Search Results (3,868)

Background: Forensic DNA phenotyping (FDP) enables the inference of externally visible characteristics (EVCs) and biogeographic ancestry when conventional STR profiling is inconclusive. The ForenSeq™ Imagen kit (107 SNPs) integrates phenotype-, ancestry-, and Y-SNPs markers; however, its performance under partial genotyping conditions has not been systematically evaluated. Methods: Ninety-four samples from a Mexican mestizo population were analyzed using the ForenSeq™ Imagen kit on the MiSeq FGx™ platform. Due to incomplete genotype recovery, 41 samples with >60% locus detection were selected for downstream analyses. Phenotype prediction was performed using the HIrisPlex-S model, and ancestry inference was assessed through principal component analysis. In silico simulations were conducted to evaluate locus-specific dropout effects. Results: Eye color prediction showed both reduced feasibility (68.3%) and lower overall accuracy (56.1%), primarily driven by systematic prediction failure when rs12913832 (HERC2) was absent, although accuracy among successfully predicted samples remained high (82.1%). In contrast, hair and skin color inference remained feasible in >97% and 100% of evaluable samples, respectively; however, classification accuracy was moderate (70% for hair and 61% for skin), improving substantially when allowing adjacent-category concordance (90.2% for skin). Ancestry inference was robust when at least 27 aiSNPs were detected, and Y-SNPs reliably distinguished male and female samples. In silico analyses confirmed the critical contribution of rs12913832 to eye color model operability. Conclusions: FDP performance under partial genotyping reflects a trade-off between prediction feasibility and accuracy and depends on locus-specific integrity rather than overall genotype completeness. The ForenSeq™ Imagen kit shows robustness for ancestry, sex, hair, and skin prediction, although with variable accuracy, whereas eye color inference remains structurally vulnerable to drop out of high-impact variants. Evaluating FDP systems under realistic non-ideal conditions is essential to define their true operational limits and ensure scientifically robust and responsible implementation. Full article

Broccoli (Brassica oleracea var. italica) is an important crop valued for its nutritional and health-promoting properties, yet its biotechnological improvement is limited by low effectivity and genotype-dependent transformation protocols. The absence of reliable transient expression systems further constrains functional genomics and genome-editing applications. Here, we optimized regeneration and transformation protocols for different broccoli genotypes. Endoreduplication patterns in young tissues were analyzed by flow cytometry to identify suitable explants, and combinations of plant growth regulators were tested to develop an efficient organogenic medium. Stable transformation was achieved via Agrobacterium tumefaciens using nptII and eGFP markers. Cotyledons and hypocotyls up to day 7 showed similar endoreduplication patterns, with abundant 2n cells, but hypocotyls exhibited higher regeneration capacity. The optimized medium supported efficient organogenesis while maintaining diploidy. Transformation efficiency reached 10.4% in ‘S1’ and 2.8% in ‘Naxos’, highlighting genotype dependence. In parallel, a transient expression system was established using cotyledon-derived protoplasts and electroporation-mediated DNA delivery. GFP expression was confirmed through fluorescence microscopy, confocal imaging, and Western blotting. These protocols provide a robust toolkit for broccoli genetic manipulation, facilitating molecular biology studies in the native plant, functional genomics and genome-editing strategies, including CRISPR-based approaches. Full article

Background/Objectives: Paediatric cataract is among the most common treatable causes of childhood blindness, caused by a genetically diverse disorder with variable clinical features. Although genetic factors significantly contribute to the development of paediatric cataracts, recent data on their genetic makeup and genotype–phenotype relationships in Saudi Arabia is limited. This study aims to investigate the genetic spectrum, inheritance patterns, and genotype–phenotype correlations of paediatric cataract in a Saudi population over twenty years. Methods: We conducted a retrospective cohort study of children diagnosed with congenital or juvenile cataracts between 2000 and 2019 at two major referral centres in Riyadh. Clinical, ocular, and systemic data were collected through multidisciplinary evaluations. Genetic analysis involved whole-exome and whole-genome sequencing performed at College of American Pathologists (CAP)-accredited laboratories. Variant interpretation was supported by bioinformatic and Artificial Intelligence (AI) prediction tools. Genotype–phenotype relationships were systematically analysed. Results: The study included 28 cases of genetically confirmed paediatric cataracts. Variants classified as pathogenic or likely pathogenic were identified in 13 genes. Autosomal recessive inheritance was predominant, with many patients exhibiting homozygous variants, often due to consanguinity. Two novel variants were identified in the Collagen Type XVIII Alpha 1 Chain (COL18A1) and the RAB3 GTPase-activating protein catalytic subunit 2 (RAB3GAP2) genes. Considerable phenotypic variability was observed, even among patients with the same mutation, particularly those with the recurrent CRYBB1 c.171del (p.Asn58fs) mutation. Syndromic cataracts were more frequently associated with loss-of-function variants and multisystem features. Conclusions: This study offers updated insights into the genetics and clinical presentation of paediatric cataract in Saudi Arabia. It highlights high genetic diversity, unique inheritance patterns, and notable genotype–phenotype variability, emphasising the importance of early genetic testing and multidisciplinary assessment for improved diagnosis, management, and counselling. Full article

In recent years, plant genotyping has been shifting from the accumulation of whole-genome data toward their effective use in breeding programs This review examines key genotyping platforms, including single-nucleotide polymorphism (SNP) arrays, reduced-representation sequencing methods such as genotyping-by-sequencing (GBS) and restriction site-associated DNA sequencing (RAD-seq), targeted genotyping approaches, and whole-genome sequencing (WGS), analyzing their informativeness, cost, and computational limitations. The transition to pangenome-based genotyping and graph genomes is discussed, as these approaches reduce reference bias and increase sensitivity for detecting structural variants, introgressions, and rare alleles that are important for adaptation and breeding. The growing role of AI/ML is highlighted in modeling complex genotype–phenotype relationships, integrating genomic and phenotypic data, and improving the accuracy and interpretability of genomic predictions. Full article

Barley remains the fourth most cultivated cereal crop worldwide and is valued for its versatility in malting and brewing, animal feed, human nutrition, and dietary supplements. The identification of genotypes suitable for breeding or specific end-use applications requires multi-environment testing to evaluate agronomic performance, grain quality, and trait stability. In this study, a panel of 50 winter barley genotypes (two-row and six-row) originating from diverse genetic backgrounds was evaluated over three growing seasons (2021–2023) under the environmental conditions of southeastern Romania. Seven traits were analyzed, including three phenological traits (heading time, flowering time and plant height), grain yield, and three quality parameters (thousand-grain weight, protein content, and starch content). Environmental conditions had a strong influence on phenological development and grain yield, whereas grain quality traits showed relatively greater stability, indicating a stronger genetic control. Multivariate analyses (Principal Component Analysis (PCA) and Genotype plus Genotype-by-Environment interaction biplot (GGE biplots)) revealed clear relationships among traits and highlighted contrasting adaptive strategies between the two barley types. In two-row barley, genotypes such as Idra and Sandra combined favorable yield performance with stable grain quality traits and therefore represent promising candidates for breeding programs and large-scale cultivation. In six-row barley, SU-Ellen and LG Zebra showed high productivity and strong starch accumulation, making them valuable genetic resources for yield-oriented breeding, although further improvement in nitrogen use efficiency may be beneficial. The 2022–2023 growing season represented the most restrictive environment, emphasizing the importance of stability under stress conditions. Genotypes located close to the Average Environment Coordination axis (AEC axis) during that season, such as Ametist (six-row) and Lardeya (two-row), may represent promising material for breeding programs targeting drought resilience. Overall, the results expand the phenotypic characterization of winter barley germplasm and identify valuable genetic resources that can support pre-breeding efforts and the development of climate-resilient barley cultivars. Full article

Ulluco (Ullucus tuberosus Caldas) is an Andean tuber crop of high nutritional and genetic importance. However, its vegetative propagation promotes the accumulation of pathogens and limits the availability of uniform, high-quality planting material. In this study, an efficient and reproducible in vitro micropropagation protocol was established for an ulluco genotype from the Amazonas region of Peru. Nodal segments were cultured on MS (Murashige and Skoog) medium supplemented with 6-benzylaminopurine (BAP) or kinetin (KIN) at increasing concentrations (0.0–2.0 mg L⁻¹). For rooting, in vitro-derived shoots were transferred to MS medium supplemented with indole-3-butyric acid (IBA) or 1-naphthaleneacetic acid (NAA) at the same concentration range (0.0–2.0 mg L⁻¹). The explants exhibited a high basal morphogenetic capacity; however, the addition of cytokinins significantly enhanced the response. KIN at 2.0 mg L⁻¹ achieved 100% regeneration, whereas BAP at 0.2 mg L⁻¹ maximized shoot proliferation, producing 2.07 shoots per explant. Shoot elongation was greater with KIN at 1.0 mg L⁻¹, reaching 39.15 mm. In the rooting phase, the response varied depending on the type and concentration of auxin. NAA at 0.1 mg L⁻¹ resulted in 100% rooting and produced the greatest root length (41.93 mm), whereas IBA at 0.1 mg L⁻¹ maximized the number of roots (4.67), although roots were shorter. Rooted plantlets exhibited 100% survival after eight weeks of acclimatization. This protocol provides an effective system for the rapid production of vigorous and uniform clonal plants and represents a useful tool for the propagation, conservation, and future biotechnological improvement of ulluco. Full article

Background: Measles and rubella remain major public health concerns in the Eastern Mediterranean Region (EMR), despite regional elimination goals. In 2023, the region experienced an increase in measles outbreaks. This study assessed outbreak detection and response challenges in either case definition or data analysis, in addition to gaps in laboratory and genotyping data integration to improve preparedness and response. Method: A retrospective epidemiological study was conducted using official World Health Organization (WHO) data on measles and rubella (MR) in EMR countries, from 1 January to 31 December 2023. Routine MR surveillance line list, genotyping data and supplemental immunization activity (SIA) reported by countries were used. Results: In 2023, 1206 suspected measles outbreaks were reported in 13 countries; 942 (78%) were confirmed. Rubella accounted for 158 confirmed outbreaks. Children under 5 years old comprised 76% of cases, with 62% zero dose. Timely detection was achieved in only 46% of outbreaks, with wide national variation. Genotype B3 predominated, but missing genotyping data limited verification. Six immunization campaigns occurred; however, outbreaks persisted due to high zero dose, limited targeting, and delayed responses. Conclusions: Persistent immunity gaps, under detection, inconsistent genotyping, and delayed response hindered MR control in EMR. Strengthening surveillance, integrating epidemiological and molecular data, expanding targeted supplementary immunization activities, and ensuring timely response are essential tasks. Standardized outbreak definitions, capacity building, and regular subnational analyses remain critical to regional elimination goals. Full article

Pea (Pisum sativum L.) is an important source of food and feed and contributes to soil improvement through its association with nitrogen-fixing bacteria. By enabling higher yields and selection of tolerant genotypes, controlled environment agriculture (CEA) could meet increasing nutritional needs despite adverse conditions. The main objective of this study was to investigate the effects of drought stress on the development of vegetable pea genotypes under controlled vertical farming conditions. Plants were grown in CEA and exposed to drought stress at different developmental stages, after flowering and after pod formation. Drought significantly reduced pod and seed numbers, showing a stronger effect than genotype. For example, genotype Favorit produced 7.67 and 9.00 seeds per plant under control conditions, compared with only 2.00 and 2.67 seeds per plant under drought treatments. Pod length, seed number, and seed weight were also lower under stress, highlighting the importance of water availability during seed setting and filling. Fresh and dry biomass were mainly influenced by genotype, indicating differences in stress adaptability. The results also demonstrate that CEA can be used for reproducible abiotic stress experiments relevant to plant breeding and crop production. Full article

Organic acidemias (OADs) are a group of inherited metabolic disorders with a high false-positive rate in newborn screening. In this study, we aimed to evaluate the clinical performance of next-generation sequencing (NGS) as a combined genetic test for OADs. From September 2022 to August 2025, 154,634 newborns underwent primary screening using tandem mass spectrometry (MS/MS). Among them, 151 neonates with suspected OADs underwent combined genetic screening using a pre-designed NGS panel. Of these, 55 cases tested positive on genetic screening, and 17 were ultimately diagnosed with OADs, yielding a prevalence of 1 in 9096. The positive predictive value of NGS was 30.91% (17/55). The genotypes of nine patients (9/17, 52.9%) were identified through NGS screening. Notably, one case of methylmalonic acidemia that would have been missed by MS/MS screening was successfully identified using the combined genetic screening. Additionally, 37 neonates with positive biochemical screening results were confirmed to be either carriers or unaffected individuals. Two cases of Wilson’s disease were also identified through combined genetic screening. Therefore, integrating NGS into conventional MS/MS-based screening can significantly reduce the false-positive rate and shorten the time from screening to definitive diagnosis. This approach provides a valuable model for improving the efficiency and accuracy of newborn genetic screening. Full article

Background: Inherited kidney diseases represent a genetically and clinically heterogeneous group of disorders affecting both pediatric and adult populations. Advances in next-generation sequencing (NGS) have improved diagnostic precision; however, genotype–phenotype correlations and diagnostic yield vary substantially across disease entities. Methods:We retrospectively evaluated 165 patients referred for genetic testing due to suspected inherited kidney disease. Patients were classified into three clinical groups: polycystic kidney disease, Alport syndrome, and other syndromic patients with inherited kidney diseases. Genetic analysis was performed using NGS with Human Phenotype Ontology–based gene filtering and included evaluation of both single-nucleotide variants and copy number variations. Results: Overall diagnostic yield differed markedly between groups. A molecular diagnosis was achieved in 71.4% of Alport patients, 41.0% of PKD patients, and 70.2% of patients in the Other syndromic group. In the Alport group, variants were identified exclusively in COL4A3, COL4A4, and COL4A5, with pathogenicity and gene involvement correlating with disease severity and the presence of extrarenal manifestations. The PKD group showed predominant involvement of PKD1, followed by PKHD1 and PKD2, while a substantial proportion of patients remained genetically negative, reflecting technical and biological complexity. The Other group exhibited pronounced genetic heterogeneity, with variants distributed across multiple genes involved in tubular, glomerular, metabolic, and ciliopathy-related pathways. Computational assessments demonstrated that several variants of uncertain significance (VUS) were located in functionally critical domains and were predicted to disrupt protein stability, intermolecular interactions, or conserved structural motifs, thereby supporting the biological plausibility of their potential pathogenic impact. Conclusions: Phenotype-driven NGS enables effective molecular diagnosis across diverse inherited kidney diseases while revealing disease-specific differences in diagnostic yield and genotype–phenotype correlations. Systematic inclusion of variants of uncertain significance and careful integration of genetic and clinical data are essential for accurate interpretation and long-term patient management. Collectively, this study enhances understanding of inherited kidney diseases and underscores the value of integrating comprehensive genomic and computational approaches into routine nephrogenetic practice. Full article

Background/Objectives: Responses to lifestyle interventions vary widely in obesity, and genetic factors may enhance outcomes. This study evaluated whether a 12-week genotype-informed personalized nutrition education (GEN) program improved weight and overall body composition among adults with obesity. Methods: Adults with a body mass index ≥ 25 kg/m² were randomized to a genotype-informed personalized nutrition education (GEN) group or a control group receiving standard nutrition education. The GEN group received weekly counseling tailored to nine obesity-related genetic traits. Changes were evaluated using paired t-tests and repeated-measures analysis of variance, with significance defined as p < 0.05. Results: Forty-three participants (GEN: n = 19; CON: n = 24) were analyzed. After 12 weeks, the GEN group showed significantly greater reductions than the CON group in body weight (−3.35 ± 0.7 vs. –0.91 ± 0.4 kg, p = 0.004), BMI (–1.17 ± 0.3 vs. –0.32 ± 0.1 kg/m², p = 0.005), and waist circumference (–5.56 ± 0.8 vs. –2.53 ± 0.7 cm, p < 0.001). Energy (–415 kcal, p = 0.003) and carbohydrate intake (–65 g, p = 0.003) also decreased significantly in the GEN group. Exploratory subgroup analyses suggested that participants classified as high genetic risk showed more pronounced improvements when receiving genotype-informed counseling. No serious adverse events were reported. Conclusions: The genotype-informed personalized nutrition program was associated with greater improvements in body composition than general nutrition education. Integrating genetic risk information into structured nutrition education may enhance perceived personal relevance and support effective weight management. Full article

Background: Persistent infection with high-risk human papillomavirus (hr-HPV) is the necessary agent of cervical cancer, yet its molecular definition remains heterogeneous. Multiple molecular approaches have been developed to characterize HPV persistence, including repeated detection of viral DNA, assessment of viral oncogene expression, and analysis of HPV-related DNA methylation. These approaches originate from different scientific traditions and reflect distinct conceptualizations of persistence. Objective: To synthesize and compare molecular methods used to detect persistent HPV infection through a narrative review and to clarify how different biomarkers conceptualize HPV persistence and disease progression. Methods: We conducted a narrative review in accordance with the RAMESES guidelines. Medline, Scopus, and the Cochrane Library were searched for original studies published between 2016 and 2025 investigating molecular markers of HPV persistence. An interpretive synthesis was performed to identify research traditions, underlying assumptions, and clinical implications. Results: Three major molecular narratives were identified. Persistent DNA positivity defines persistence as repeated detection of the same HR-HPV genotype over time and reflects an epidemiological–virological perspective with high sensitivity but limited specificity. Persistent oncogene expression, assessed by E6/E7 mRNA detection, conceptualizes persistence as active viral oncogenic activity and shows improved specificity for clinically relevant lesions. Persistent epigenetic imprint, measured by DNA methylation of viral and host genes, captures cumulative biological effects of long-term infection and is strongly associated with high-grade lesions and cervical cancer. These narratives represent complementary stages along a continuum of molecular persistence. Conclusions: Molecular markers of HPV persistence reflect the evolving understanding of cervical carcinogenesis, progressing from repeated viral DNA detection to oncogenic activity and stable epigenetic alterations. These complementary biomarkers represent different biological stages of persistent infection and may improve risk stratification in HPV-based screening and triage strategies. Full article

A detailed characterization of root system architecture (RSA) and growth dynamics is key to develop stress-resilient maize varieties. We evaluated sixty-five Mediterranean maize inbred lines using automated high-throughput phenotyping under controlled conditions. Shoot and root traits were extracted from imaging data during early vegetative development, revealing significant genotype-specific variation in root biomass-related traits (total root length, total root volume), root architecture (root angle, root system depth, root system width), and relative growth rates. Notably, lines previously classified as heat and drought stress-resilient or stress-sensitive based on above-ground development did not group according to particular root traits, indicating that multiple strategies may underlie tolerance to combined stress. We identified lines with contrasting RSA, including deeper roots, shallower roots, or overall larger root systems, that offer new opportunities for resilience breeding. Our results underscore root traits as critical yet underexploited targets for improving stress resilience and resource efficiency. Full article

Broccoli is rich in glucosinolates (GSLs), secondary metabolites that contribute to both plant defense and human health. Optimizing the composition of major aliphatic GSLs is an important breeding objective, yet robust molecular markers for marker-assisted selection (MAS) remain limited. In this study, candidate gene-based kompetitive allele-specific PCR (KASP) markers were developed from conserved GSL biosynthesis genes, focusing on AOP2 and GSL-OH selected from 19 GSL-related genes. Marker–trait associations were evaluated in a natural broccoli population and further validated in an independent F₂ population. Among the tested markers, S101, located in AOP2, exhibited consistent genotype-dependent effects on GNA and PRO across both populations, supporting its stable predictive value. Receiver operating characteristic (ROC) analysis further confirmed strong classification performance of S101 for distinguishing high- and low-content genotypes of these traits in the F₂ population. In contrast, S074 and S035 showed population-dependent effects, with significant associations detected only in the natural population. Although association signals were reduced under mixed linear model (MLM) analysis with false discovery rate (FDR) correction, major loci identified under the general linear model (GLM) framework remained detectable. Overall, these results demonstrate the potential of candidate gene-based KASP markers for improving aliphatic GSL composition in broccoli through marker-assisted selection. Full article

Multidrug-resistant tuberculosis is a major global health concern. Newer agents, including bedaquiline (BDQ), delamanid (DLM), pretomanid (PMD), and linezolid (LZD), are essential for treatment; however, the resistance mechanisms of these drugs remain poorly understood in South Korea. This study aimed to investigate correlations between phenotypic and genotypic resistance to these drugs using 49 clinical Mycobacterium tuberculosis isolates collected in South Korea between 2017 and 2022. The minimum inhibitory concentrations were determined using the 7H9 broth microdilution method, and whole-genome sequencing (WGS) results were compared with the May 2024 World Health Organization (WHO) mutation catalogue. Phenotypic drug susceptibility testing (pDST) revealed elevated MICs to BDQ in 12 isolates (24.5%), DLM in nine (18.4%), and PMD and LZD in two each (4.1%). No Group 1 or 2 resistance-associated mutations were detected in BDQ-, PMD-, or LZD-elevated-MIC isolates. A Group 2 mutation (fbiC_LoF) was observed in one DLM-elevated-MIC isolate, whereas fbiC_p.Ala855fs (WHO Group 2) mutations occurred in four susceptible isolates. These findings suggest resistance mechanisms beyond the current WHO catalog. Discrepancies between pDST and WGS highlight the need for integrated diagnostics and reinforce the importance of ongoing surveillance and refinement of mutation classification systems to improve genotypic resistance prediction. Full article