Search Results (950)

Objectives: Isatis indigotica is a core medicinal crop for producing Radix Isatidis and Folium Isatidis, although cultivar genotype severely affects medicinal quality. This study aimed to systematically dissect the phenotypic, physiological, metabolomic, and transcriptomic differences between two cultivars, Songming No. 1 (SL, new elite line) and Dinglan No.1 (DL, conventional cultivar), and uncover the molecular mechanisms underlying SL’s superior agronomic and medicinal traits. Methods: Agronomic phenotypes, photosynthetic pigments, antioxidant enzyme activities, and leaf indirubin content were measured across seven growth stages (A–G). Untargeted LC-MS/MS metabolomics analyses were conducted at stages A, B, and E, and full-stage transcriptome sequencing was performed followed by qRT-PCR validation. Multi-omics correlation was visualized via nine-quadrant analysis. Results: SL exhibited a significantly larger leaf size, higher leaf biomass, and persistently elevated indirubin concentration at all stages. Its chlorophyll, carotenoid, Calvin-cycle enzyme, and AsA-GSH antioxidant enzyme activities were mostly higher than those in DL. A total of 1217 metabolites and massive differentially expressed genes (DEGs) were identified; flavonoids, especially peonidin-3-glucoside, stably accumulated in SL and mapped to anthocyanin biosynthesis. Transcriptional variations between cultivars concentrated on chloroplast pathways, with two candidate genes, LOC18994026 and LOC104719239, potentially boosting SL photosynthesis. Seventeen differential metabolites correlated with 170 DEGs, while DL showed stronger cold tolerance linked to tryptophan-synthesis gene overexpression, and SL was inferred to be more sensitive to high light. Conclusions: In conclusion, SL possesses comprehensive advantages in yield, photosynthetic performance, and medicinal ingredient accumulation, serving as an excellent germplasm for large-scale cultivation. This multi-omics study clarifies genotypic divergence mechanisms and provides theoretical support for high-quality I. indigotica breeding. Full article

Objective: The objective of this study was to analyze the clinical phenotypes and genetic variant characteristics of four unrelated Chinese children carrying pathogenic variants in the CTCF gene and to explore the genotype–phenotype heterogeneity of autosomal dominant intellectual disability type 21 (MRD21, OMIM 615,502). Methods: Four pediatric patients admitted to Beijing Children’s Hospital, Capital Medical University, from 2020 to 2024 were enrolled in this retrospective study. All patients underwent medical history collection, physical examination, laboratory tests and high-throughput sequencing. Identified variants were verified in the probands and parents via Sanger sequencing or CNV-seq. Results: Four distinct heterozygous CTCF variants were identified: a missense variant c.1117C>T (p.His373Tyr); an 8.92 Mb microdeletion at 16q21-q22.1 (arr[GRCh37] 16q21q22.1(58,986,875–67,907,636)×1), encompassing the entire CTCF gene; a frameshift deletion c.615_618delGAAA (p.Lys206Profs*15); and an intragenic deletion of exons 8–10. Parental testing confirmed that all identified variants were of de novo origin. The missense variant and the frameshift deletion have been reported previously in ClinVar (VCV000521287.19 and VCV001308122.2), but the two deletions were not found in public databases. Three patients presented with global developmental delay consistent with MRD21, with variable additional features including autistic-like behavior and facial dysmorphism. Notably, two of these patients showed somatic overgrowth with height and weight above the 97th percentile, contrasting with the short stature classically emphasized in MRD21. The fourth patient was a preterm infant with neonatal chylothorax, cardiopulmonary failure, and multiple congenital cardiovascular malformations; developmental assessment at a corrected age of 11 months showed only mild lags. Conclusions: This study expands the spectrum of pathogenic CTCF variants in the Chinese population and underscores the marked phenotypic heterogeneity of CTCF-related disorders, ranging from benign developmental outcomes with complete catch-up to severe neonatal multisystem involvement. In neonates presenting with unexplained chylothorax and multisystem abnormalities, especially when accompanied by features suggestive of a neurodevelopmental syndrome, CTCF should be considered in the differential diagnosis. Given this heterogeneity, a broad genomic approach rather than targeted CTCF screening is recommended in patients with complex presentations. Full article

Background: Acute renal colic is a common urological emergency characterized by substantial interindividual variability in analgesic response. Pharmacogenetic variation in OPRM1, COMT, and ABCB1 may contribute to differences in opioid efficacy and pain control. This study primarily evaluated the associations of OPRM1 A118G (rs1799971), COMT Val158Met (rs4680), and ABCB1 C3435T (rs1045642) polymorphisms with opioid analgesic response in patients with acute renal colic. As a secondary exploratory analysis, genotype and allele frequencies were compared between patients and healthy controls. Methods: This prospective case–control study included 150 patients with acute renal colic and 100 healthy controls. Genotyping was performed using TaqMan SNP Genotyping Assays based on real-time polymerase chain reaction. Genotype frequencies were compared between groups using dominant and recessive genetic models, and Hardy–Weinberg equilibrium was assessed. In addition, genotype–phenotype associations were evaluated using pain severity, early analgesic response, initial opioid dose, rescue analgesic requirement, and multivariable logistic regression analyses. Results: In the secondary exploratory case–control analysis, no statistically significant differences in genotype or allele frequencies of OPRM1 rs1799971, COMT rs4680, or ABCB1 rs1045642 were observed between patients with acute renal colic and healthy controls. Within the patient cohort, however, genotype–phenotype analyses identified differences in early analgesic outcomes. Baseline-adjusted 30 min VAS differed according to OPRM1, COMT, and ABCB1 genotype, with the most pronounced difference observed for ABCB1 rs1045642. Patients with the ABCB1 TT genotype had higher adjusted 30 min VAS scores and showed a pattern of greater opioid requirement and more frequent rescue analgesia. In exploratory multivariable analysis, the ABCB1 TT genotype was associated with higher odds of inadequate early analgesic response (adjusted OR = 2.74, 95% CI 1.18–6.37; p = 0.019). Given the limited number of outcome events, this adjusted association should be considered preliminary and hypothesis-generating. Conclusions: No significant differences in the distributions of the polymorphisms investigated were observed between patients with acute renal colic and healthy controls. Within the patient group, ABCB1 genetic variation was associated with early opioid analgesic response, although this finding should be considered preliminary and requires confirmation in larger prospective pharmacogenetic studies before clinical implementation. Any potential future pharmacogenetic application should be considered as an adjunct to established first-line renal–colic management and specifically in patients for whom opioid therapy is clinically indicated. Full article

Silver–Russell syndrome (SRS) is most commonly caused by epigenetic alterations at 11p15.5 or maternal uniparental disomy of chromosome 7 [upd(7)mat], though other molecular mechanisms remain unclear. While microdeletions encompassing MEST have been associated with SRS-like phenotypes, no pathogenic intragenic MEST variants have been reported to date. We describe a 6-month-old male infant with clinical features suggestive of a SRS-like phenotype, including intrauterine and postnatal growth restriction, triangular facies, prominent forehead, and small extremities. Methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA) revealed neither methylation abnormalities at 11p15.5, 7p13, or 7q32 nor copy number variations (CNVs) in these regions. Trio whole-exome sequencing (trio-WES) identified a paternally inherited splice-site variant (c.890 + 1G > A) in MEST. Given the paternal-specific expression of MEST, this variant resides on the functionally active allele. Based on in silico predictions and clinical correlation, this case identifies MEST as a plausible candidate gene for SRS and provides a rationale for further functional studies. Phenotypic variation exists across molecular subtypes, yet definitive genotype–phenotype correlations await larger, systematically ascertained cohorts. Full article

Seed transfer guidelines are used in ecological restoration to reduce the maladaptation risk from non-local genotypes. Researchers often examine second-generation populations under uniform conditions to isolate adaptation from environmental responses. However, in outcrossing species, interpreting these traits may be challenging if uncontrolled gene flow and recombination among provenances influence offspring phenotypes. We compared seed germination and seedling traits of the wind-pollinated grass Festuca vaginata, a dominant species of open sand grasslands in Hungary, across seed transfer zones (STZs) and localities. We used a two-generation common garden experiment with uncontrolled gene flow. Our results reveal that under common garden cultivation, the transgenerational stability of population differentiation is traitspecific. While locality effects on germination disappeared in the second generation, phenotypic variation in biomass and leaf length persisted, suggesting that shared environments homogenize germination faster than vegetative traits. As wind-pollinated species often exhibit weak regional genetic structuring, STZs may not capture the primary axis of phenotypic variation in specific traits. While not invalidating the use of STZs, our findings suggest that seed sourcing strategies should, if feasible, consider locality-level variation when using wind-pollinated grasses for species reintroduction. Full article

Context: Forage bermudagrass (Cynodon dactylon) is widely used in warm-season livestock production systems because of its high productivity and adaptability. However, systematic evaluation of forage-type germplasm remains limited, restricting the identification of superior breeding materials. Aims: This study aimed to evaluate phenotypic variation, identify key yield-related traits, and identify high-performing forage bermudagrass germplasm with contrasting interannual phenotypic responses derived from a ‘Wrangler’ × ‘CD-21’ hybrid population. Methods: Two evaluation populations were established. A single-genotype population of 621 individuals was used to assess plant and canopy height variation, whereas 16 representative entries were evaluated for biomass yield and major agronomic traits during 2024–2025. Frequency distribution, principal component, correlation, and path analyses were conducted. Key results: Stem height and canopy height showed unimodal, approximately normal distributions, indicating continuous phenotypic variation and supporting their characterization as quantitative traits. Biomass yield was positively associated with stem height (r = 0.79), canopy height (r = 0.82), and internode length (r = 0.63). Path analysis indicated that stem height had the largest estimated direct effect (β = 0.45) on biomass yield within the proposed path model. Multivariate analyses revealed distinct phenotypic differences among entries and years, allowing classification into high-performing, environmentally responsive, and leaf-structure efficient groups. Conclusions: Stem height, canopy height, and internode length were identified as key traits associated with forage biomass production. Integrating multivariate and path analyses effectively differentiated forage bermudagrass germplasm based on yield performance and agronomic traits. Implications: The identified germplasm and trait relationships provide useful information for further breeding evaluation and selection decisions and support the development of improved forage bermudagrass cultivars. Full article

Barley (Hordeum vulgare L.) is a major cereal in Kazakhstan, where diverse breeding material supports crop improvement. We characterized 86 two-row spring barley accessions from six breeding organizations using the Illumina Infinium 50K Barley SNP Array. Analysis of 29,920 high-quality SNPs revealed moderate diversity (H_e = 0.346, PIC = 0.278, Shannon = 0.752), with 80.84% of molecular variation occurring within and 19.16% among breeding organizations. A minor allele frequency-free (MAF-free) analysis showed that 95.61% of marker–allele combinations at polymorphic loci were shared by at least two organizations. Although PCA, kinship, and neighbor-joining analyses indicated extensive overlap, discriminant analysis of principal components (DAPC) cluster membership was significantly associated with breeding origin (χ² = 106.38, Monte Carlo p = 1 × 10^–5; bias-corrected Cramér’s V = 0.513), demonstrating substantial but incomplete differentiation among breeding programs. Phenotypic differentiation was evaluated using environment-adjusted genotype BLUPs. All seven traits differed significantly among five DAPC clusters. In a reduced six-trait linear discriminant analysis (LDA) excluding vegetation period, LD1 was associated most strongly with number of kernels per spike, followed by heading time, spike length, and heading-to-maturity time. Leave-one-out cross-validation (LOOCV) accuracy was 36.47%, exceeding the permutation mean of 19.83% but indicating considerable phenotypic overlap. The examined materials therefore constitute a diverse, interconnected breeding panel that may support germplasm management and parent selection and provide a genomic and phenotypic framework for future GWAS, genomic selection, and targeted validation of molecular markers within the represented collections. Full article

Vivipary adversely affects the production process of the cucumber seed industry and greatly limits the popularization of cucumber varieties. Identification of the cucumber seed vivipary phenotype and screening of vivipary-associated genes will provide important theoretical value and practical significance for solving this problem in agricultural production. In this study, cucumber near-isogenic lines with significant differences in vivipary traits (viviparous line F and non-viviparous line BF) were successfully screened and used to construct genetic populations. Bulk segregant analysis (BSA) and QTL-seq were performed to fine-map the major-effect quantitative trait locus associated with vivipary variation. Based on QTL and BSA analyses, CsaV3_3G044640 (designated CsCYP82D47), which encodes a cytochrome P450 family protein, was identified as a candidate gene associated with cucumber vivipary. CsCYP82D47 exhibits obvious tissue specificity and is highly expressed in leaves, sprouts, and seeds. However, no significant difference in CsCYP82D47 expression was detected between viviparous and non-viviparous cucumber materials. Further sequence analysis revealed multiple mutation sites in this gene between different genotypes. Specifically, the CYP82D47 protein in viviparous materials harbours one amino acid insertion (L63) and two missense mutations (M71L and S124L). In addition, the altered leucine residue distribution in viviparous cucumber may enlarge the substrate channel and enhance substrate catalytic efficiency, which may contribute to the vivipary phenotype. In summary, this study identifies a promising candidate gene potentially related to cucumber vivipary, which lays a foundation for further exploration of the molecular mechanism underlying cucumber vivipary and provides a potential genetic resource for cucumber molecular breeding. Full article

Rainbow trout (Oncorhynchus mykiss) is an important cold-water aquaculture species and a tractable salmonid model for functional genomics. Rapid advances in chromosome-level genome assemblies, genetic variation resources, regulatory annotations, tissue and cell models, controlled challenge systems, and genome-editing technologies have established an increasingly integrated framework for linking genomic variation with measurable phenotypes. Evidence from studies of mucosal immunity, disease-resistance genetics, and environmental stress responses indicates that these resources can improve candidate-gene prioritization and mechanistic interpretation across molecular, cellular, tissue, and whole-fish levels. However, differential gene expression, quantitative trait locus and genome-wide association signals, genomic predictions, and cell-type localization remain largely associative and rarely provide direct evidence of causality. Interpretation is further complicated by salmonid-specific whole-genome duplication, because retained paralogues may exhibit tissue-specific divergence, functional redundancy, and compensatory responses. Further progress will require the integration of pangenomics, regulatory annotation, single-cell and spatial analyses, and paralogue-aware functional perturbation in both cell-based and whole-fish systems. Such integration will strengthen causal inference, clarify genotype–phenotype relationships, and support disease-resistant breeding, healthy aquaculture, and environmental risk assessment. Full article

Phyllosphere microorganisms interact with host plants to regulate growth, promote nutrient uptake and enhance stress tolerance with host specificity, while arbuscular mycorrhizal fungi facilitate plant nutrient absorption and stress adaptation. Current poplar microbial studies mostly focus on hermaphroditic species, with limited research on dioecious poplars. This study selected four poplar species commonly hybridized with Populuscathayana and Populus deltoides in the Xinmin area of Liaoning Province as research subjects: two female plants, DM-9-18 and DX-08-01, and two male plants, 2111 and Qingshan poplar. We performed MiSeq high-throughput sequencing targeting bacterial 16S rRNA, fungal ITS, and arbuscular mycorrhizal fungal (AMF) marker genes from poplar phyllosphere, coupled with chemical quantification of leaf, root and rhizosphere soil, to disentangle clone- and sex-associated divergence in microbial assemblages and their core environmental drivers. No significant gender differences were observed in leaf and rhizosphere nutrient levels and microbial α diversity, whereas male poplars had higher rhizosphere soil nutrients. Male and female poplars genotypes harbored distinct microbial ASVs. The dominant phyllosphere microbes and arbuscular mycorrhizal fungi exhibited gender-specific abundance variations, and nutrient content was the key factor shaping microbial communities. This study clarifies microbial community differences among the four selected hybrid poplar clones. While the experimental design confounds sex with host genotype, the observed patterns provide insights into potential sex-related variations. Our results advance the mechanistic understanding of how dioecious poplar genotype and sexual phenotype jointly filter leaf and root-associated microbial symbionts, with applied implications for hybrid poplar breeding and shelterbelt microbial regulation. Full article

Polyploidy is widely used in plant breeding to increase phenotypic variation and potentially improve stress-related traits; however, its effects in common bean remain poorly characterized. Here, colchicine-induced polyploidy was evaluated in Phaseolus vulgaris cv. Zorzal to determine whether tetraploid lines exhibit coordinated changes in stomatal anatomy, physiology, pigment composition, oxidative balance, and ploidy inheritance. Polyploidy was induced using different colchicine exposure regimes and confirmed by flow cytometry. Stomatal traits, gas-exchange parameters, photosynthetic pigments, oxidative stress markers, antioxidant capacity, and multivariate phenotypic relationships were subsequently analyzed in confirmed tetraploid lines. Colchicine treatments successfully generated tetraploid and mixoploid plants, although induction efficiency was highly variable among replicates. Tetraploid lines showed heterogeneous physiological responses, including increases in the photosynthetic rate and stomatal conductance in some genotypes, but no consistent reduction in stomatal pore area index. Pigment composition and antioxidant-related traits also varied among lines, without a uniform response pattern. Multivariate analyses revealed coordinated but highly divergent phenotypic profiles among tetraploid genotypes. Importantly, the induced tetraploids were not stably transmitted to the C1 generation, with a predominance of diploid progeny among the evaluated offspring. Overall, colchicine-induced polyploidization generated substantial physiological variability among independently derived tetraploid plants of P. vulgaris cv. ‘Zorzal’; however, the predominance of diploid individuals among the evaluated C1 progeny indicates limited transmission of the induced tetraploid state to the subsequent generation. Full article

Low-coverage whole-genome resequencing (lcWGS) is emerging as a powerful population-scale genomic strategy for livestock and poultry research. By integrating sparse sequencing reads with genotype likelihoods, haplotype information and imputation models, lcWGS enables genome-wide variant discovery and genetic inference across large animal cohorts. This feature is particularly valuable for breeding populations, indigenous breeds and conservation resources, where broad sampling is essential for capturing population-specific variation and linking genomic diversity with economically and adaptively important traits. In this review, we synthesize the statistical foundations, analytical workflows and major applications of lcWGS in livestock and poultry genomics. We discuss how lcWGS supports genetic diversity assessment, population structure analysis, genome-wide association studies, genomic selection, selection-signature detection, environmental adaptation research and genetic resource conservation. We further highlight the importance of coordinated study design, including sequencing depth, sample size, reference-panel construction, imputation strategy, phenotype quality and downstream analytical models. Beyond its role as a cost-efficient genotyping approach, lcWGS provides a flexible framework for integrating population genomics with functional annotation, multi-omics resources, long-read assemblies, graph pan-genomes and interpretable prediction models. These developments are expanding the potential of lcWGS from variant discovery toward biological interpretation, precision breeding, climate-resilient animal production and the sustainable management of livestock and poultry genetic resources. Full article

Pain is a leading cause of morbidity and healthcare utilization in sickle cell disease (SCD), and opioids remain central to treating vaso-occlusive and chronic pain. Yet opioid response varies widely, raising the question of whether pharmacogenetic testing should inform opioid prescribing. Our review examined the PubMed literature on pharmacogenomics and opioid efficacy in SCD. We focus on CYP2D6 as the clearest current pharmacogenetic signal for codeine and tramadol, and assess SCD-specific implementation studies, preemptive testing, and African pharmacoequity. The current evidence supports targeted CYP2D6-informed prescribing in selected contexts rather than universal testing for all opioids, while highlighting the need to integrate genotype with pain phenotype, drug–drug interactions, liver function, and clinically grounded implementation studies, and better characterize African and African-ancestry pharmacogene variation. Full article

Phenotypic variation does not always correspond closely to genetic structure within species, particularly for morphological traits that are also influenced by environmental conditions. We examined whether leaf morphology in Daphne blagayana reflects previously identified phylogeographic structures and whether size- and shape-related traits differ in the hierarchical distribution of variation. Leaf morphometric analyses were performed on 3439 leaves collected from 596 shrubs in 21 populations covering the entire distribution range of the species. Ten leaf morphological traits were analysed using nested mixed-effects models, principal component analysis (PCA), MANOVA, Mantel tests and additional conservative mixed-effects models accounting for population-level structure. Leaf size-related traits showed stronger population-level differentiation and clearer geographic structuring, whereas shape-related traits exhibited higher within-shrub variation and weaker correspondence with phylogeographic structure. PCA and MANOVA revealed significant morphological differentiation among the three previously defined evolutionarily significant units (ESUs), although overlap among groups remained considerable. When population-level structure was taken into account, ESU effects were reduced but remained detectable for leaf length and selected shape-related traits. The northwestern ESU was characterized by larger and broader leaves, while differences between the central–southeastern and central ESUs were associated mainly with leaf shape traits. Mantel analysis revealed a weak but significant correlation between geographic and morphological distances among populations, indicating that geographic distance contributes to, but does not fully explain, morphological differentiation. The results show that leaf morphology in D. blagayana is associated with the previously identified phylogeographic structure of the species and that size- and shape-related traits differ markedly in their degree of geographic differentiation and hierarchical variation. However, because phylogeographic and geographic structure are spatially confounded in the present dataset, their individual effects on leaf morphology cannot be statistically separated. The study also highlights the importance of hierarchical sampling, appropriate statistical analyses, and cautious interpretation of genotype–phenotype correspondence in observational studies of intraspecific morphological variation. Full article

Methane (CH₄) emissions from dairy cattle contribute substantially to agricultural greenhouse gas production and are influenced by genetic, physiological, environmental and management-related factors. The present study investigated CH₄-related traits and genotype–system interactions in Holstein Friesian (HF) dairy cows using repeated laser methane detector (LMD)-based measurements. A total of 134 cows from one research herd reflecting a commercial production system were repeatedly recorded for CH₄ traits (739 observations per trait) between 2020 and 2024 and linked with milk performance test-day data, behavioral observations, environmental measurements and genomic breeding values. CH₄ traits were derived separately for respiration- and eructation-related emissions. Generalized linear mixed models revealed significant effects of wind speed, rumination behavior, interaction behavior and days in milk on several CH₄ traits. Across lactation, respiration-related CH₄ traits slightly decreased, whereas eructation-related traits increased toward later lactation stages. Correlations between CH₄-related breeding values and production traits were generally low to moderately negative, ranging from −0.24 to 0.08, indicating that selection for reduced CH₄ emissions may be achievable without major unfavorable effects on milk production traits. To evaluate the complex relationships among CH₄ emissions, production, behavior, environment, diet and genetic background, a structural equation model (SEM) was applied. Environmental conditions, particularly temperature and humidity, showed the strongest positive association with CH₄ emissions, while eructation-related CH₄ traits contributed more strongly to the latent CH₄ construct than respiration-related traits. Behavioral activity, especially rumination, indicated relevant associations with CH₄ expressions. The SEM further suggested that CH₄ emissions are shaped by interconnected environmental, physiological and genetic pathways rather than by a single dominant factor. Overall, the results highlight the importance of environmental sensitivity and longitudinal biological variation in CH₄ phenotypes under commercial dairy production conditions. Repeated on-farm CH₄ measurements, particularly eructation-associated traits, may provide valuable indicator traits for future genomic breeding and management strategies to reduce the environmental footprint of dairy cattle production. Full article