Search Results (3,137)

Triploid breeding is a promising approach for developing seedless varieties, but the long juvenile phase of perennial fruit trees necessitates efficient early selection. In loquat (Eriobotrya japonica), a fruit crop with high demand for seedlessness, the relative contributions of hybridity, ploidy level, and parent-of-origin effects (POEs) to triploid seedling vigor remain elusive. To dissect these factors, we established a comprehensive experimental system comprising reciprocal diploid (2x), triploid (3x), and tetraploid (4x) hybrids from two genetically distinct cultivars. The ploidy, hybridity and genetic architecture of hybrid and parental groups were verified using flow cytometry, chromosome counting, newly developed InDel markers and genome-wide SNP analysis. Phenotypic evaluation of eight vigor-related traits revealed that plant height and soluble starch content were the most robust indicators of triploid heterosis in loquat. Notably, paternal-excess triploids [3x(p)] consistently outperformed all other groups. Quantitative analysis revealed POE as the main positive driver of triploid heterosis (+10.37% for plant height), far exceeding the negative impacts of hybridity (−12.75%) and ploidy level (−20.87%). These findings demonstrate that POE predominantly drives seedling vigor heterosis in triploid loquat. We propose a practical breeding strategy that combines prioritizing paternal-excess crosses with novel InDel markers for rapid verification of superior seedless progeny. Full article

In this paper, we research multi-robot coverage path planning (MCPP), which generates paths for agents to visit all target areas or points. This problem is common in various fields, such as agriculture, rescue, 3D scanning, and data collection. Algorithms to solve MCPP are generally categorized into online and offline methods. Online methods work in an unknown area, while offline methods generate a path for the known. Recently, offline MCPP has been researched through various approaches, such as graph clustering, DARP, genetic algorithms, and deep learning models. However, many previous algorithms can only be applied on grid-like environments. Therefore, this study introduces an offline MCPP algorithm that applies graph-adapted K-means and spanning tree coverage for robust operation in non-grid-structure maps such as road networks. To achieve this, we modify a cost function based on the travel distance by adjusting the referenced clustering algorithm. Moreover, we apply bipartite graph matching to reflect the initial positions of agents. We also introduce a cluster-level graph to alleviate local minima during clustering updates. We compare the proposed algorithm with existing methods in a grid environment to validate its stability, and evaluation on a road network digital twin validates its robustness across most environments. Full article

Karyotype analysis and the investigation of chromosomal variations in Populus are challenging due to its small and morphologically similar chromosomes. Despite its utility in chromosome identification and karyotype evolutionary research, satellite DNA (satDNA) remains underutilized in Populus. In the present study, 12 satDNAs were identified from P. trichocarpa, and the copy numbers and chromosomal distributions of each satDNA were analyzed bioinformatically in the reference genomes of P. trichocarpa, P. simonii, and P. nigra. Ten satDNA probes for fluorescence in situ hybridization (FISH) were successfully developed and validated on chromosomes of P. xiaohei (poplar hybrid P. simonii × P. nigra). By integrating bioinformatic genomic satDNA distribution patterns with experimental FISH signals, we constructed a molecular karyotype of P. xiaohei. Comparative analysis revealed errors in current poplar genome assemblies. Comparative karyotype analysis of P. xiaohei and its doubled haploid (DH) lines revealed chromosomal variations in the DH lines relative to the donor tree. The results demonstrate that the newly developed satDNA probes constitute robust cytogenetic tools for detecting structural variations in Populus, while molecular karyotyping provides new insights into the genetic mechanisms underlying chromosome variations in P. xiaohei and the DH plants derived. Full article

The European sweet chestnut (Castanea sativa Mill.) is an ecologically and culturally significant forest tree species in Croatia; however, its genetic diversity and population structure remain insufficiently characterized. This study aimed to evaluate the genetic diversity, structure, and connectivity of chestnut populations on Zrin Mountain, the country’s largest continuous chestnut area. Using seven nuclear SSR markers, we genotyped 153 individuals from three populations (PET, HRK, and BAC). All populations exhibited moderate genetic diversity (mean He = 0.571), with BAC showing the highest allelic richness and number of private alleles. AMOVA revealed that most genetic variance (67%) occurred among individuals, while population differentiation was low to moderate (FST = 0.064; PhiPT = 0.146), consistent with high inferred gene flow (Nm = 7.48). Both STRUCTURE and PCoA indicated that HRK was the most genetically distinct population, whereas PET and BAC were more similar. Overall, these findings demonstrate substantial gene flow and connectivity among Croatian chestnut populations, providing a foundation for sustainable management and conservation strategies in a broader European context. Full article

Paulownia trees are grown globally for their robust timber, agroforestry, and effective carbon dioxide drawdown. China possesses rich Paulownia germplasm resources, offering favorable material for the genetic improvement. Understanding the taxonomy and phylogenetic relationships of Paulownia species is essential for the advancement of germplasm innovation. In this study, we re-sequenced 67 typical accessions of 11 species within the Paulownia genus. A total of 16,163,790 high-quality single nucleotide polymorphisms (SNPs) were identified. Based on these markers, these accessions were classified into three groups: P. fortunei and P. lampropylla (Group I); P. tomentosa, P. fargesii, and P. kawakamii (Group II); and P. taiwaniana, P. jianshiensis, P. catalpifolia, P. elongata, P. ichangensis, and P. albiphloea (Group III). Using maximum likelihood estimation, population genetic structure analysis revealed that the 11 species originated from four different ancestral populations. The two predominant breeding species—P. fortunei and P. tomentosa—exhibit divergent origins: P. fortunei arose from hybridization between two ancestral species followed by complex admixture, whereas P. tomentosa retains a predominantly singular ancestral lineage, with traces of P. kawakamii. The genetic diversity (π) of P. tomentosa was 0.002588, which was considerably lower than that of P. fortune (0.004181) suggesting that P. tomentosa is subjected to a stronger breeding selection during the evolution than P. fortune. A total of 59 selected regions and 65 genes were identified by selective sweep analysis. These genes may be involved in biological processes such as morphological development and response to abiotic stress and hormonal activity regulation. These findings provide valuable references for further research on the genetic differentiation and adaptive evolutionary mechanisms of Paulownia species, laying a foundation for future germplasm innovation and variety improvement. Full article

China has the largest population of pigeons globally, particularly for commercial meat production. Due to insufficient emphasis on bloodline preservation, there is a significant occurrence of breed hybridization, which presents challenges to the differentiation and identification of various pigeon breeds. In this study, a single-nucleotide polymorphism chip was developed to elucidate genomic relationships and genetic diversity among 10 pigeon breeds, encompassing meat, racing, and ornamental varieties. Principal component analysis revealed that this resource population could be classified into three major clusters: homing and Tarim pigeons; the Dianzi (DZ) and Xinjiang Roller (XR) varieties; and commercial meat pigeon breeds, including the Euro-pigeon (EP), Danish King (DK), Silver King (SK), Yellow Carneau (YC), Red Carneau (RC), and Taishen (TS) varieties. Phylogenetic tree analysis indicated that the HP, TR, DZ, and XR varieties clustered into a large group. Of these, the HP and TR groups and the DZ and XR group were closely genetically related. Other meat pigeon varieties clustered into a large group. The genetic relationship between the YC and RC pigeons was intertwined, suggesting that although there were differences in feather color, the genetic backgrounds are similar. The phylogenetic tree results also demonstrated that the DK and SK pigeons had a considerable genetic distance, indicating that although the feather color was similar, the birds belong to two distinct genetic groups. The Pigeon 5 K liquid chip can effectively discriminate among different pigeon populations and provides a method for the identification and evaluation of pigeon germplasm resources, especially for pure breed identification and exploration of new resources. Full article

The wild yak (Bos mutus) is a flagship species on the Qinghai–Tibet Plateau, possessing significant ecological functions and conservation value. Using single-nucleotide polymorphism markers from whole-genome resequencing, we systematically analyzed golden wild yak (n = 37), common wild yak (n = 106), and domestic yak (Bos grunniens) (n = 20) to characterize the population genetic structure and adaptive selection signals in the golden wild yak. Genetic diversity analyses revealed that the golden wild yak had the lowest nucleotide diversity (π = 0.00148) and the highest inbreeding coefficient (F_Hom = 0.043). Population structure analyses integrating principal component analysis, phylogenetic tree, and ancestral component clustering indicated that the golden wild yak formed a relatively independent evolutionary lineage. However, its genetic differentiation from sympatric common wild yak population was limited (fixation index = 0.031). Selective sweep analysis identified a set of candidate positively selected genes in the golden wild yak genome associated with key traits and physiological functions, including coat color (TYRP1), hypoxia adaptation (MYH11, POLQ), reproductive function (SLC9C1, SPAG16, CFAP97D1), and immune response (CASP8, PGGT1B, BIRC6). Overall, our study reveals a distinct genetic background and selection signatures in the golden wild yak and provides genomic insights to inform the conservation and management of the wild yak. Full article

Bamboo (subfamily Bambusoideae, Poaceae) ranks among the fastest-growing plants on Earth, achieving up to 1 m day⁻¹, significantly faster than other fast growing woody plant such as Eucalyptus (up to 0.6 m day⁻¹) and Populus (up to 0.5 m day⁻¹). Native to Asia, South America and Africa, and cultivated on approximately 37 million ha worldwide, bamboo delivers multifaceted environmental, social, and economic benefits. Historically central to construction, handicrafts, paper and cuisine, bamboo has evolved into a high-value cash crop and green innovation platform. Its rapid renewability allows multiple harvests of young shoots in fast-growing species such as Phyllostachys edulis and Dendrocalamus asper. Its high tensile strength, flexibility, and ecological adaptability make it suitable for applications in bioenergy (bioethanol, biogas, biochar), advanced materials (engineered composites, textiles, activated carbon), and biotechnology (fermentable sugars, prebiotics, biochemicals). Bamboo shoots and leaves provide essential nutrients, antioxidants and bioactive compounds with documented health and pharmaceutical potential. With a global market value exceeding USD 41 billion, bamboo demand continues to grow in response to the call for sustainable materials. Ecologically, bamboo sequesters up to 259 t C ha⁻¹, stabilizes soil, enhances agroforestry systems and enables phytoremediation of degraded lands. Nonetheless, challenges persist, including species- and age-dependent mechanical variability; vulnerability to decay and pests; flammability; lack of standardized harvesting and engineering codes; and environmental impacts of certain processing methods. This review traces bamboo’s trajectory from a traditional resource to a strategic bioresource aligned with Industry 5.0, underscores its role in low-emission, circular bioeconomies and identifies pathways for optimized cultivation, green processing technologies and integration into carbon-credit frameworks. By addressing these challenges through innovation and policy support, bamboo can underpin resilient, human-centric economies and drive sustainable development. Full article

Background/Objectives: The Chinese dwarf cherry (Cerasus humilis) is an endemic shrub fruit tree species in China. Its fruit is flavorful, nutrient-rich, and has considerable research and utilization potential. However, most currently cultivated varieties of C. humilis are highly acidic and primarily used for processing. Consumer-preferred, low-acid, fresh-eating varieties are scarce, limiting industrial development. We used 208 F₁ individuals derived from a cross between high-acid “Nongda 4” and the low-acid “DS-1”. Methods: Restriction site-associated DNA sequencing (RAD-seq) was used to develop single-nucleotide polymorphism (SNP) markers and construct a high-density genetic linkage map. Using two years of fruit titratable acidity phenotypic data, quantitative trait locus (QTL) mapping and candidate gene screening were performed. Results: The genetic map contained 2491 SNP markers, assigned to eight linkage groups. The total genetic distance was 672.71 cm, with an average distance of 0.27 cm between markers, indicating high map quality. QTL mapping identified 18 loci associated with fruit titratable acidity, including 11 major-effect QTLs (logarithm of odds, LOD ≥ 3.5). These major-effect QTLs were concentrated on linkage groups LG2 and LG5, with an explained phenotypic variation of 8.6–31.13%. Two candidate genes were identified within QTL intervals: phosphoester phosphatase and MATE transmembrane transporter. The phosphatase gene’s expression showed a strong correlation with titratable acid content (p < 0.01, correlation coefficient 0.93), suggesting that it plays an important role regulating fruit acidity in C. humilis. Conclusions: This study supports marker-assisted breeding of low-acid, fresh-eating varieties, aiding commercial promotion of C. humilis. Full article

The rising prevalence of food allergies, particularly to peanuts and tree nuts, poses significant challenges for pediatric health worldwide. These allergens are among the leading causes of severe allergic reactions, including anaphylaxis, often manifesting in early life. This review synthesizes the current knowledge on the immune mechanisms underlying these allergies, emphasizing the interplay between genetic, immunologic, and environmental factors in shaping allergic sensitization. Advances in prevention strategies, including early allergen introduction, have been critically evaluated. Predictive and diagnostic methodologies, from traditional IgE evaluation to cutting-edge proteomics and metabolomics approaches, have been explored to identify biomarkers that predict allergy onset and severity. By unraveling early immunological and molecular signatures, this study aimed to summarize the early prediction, prevention, diagnosis, and treatment of peanut and tree nut allergies, ultimately contributing to more effective interventions and a better quality of life for affected children. Full article

Chronic metabolic disorders have increased recently due to changes in dietary habits and lifestyle. Red-coloured fruits, such as sweet cherries, are rich in anthocyanins and other (poly)phenolic compounds with health-promoting properties, which has garnered growing scientific interest. Melatonin elicitation has emerged as a promising strategy to improve the functional quality of these fruits. This research investigates, for the first time, the combined effect of pre- and postharvest melatonin treatments, followed by a cold storage (2 °C) of 21 days, on the endogenous melatonin and phenolic compound levels of 90 sweet cherries (n = 3) from the ‘Sunburst’ cultivar and harvested from 9 trees per treatment. Single preharvest or postharvest melatonin treatments increased the endogenous melatonin content via direct absorption and activation of key biosynthetic genes, while they reduced anthocyanin, hydroxycinnamic acid, and flavonol levels, likely due to a ripening-delaying effect at harvest. Nevertheless, the combined treatment increased endogenous melatonin levels 5-fold compared to harvest and increased all measured polyphenolic compound levels, including a 29% rise in total anthocyanins reverting the delay in the ripening process. These effects suggest upregulation of genes in the phenylpropanoid pathway and could improve fruit’s functional quality. The response to melatonin is cultivar- and dose-dependent. Future research should investigate genetic and transcriptomic validation to confirm these potential effects and assess whether increased bioactive compound content would translate into measurable human health benefits. Full article

Leaf pigment composition and concentration are crucial indicators of plant physiological status, photosynthetic capacity, and overall ecosystem health. While spectroscopy techniques show promise for monitoring vegetation growth, phenology, and stress, accurately estimating leaf pigments remains challenging due to the complex reflectance properties across diverse tree species. This study introduces a novel approach using a two-dimensional convolutional neural network (2D-CNN) coupled with a genetic algorithm (GA) to predict leaf pigment content, including chlorophyll a and b content (C_ab), carotenoid content (C_ar), and anthocyanin content (C_anth). Leaf reflectance and biochemical content measurements taken from 28 tree species were used in this study. The reflectance spectra ranging from 400 nm to 800 nm were encoded as 2D matrices with different sizes to train the 2D-CNN and compared with the one-dimensional convolutional neural network (1D-CNN). The results show that the 2D-CNN model (nRMSE = 11.71–31.58%) achieved higher accuracy than the 1D-CNN model (nRMSE = 12.79–55.34%) in predicting leaf pigment contents. For the 2D-CNN models, C_ab achieved the best estimation accuracy with an nRMSE value of 11.71% (R² = 0.92, RMSE = 6.10 µg/cm²), followed by C_ar (R² = 0.84, RMSE = 1.03 µg/cm², nRMSE = 12.29%) and C_anth (R² = 0.89, RMSE = 0.35 µg/cm², nRMSE = 31.58%). Both 1D-CNN and 2D-CNN models coupled with GA using a subset of the spectrum produced higher prediction accuracy in all pigments than those using the full spectrum. Additionally, the generalization of 2D-CNN is higher than that of 1D-CNN. This study highlights the potential of 2D-CNN approaches for accurate prediction of leaf pigment content from spectral reflectance data, offering a promising tool for advanced vegetation monitoring. Full article

Prosopis cineraria (L.) Druce is a keystone tree species in the arid and semi-arid regions of West and South Asia, with critical ecological, cultural, and conservation significance. In the United Arab Emirates (UAE) and other regions of the Arabian Peninsula, this beneficial tree is called Ghaf. Despite its importance, genomic resources and population-level diversity data for the tree remain limited. Here, we present the first comprehensive population genomics study of Ghaf based on whole-genome resequencing of 204 individual trees collected across the UAE. Following Single-Nucleotide Polymorphism (SNP) discovery and stringent filtering, we analyzed 57,183 high-quality LD-pruned SNPs to assess population structure, diversity, and gene flow. Principal component analysis (PCA), sparse non-negative matrix factorization (sNMF), and discriminant analysis of principal components (DAPC) revealed four well-defined genetic clusters, broadly corresponding to geographic origins. The genetic diversity varied significantly among the groups, with observed heterozygosity (Ho), inbreeding coefficients (F), and nucleotide diversity ($\pi$) showing strong population-specific trends. Genome-wide fixation index F_ST scans identified multiple highly differentiated genomic regions, enriched for genes involved in stress response, transport, and signaling. Functional enrichment using Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Pfam annotations indicated overrepresentation of protein kinase activity, ATP binding, and hormone signaling pathways. TreeMix analysis revealed gene flow into one of the genetic clusters from both others, suggesting historical admixture and geographic connectivity. This work provides foundational insights into the population genomic profile of P. cineraria, supporting conservation planning, restoration strategies, and long-term genetic monitoring in arid ecosystems. Full article

The “divergence problem” in recent decades is a tendency for trees in high latitudes to lose climate sensitivity. Growth divergence has been reported for certain tree species in alpine or northern latitude locations but has yet to be found in species with southern distributions. This retrospective study used tree ring data collected from longleaf pine trees (Pinus palustris Mill.) in natural stands and a young plantation to test whether divergence exists in this important southeastern tree species. Our results demonstrate that a growth divergence in basal area increment (BAI) occurred among individual longleaf pines within stands. The BAI of each tree followed Taylor’s law but with differing exponents, which varied from 0.75 to 6.4. Divergence of BAI among trees increased with time, and it might be related to the local drought, as the highest BAI divergence occurred when the SPEI (standardized precipitation-evapotranspiration index) was approximately 0 (−0.3–0.3). Hourly dendrometer measurements confirmed growth divergence among individuals. Collectively, our study provides new information about the growth characteristics of longleaf pine, which may partially explain how this species persists and thrives in southeastern environments. Our current management strategy on longleaf pine forests, such as prescribed burning and genetics improvement efforts, needs to be adapted. Full article

The Flaviviruses Dengue virus (DENV), West Nile virus (WNV), Zika virus (ZIKV), and Yellow Fever virus (YFV), are mosquito-borne viruses that represent a persistent challenge to global health due to the emergence and re-emergence of outbreaks of significant magnitudes. Their positive-sense RNA genome, about 11,000 nucleotides long, encodes structural and nonstructural proteins. These viruses evolve rapidly through mutations and genetic recombination, which can lead to more virulent and transmissible strains. Although whole-genome sequencing is ideal for studying their evolution and geographic spread, its cost is a limitation. We investigated the genetic variability of DENV, ZIKV, WNV, and YFV to identify genomic regions that accurately reflect the phylogeny of the complete coding sequence and evaluated the utility of these regions in reconstructing the geographic dispersal patterns of viral genotypes and lineages. Publicly available sequences from GenBank were examined to assess variability, reconstruct phylogenies, and identify the most informative genomic regions. Once representative regions were identified, they were used to infer the global phylogeographic structure of each virus. The virus depicted distinct variation patterns, but conserved regions of high and low variability were common to all. Highly variable regions of ~2700 nt offered greater resolution in phylogenetic trees, improving the definition of internal branches and statistical support for nodes. In some cases, combined multiple highly variable regions enhanced phylogenetic accuracy. Phylogeographic reconstruction consistently grouped sequences by genotype and geographic origin, with temporal structuring revealing evolutionarily distinct clusters that diverged over decades. These findings highlight the value of targeting genomic regions for phylogenetic and phylogeographic analysis, providing an efficient alternative for genomic surveillance. Full article