Search Results (568)

This study presents a cytogenetic and comparative analysis of three rare terrestrial orchid species from Thailand: Habenaria janellehayneana, H. rhodocheila, and Nervilia khaoyaica. Somatic chromosome numbers, karyotype structures, and chromosomal morphology were investigated using conventional cytological techniques. The results revealed that both H. janellehayneana and H. rhodocheila possess a chromosome number of 2n = 42 with a fundamental number (NF) of 84, whereas N. khaoyaica has 2n = 36 and NF = 72. Karyotype formulas were determined as 11m + 10sm for H. janellehayneana, 21m for H. rhodocheila, and 2m + 16sm for N. khaoyaica, all indicating symmetrical karyotypes. Multivariate analyses, including Principal Component Analysis (PCA) and hierarchical clustering, were applied to both morphological and karyological datasets. The results demonstrated clear separation between genera along the primary component axis, while species within Habenaria were distinguished along the secondary axis. Karyotype-based PCA further supported distinct chromosomal patterns among all three species, despite identical chromosome numbers in the two Habenaria taxa. This study provides the first cytogenetic report for these species and highlights the importance of chromosome structure, particularly centromere position and arm ratio, in species delimitation. The findings contribute valuable baseline data for taxonomy, evolutionary studies, and conservation of Orchidaceae in Thailand. Full article

Carex is among the most species-rich genera of angiosperms and plays important ecological roles in wetlands, alpine regions, and temperate ecosystems worldwide. However, research on this genus has long been challenged by pronounced phenotypic plasticity, reduced floral morphology, frequent hybridization, and complex chromosomal evolution. Although recent advances in molecular phylogenetics, comparative genomics, reproductive biology, and ecophysiology have substantially expanded the knowledge of Carex, these findings remain fragmented across disciplines. Here, we synthesize current evidence on Carex taxonomy and phylogeny, genomic and karyotypic evolution, reproductive and life history strategies, abiotic stress responses, ecosystem functions, and bioresource potential within a cross-scale framework. This review emphasizes how genomic architecture, life history variation, and ecophysiological adaptation jointly shape species diversification and ecosystem functioning, while clarifying their implications for habitat restoration and the sustainable use of Carex resources. Finally, we identify key priorities for future research, including improved phylogenomic resolution, comparative functional studies, climate-resilience assessment, and germplasm conservation and sustainable use. Full article

Glycogen synthase kinase 3 (GSK3/Shaggy-like) belongs to evolutionarily conserved serine/threonine protein kinases that regulate plant morphological development, multi-hormone crosstalk and adaptation to abiotic stresses. However, systematic genome-wide characterization of CmGSK3 is still absent in melon (Cucumis melo L.). This study identified six CmGSK3 members on a whole-genome level, unevenly distributed among four chromosomes. Combined phylogenetic and synteny profiling separated these six genes into four conserved subclades; orthologous links were discovered between melon, Arabidopsis, and rice, revealing evolutionary conservation between monocot and dicot crops. Prediction of promoter cis-regulatory motifs combined with transcriptome datasets suggested that CmGSK3 genes participate in hormone transduction and environmental stress adaptation. Quantitative real-time PCR further verified that exogenous brassinosteroid (BR) application dramatically induced transcriptional accumulation of CmSK21 and CmSK22. Heterologous overexpression of these two genes in wild-type Arabidopsis significantly lowered plant sensitivity to BR, confirming they may function as negative modulators of the BR signaling cascade. Collectively, CmGSK3 members coordinate multiple metabolic routes, dominated by BR-related signal transduction, to manipulate melon growth and stress adaptability. This study establishes the first systematic research on the melon GSK3 family and supplies elite candidate genes for molecular breeding targeting fruit quality and stress resistance improvement in melon. Full article

Background/Objectives: Sex estimation is a cornerstone of research and practice in bioarchaeology and forensic anthropology. However, morphological and metric methods are often hampered by population-specific variation, subjectivity in assessment, and taphonomy. This study compares morphological analysis and ancient DNA (aDNA)-based sex assessment in a 19th-century Portuguese sample to evaluate the accuracy of osteological (anthropological) criteria. Methods: This study analysed 37 skeletons from the Venerável Ordem Terceira da Nossa Senhora do Carmo burial grounds in Porto. Sex estimation was based on (1) the bioanthropological assessment of morphological traits of the os coxae and the skull (2) through aDNA analysis using a multi-marker approach, including real-time PCR (qPCR) targeting autosomal loci, the amelogenin locus, a Y-chromosomal INDEL, and Y-STRs. aDNA was extracted via a non-destructive protocol. Results: Whilst anthropological analysis was possible on all 37 individuals, estimation of sex through aDNA analysis was possible for 26 individuals. A 20% discordance rate was found between morphological and aDNA results. Many individuals morphologically classified as “possible female” or “indeterminate” were genetically identified as male. Genetic analysis resolved most cases that biological anthropologists concluded were “indeterminate”. Conclusions: The high discordance in the Carmo sub-sample may indicate reduced skeletal sexual dimorphism, with males exhibiting skeletal traits typically associated with females, suggesting a sample-specific reduction in sexual dimorphism likely influenced by environmental, nutritional, and/or genetic stressors. A limitation of this study is its small sample size: only 26 of 37 individuals yielded usable genetic results, and only a portion of these individuals provided sufficient data for a direct comparison between morphological and genetic data. Nevertheless, these findings highlight the risk that applying generalised osteological standards relying solely on morphology can lead to systematic misclassification, emphasising the need for a critical, multidisciplinary approach to sex estimation. Full article

Primary hepatocytes are limited by poor proliferative capacity and a finite replicative lifespan, restricting their utility in long-term in vitro studies. Here, we report the generation of expandable hepatocyte-like progenitor cells from GGTA1 knockout pigs, a large-animal model with reduced immunogenicity. Porcine fibroblasts were directly reprogrammed using a non-integrative episomal system encoding hepatic transcription factors, enabling stable lineage conversion without genomic integration. A simplified two-vector configuration combined with codon optimization enabled evaluation of vector-dependent effects while maintaining genomic safety without viral integration. The resulting cells exhibited hepatocyte-like morphology and gene expression, and transcriptomic analysis revealed a progressive shift toward liver-associated profiles during extended culture. Chromosomal analysis revealed vector-dependent differences in genomic stability, with codon-optimized cells showing increased aneuploidy, indicating a trade-off between proliferative capacity and genomic integrity. The cells also demonstrated sustained proliferative capacity, supported by maintenance of telomere length, increased expression of TERT and MYC, and reduced CDKN1A levels. Importantly, sustained proliferation was supported by complementary evidence from chromosomal and telomeric analyses. Although chromosomal alterations were observed during long-term culture, their biological significance remains to be fully determined. These cells partially recapitulate hepatocyte functions and provide a renewable in vitro system for studies of hepatic biology, proliferation, drug metabolism, toxicity, and repeated in vitro applications. Full article

Indigenous goat populations are valuable genetic resources for livestock production in arid and semi-arid environments, yet many remain insufficiently characterized at the phenotypic and genomic levels. This study investigated phenotypic variation and genome-wide associations in two local Ardi goat lines in Bahrain: Ardi Bahraini and Ardi Mu’atar, the latter being distinguished by a characteristic facial marking pattern. A total of 280 goats were phenotypically characterized for qualitative traits and body measurements, and 76 animals were genotyped using the Illumina Caprine 60K single nucleotide polymorphism (SNP) BeadChip. After quality control, 49,716 autosomal SNPs were retained for genome-wide association analysis. Phenotypic analysis showed that the two lines differed significantly in body weight, body length, hip height, face width, tail length, ear width, and tail circumference, while discriminant analysis identified tail length, ear width, tail circumference, and facial patterns differentiating the lines. Principal component analysis (PCA) showed partial genomic clustering of the two lines, and genome-wide significant and suggestive SNPs based on Bonferroni and false discovery rate (FDR) thresholds on chromosomes 6, 13, 14, and 29. The strongest association was observed for rs268277393 on chromosome 13, located near DOK5 (Docking Protein 5) and TRNAC-GCA (transfer RNA cysteine, anticodon GCA), and was associated with the Ardi Mu’atar facial pattern. Additional candidate regions were located near genes with possible roles in pigmentation, development, or morphological variation. These findings provide preliminary genomic evidence supporting the phenotypic distinctiveness of Ardi Mu’atar goats and identify candidate markers that may contribute to future conservation and breeding programs. Further validation in larger populations and functional studies will be required to confirm the biological role of these candidate regions. Full article

Background/Objectives: Popcorn (Zea mays L. var. everta) is an important specialty maize type; however, the genetic variation underlying popping-related quality traits remains insufficiently characterized in breeding. Methods: In this study, 18 popcorn inbred lines were analyzed using 25 simple sequence repeat (SSR) markers distributed across all 10 maize chromosomes, and 16 lines were further evaluated for popping performance and image-based flake morphology. Results: Substantial phenotypic variation was observed among the tested lines, with expansion volume ranging from 173.33 to 343.33 mL and expandability ranging from 16.79- to 32.46-fold. Image-based analysis of 957 popped kernels revealed continuous variation in flake circularity, indicating that flake morphology represents a quantitative trait rather than a strictly discrete classification. SSR analysis detected 2 to 11 alleles per locus, with polymorphism information content values ranging from 0.05 to 0.85, indicating moderate-to-high genetic diversity among the tested lines. Principal component analysis (PCA), unweighted pair group method with arithmetic mean (UPGMA) clustering, and population structure analysis revealed clear genetic differentiation and heterogeneous genetic backgrounds within the germplasm collection. Marker–trait association analysis identified several putative SSR loci associated with expansion efficiency, flake morphology, pericarp retention, and popping dynamics. Notably, marker M18 was putatively associated with both expansion volume and expandability. Conclusions: Based on these results, a conceptual framework was proposed in which popping-related traits were organized into partially independent but interconnected functional modules. Overall, this study provides SSR-based genetic information for popcorn germplasm characterization and offers preliminary marker resources for quality-oriented popcorn breeding. Full article

Congenital heart defects (CHDs) are the most common congenital anomalies, with identifiable genetic etiologies in approximately 5–30% of affected infants, depending on the clinical presentation and comorbidities. This study included 216 children with CHD, predominantly syndromic, to explore the role of genetic variants in their morphological phenotypes. Chromosomal microarray (CMA) and whole-exome sequencing (WES) were performed, revealing clinically significant copy number variations (csCNVs) in 59 (27.3%) patients. The most frequent were 22q11.21 (8/59; 13.6%) and 7q11.23 (5/59; 8.5%) deletions. WES was conducted in 28.0% of cases, achieving a detection rate of 29.5%, primarily identifying variants related to Noonan syndrome. Genetic diagnoses were confirmed in 33.3% of patients, with clinically significant CNVs and SNV/INDELs found exclusively in those with syndromic CHD, leading to a 36.5% diagnosis rate in those patients. The identified variants most frequently affected genes encoding transcription factors (40.4%), followed by genes involved in the RAS signaling pathway and structural proteins (17.0%), and chromatin remodeling proteins (12.8%). Full article

The potential effects of microplastics (MPs) on humans and ecosystems are of great concern, and it has been reported that the ingestion of contaminated food is the main route of exposure. In the present study, Perca fluviatilis was selected as a vertebrate model to evaluate the possible cellular effects induced by five different plastic polymers and car tire debris (CT) after 4- and 7-month exposure periods. The Cytome assay was chosen to check chromatin alteration in perch’s peripheral blood. The results indicated an increase in micronuclei and cytotoxic effect in specimens co-exposed to MPs + CT for 7 months. Increases in dicentric chromosomes were observed in specimens exposed both to MPs alone and to the mixture of MPs + CT, indicating for the first time a genotoxic effect induced by CT debris in fish in terms of structural aberrations. Increases in micronucleated erythrocyte frequency assessed after 7 months only after the addition of CT debris to the mixture of MPs might suggest an aneugenic action of CT in fish. In the same groups, the higher values of frequency in 8-shaped erythrocytes also indicate possible cell cycle toxicity exerted by CT exposure. An association between total erythrocyte nuclear morphology abnormalities (ENA) and glutathione reductase activity was also found, indicating a potential involvement of oxidative processes in modulating the genotoxicity observed. The present experimental model is a useful tool to study cellular mechanisms related to both MP- and CT-induced chromatin structure alterations indicating possible interference with human health as well. Full article

Due to overfishing, eutrophication of rivers and lakes, and irrational stocking practices, the diversity of wild native carp populations has declined, leading to germplasm degradation and a decrease in fish quality, thereby affecting the sustainable development of fisheries. In this study, a novel hybrid crucian carp lineage (designated LWR) was successfully established via distant hybridization using Dongting Lake crucian carp (LC, ♀) and Hefang crucian carp (WR, ♂) as parental stocks. Systematic analyses were conducted on the morphology, ploidy, fertility, growth performance, survival rate, and molecular genetics of LWR. The results reveal that LWR is an allodiploid (2n = 100), with a chromosome number identical to that of its parents. Gonadal development in the hybrid progeny (LWR) was normal, with both sexes being fertile and reaching sexual maturity at one year of age. Morphologically, LWR exhibited intermediate traits with a paternal bias, characterized by a deep-bodied and elongated shape. In terms of growth performance, LWR displayed significant heterosis (approximately 145% and 271% higher than the body weight of the maternal parent at 6 months and 1 year). Molecular genetic analysis indicated that the 5S rDNA sequences of LWR were predominantly inherited from the paternal parent WR, with insertions, deletions, recombination, and mutations detected. The mtDNA sequences exhibited 99.78% similarity to those of the maternal parent LC, following maternal inheritance with sporadic nucleotide variations. These findings offer a new paradigm for hybridization and a theoretical foundation for the improvement and sustainable utilization of indigenous crucian carp germplasm resources, the selective breeding of improved aquaculture strains, and the sustainable development of fisheries. Full article

This Y-chromosome study of Moroccan Jews, the largest conducted to date, analyzes the patrilineal origins of 288 men of genealogically verified Moroccan Jewish descent through the Avotaynu DNA Project, identifying 111 distinct founder lineages. The long-standing hypothesis of large-scale Berber Judaization has not previously been tested at full Y-chromosome resolution; our findings provide the first systematic evidence against it. Approximately 71% of founder lineages and 80% of individuals trace to haplogroups common in the Middle East. Only 4.5% of founder lineages are of autochthonous North African origin. Iberian-origin lineages account for 11% of Moroccan Jewish founder lineages reflecting sustained demographic and cultural exchange between Morocco and the Iberian Peninsula over many centuries. Split dates between Moroccan and Ashkenazi or Sephardic subclades cluster between the 5th and 8th centuries CE, suggesting that the ancestral lineages of contemporary Moroccan Jews were already present across the Mediterranean basin during late Antiquity and the early medieval period. Analysis of 190 distinct Moroccan Jewish surname roots identifies 29 polygenic and 30 monogenic surnames, and demonstrates that the linguistic origin of a surname, including surnames of Maghrebi morphology, does not necessarily reflect its bearer’s Y-chromosome ancestry. Unlike Ashkenazi Jews, Moroccan Jews show no evidence of a founder effect or genetic bottleneck, and display a remarkable patrilineal diversity. Among the individual lineages documented here are the first paleogenetic link between a contemporary Moroccan Jewish patriline and a victim of the 1348 Tàrrega pogrom, an Iberian/Ashkenazi split traceable to tenth-century al-Andalus, and an unexpected connection between a predominantly Moroccan Jewish lineage and the Saint Thomas Syrian Christian community of Kerala. Moroccan Jewish patrilineal heritage is overwhelmingly Middle Eastern in origin and has been preserved with remarkable continuity across two millennia of diaspora, persecution, and migration. Full article

Ensuring global food security under accelerating climate change requires transformative approaches to crop improvement that extend beyond the limits of traditional breeding and gene editing. While domestication and modern agriculture have delivered substantial gains in productivity, these advances often came at the cost of genetic diversity, stress resilience, and developmental plasticity. Plants, however, inherently exhibit remarkable flexibility in their morphology and development, as evidenced by the vast diversity of organ shapes, cell types, and adaptive responses that have evolved across lineages. This natural design space provides a foundation for reimagining plant architecture using synthetic biology. Recent advances in plant synthetic biology, including programmable transcription factors, CRISPR-based regulatory systems, synthetic gene circuits, orthogonal signalling pathways, and plant artificial chromosomes, now enable precise, modular, and environmentally responsive manipulation of developmental processes. These tools allow researchers to rewire hormone pathways, tune quantitative gene expression, integrate multiple environmental signals, and create novel regulatory modules that operate independently of endogenous networks. Beyond understanding plant development, these capabilities open avenues for engineering crops with dynamic architectures, enhanced plasticity, and improved resilience to complex and fluctuating stresses. In this review, we synthesise insights from natural diversity, developmental biology, and synthetic regulatory engineering to outline how plant architecture can be rationally redesigned. We argue that integrating synthetic biology with modern breeding and modelling frameworks will be essential for generating the next generation of programmable crops; i.e., varieties capable of sustaining productivity and stability in an era of unprecedented environmental and geopolitical changes. Full article

Plant genetic resources are vital for crop improvement, ecological resilience, and agrobiodiversity conservation, making their characterization through morphological and cytogenetic methods essential for breeding and germplasm management. This study comparatively analyzed two herbaceous cultivars Hibiscus moscheutos cv. ‘Carousel Jolly Heart’ and cv. ‘Carousel Pink Passion’ and two woody cultivars, Hibiscus syriacus cv. ‘Sukim’ and cv. ‘Freedom’, to assess interspecific diversity and hybridization potential. Morphological assessments revealed notable differences in flower size and leaf shape between species, with ‘Carousel Pink Passion’ exhibiting the largest flower diameter (16.70 cm) and ‘Freedom’ exhibiting the smallest (10.20 cm). Chromosome analysis confirmed diploidy (2n = 38) in H. moscheutos and polyploidy (2n = 84) in H. syriacus, highlighting a fundamental genomic distinction between the two species. Fluorescence in situ hybridization (FISH) consistently identified two 5S rDNA loci across all cultivars; however, species-specific variation in 18S rDNA loci was detected with four loci in H. syriacus and six in H. moscheutos, suggesting divergent rDNA evolution and distinct genomic organization in the two species. Flow cytometry confirmed significant differences in nuclear DNA content corresponding to ploidy levels: ‘Carousel Jolly Heart’ and ‘Carousel Pink Passion’ measured 2.06 pg and 2.05 pg, respectively, while ‘Sukim’ and ‘Freedom’ measured 4.18 pg and 4.27 pg, respectively. Full article

(1) Background: Integrated bioarchaeological approaches combining osteological and ancient DNA analyses provide powerful insights into health, disease, and population history in past societies. However, the relationship between rare skeletal variations, genetic disorders, and ancestry remains insufficiently explored within single individuals. This study aimed to investigate the combined osteological, paleopathological, and genetic characteristics of a Roman-period individual from southwestern Anatolia. (2) Methods: A multidisciplinary approach was applied to the skeletal remains of an adult male recovered from the Sekköy excavation site. Osteological analysis was conducted to assess cranial morphology, pathological lesions, and dental status. Ancient DNA was extracted from petrous bone under strict contamination control. The hemoglobin beta (HBB) gene was analyzed using Next Generation Sequencing and validated by Sanger sequencing. Y-chromosomal STR analysis was performed to determine paternal lineage. (3) Results: Osteological examination revealed a rare craniovertebral anomaly consistent with a third occipital condyle, along with porotic hyperostosis and extensive antemortem dental pathology, indicating prolonged physiological stress. Genetic analysis identified a heterozygous hemoglobin S mutation (HbAS; rs334), confirmed by both next-generation sequencing and Sanger sequencing, providing direct molecular evidence of hereditary hemoglobinopathy. Y-STR profiling assigned the individual to haplogroup R1b (predicted based on Y-STR data), indicating affiliation with Western Eurasian paternal lineages. (4) Conclusions: Despite the presence of comparable skeletal stress indicators, the integration of osteological and genetic data revealed a complex interaction between anatomical variation, chronic physiological stress, and inherited disease. The co-occurrence of a rare cranial anomaly, HbS mutation, and a defined paternal lineage represents a unique bioarchaeological case. These findings highlight the value of integrating skeletal and molecular approaches to reconstruct individual health profiles in archaeological contexts and demonstrate the methodological potential of interdisciplinary bioarcheological analysis. Full article

Fittonia Coem. is a widely cultivated ornamental foliage genus, but the taxonomy and relationships of cultivated forms remain poorly resolved because traditional classifications rely heavily on variable foliar traits. In this study, we investigated the genetic relationships and phenotypic variation among 14 commercially available Fittonia cultivars using amplified fragment length polymorphism (AFLP), methylation-sensitive amplified fragment length polymorphism (MSAP), DNA flow cytometry, chromosome counting, and comparative morphological and anatomical analyses. Morphological character states were further mapped onto AFLP- and MSAP-derived phylograms to assess their evolutionary patterns and taxonomic relevance. AFLP and MSAP analyses consistently recovered two well-supported clusters within the cultivated material examined: Clade I, comprising ‘Titanic’ and ‘Angel Snow’, and Clade II, comprising the remaining 12 cultivars. These clades were independently supported by stable differences in trichome morphology, cystolith distribution, epidermal cell form, leaf venation architecture, and stem anatomy. In contrast, several traditionally used diagnostic characters, including leaf vein color and petiole length, were found to be homoplastic or continuously variable. Chromosome counts and flow cytometry indicated that all cultivars were diploid (2n = 36) and exhibited limited variation in genome size. Together, these results provide integrative evidence for two distinct clusters within cultivated Fittonia. However, because sampling was limited to commercially available cultivars, the relationship of these clusters to currently recognized species remains unresolved. Our findings highlight the limitations of traditional trait-based classifications and underscore the need for broader sampling, including wild populations, to reassess species boundaries in the genus. Full article