattern, featuring the most genetically cohesive group from Guangxi and more differentiated geographically marginal populations from Hainan and Vietnam. STRUCTURE analysis (K = 2) indicated two main gene pools with signals of genetic admixture. Geographical isolation was suggested as a potential driver of genetic differentiation. The Guangxi population represents a genetically consistent major reservoir, while marginal populations harbor unique variations. These findings provide a scientific basis for germplasm identification, conservation, and parental selection in C. eburneum Lindl. breeding. Full article

Understanding the genetic architecture underlying growth variation is central to improving aquaculture species through genomic selection. Here, we performed a genome-wide association study (GWAS) on 303 individuals from a G₂ breeding population of channel catfish (Ictalurus punctatus) using whole-genome resequencing data. After stringent quality control, 5.64 million high-confidence single nucleotide polymorphisms (SNPs) were retained for association analyses of two key growth traits—monthly weight gain (MWG) and body depth (BH). We identified 15 and 28 loci significantly associated with MWG and BH, respectively, with the majority concentrated on chromosome 20. Two SNPs (Chr20:14,657,971 and Chr20:14,658,012) located in exon 9 of the rrp44 gene were significantly associated with both traits. Functional annotation and enrichment analyses revealed that the rrp44 gene, encoding an exoribonuclease subunit of the RNA exosome complex, participates in mitotic spindle regulation and post-transcriptional RNA decay, processes critical for cellular growth and metabolic homeostasis. We propose that rrp44 may influence growth through the modulation of feeding rhythm and circadian regulation, providing a potential molecular basis for growth heterogeneity in channel catfish. These findings enrich our understanding of growth-related genomic variation and offer valuable molecular markers for precision breeding and genetic improvement of catfish. Full article

Background/Objectives: With the acceleration of global industrialization and continuous population growth, the world is increasingly confronted with the dual challenges of food insecurity and cultivated land contamination. The screening and breeding of rice varieties with superior agronomic traits and low heavy metal accumulation have therefore become important strategies for ensuring food safety and sustainable agricultural production. Methods: In this study, rice varieties carrying the Gn1a-i gene and exhibiting specific cadmium (Cd) accumulation characteristics were screened using a combination of molecular marker detection and cadmium accumulation evaluation. Specific loop-mediated isothermal amplification (LAMP) primers targeting the Gn1a-i gene were designed and combined with a lateral flow dipstick (LFD) assay to enable rapid genetic screening of rice varieties. A six-day hydroponic experiment under cadmium stress was conducted across three temperature ranges (15–20 °C, 22–27 °C, and 30–35 °C), and cadmium accumulation in different plant organs (roots, stem sheath, and leaves) was analyzed. Results: Seven varieties carrying the Gn1a-i gene, including Xiangwanxian 12, were identified among ten tested rice varieties. Xiangwanxian 12 was subsequently selected for further evaluation, with the high-cadmium-accumulating variety Yuzhenxiang used as a control. At 144 h, the total Cd content in the measured organs of Xiangwanxian 12 was 9.6%, 4.0%, and 23.2% lower than that of Yuzhenxiang under low, medium, and high temperatures, respectively (one-tailed t-test, p < 0.01 for all three temperatures). Conclusions: The integration of LAMP-based genotyping and physiological evaluation provides a novel and reliable strategy for identifying low-Cd rice germplasm. Xiangwanxian 12, which carries the Gn1a-i allele and exhibits consistently lower Cd accumulation than Yuzhenxiang, suggests potential as a candidate for breeding high-yield, low-Cd rice cultivars. Full article