Search Results (3,358)

Background: Personalized precision medicine adapts therapeutic strategies to individual characteristics. In psychiatry, suboptimal outcomes with antipsychotics are often related to adverse drug reactions, poor adherence and therapeutic failure. Pharmacogenetics, particularly CYP2D6 genotyping, can improve clinical outcomes through genotype-guided therapy. This study aimed to design and implement a pharmacogenomic and pharmacokinetic testing program for long-acting injectable (LAI) antipsychotics within the Galician Health Service to enhance personalized psychiatric care. Methods: The pilot program encompasses pharmacogenetic and pharmacokinetic testing. Inclusion criteria were broad, covering patients initiating or receiving LAI antipsychotic therapy, as well as those with prior adverse reactions in order to explore scenarios where pharmacogenetic and/or pharmacokinetic data could help with clinical decisions. Structured workflows, interdisciplinary training and integration of results into the electronic health record supported implementation. A pharmacogenetic panel was specifically designed for psychiatric care, targeting clinically relevant variants in CYP2D6, CYP3A4 and ABCB1. Results: A total of 540 patients were included, with primary testing reasons being clinical follow-up (54.6%) and oral-to-LAI transition (38.5%). The CYP2D6 phenotypes were 55% normal, 34% intermediate, 6.3% poor and 4.3% ultrarapid metabolizers. Atypical metabolism was observed in 6.7% of patients for CYP3A4 and in over half for ABCB1. Plasma drug levels were within the therapeutic range for most patients, though some measurements were above or below expected values. Conclusions: This pilot demonstrates a scalable, evidence-based approach to precision psychiatry for LAI antipsychotics, integrating pharmacogenetic and pharmacokinetic testing into routine care. The framework facilitates genotype-guided decision-making and supports broader adoption of pharmacogenomics in psychiatric practice. Full article

Copy number variation (CNV) is a major class of genomic structural variation that can shape economically important traits by altering gene dosage and gene expression. MAX (MYC-associated factor X), a core component of the MYC-MAX-MXD1 transcriptional regulatory network, is critically involved in cell proliferation, differentiation, and development. However, the relationship between MAX CNVs and morphometric traits in cattle remains largely unknown. Here, we genotyped MAX CNVs by quantitative real-time PCR (qPCR) in 572 Chinese cattle from five breeds, including Qinchuan (QC), Ji’an (JA), Jinnan (JN), Nanyang (NY), and Xianan (XN) cattle, and evaluated the association of MAX CNVs with morphometric traits. MAX CNVs exhibited distinct breed-specific distribution patterns: the gain type predominated in QC, the loss type predominated in JN, NY, and XN, whereas JA showed a relatively balanced distribution across the three CNV types. Based on raw p values, MAX CNVs showed a nominal association with chest girth in JN cattle and nominal associations with chest girth and hucklebone width in NY cattle (p < 0.05). Individuals with the medium type showed higher least-squares means for the nominally associated traits than those with the loss or gain types. MAX CNVs explained 5.9% of the phenotypic variance in chest girth in JN cattle and 13.6% and 12.2% of the phenotypic variance in chest girth and hucklebone width in NY cattle, respectively. These results suggest that MAX CNVs may represent a breed-specific candidate locus related to morphometric traits in Chinese cattle. However, because no formal multiple-testing correction was applied and this study did not include independent population validation or functional validation, further studies are needed before considering any potential application in marker-assisted selection. Full article

Drought stress constrains potato (Solanum tuberosum L.) production, and potassium (K) fertilization may alleviate it, but genotype-dependent responses remain unclear. Six cultivars (‘V7’, ‘DXY’, ‘JZS-3’, ‘SY-2’, ‘JZS-12’, ‘ZJ-7’) were grown under four treatments: low K with normal irrigation (T1) or drought (T2), and K application with normal irrigation (T3) or drought (T4). Dry matter in roots, stems, leaves, and tubers was measured at 50–110 days after planting, starch content at 70–110 days, and final yield recorded. Drought (T2) reduced yield by 28.6–52.3% versus T1; K under drought (T4) recovered yield by 12.8–41.5%. Starch decreased by 18.5–35.2% under drought but was restored to 82.6–94.3% of T1 levels with K. SY-2 showed the highest biomass and yield across treatments, while V7 was most affected. Based on yield responses, cultivars fell into four categories: K-efficient/drought-tolerant (SY-2), K-responsive/drought-tolerant (DXY), K-non-responsive/drought-tolerant (JZS-12), and K-inefficient/drought-sensitive (V7). K application mitigates drought-induced losses, but benefits are genotype-dependent. This classification supports genotype-specific K recommendations in water-limited systems, and SY-2 is a valuable genetic resource for breeding for K-use efficiency and drought tolerance. Physiological assessments of leaf relative water content and stomatal conductance confirmed that drought treatment effectively induced water stress and revealed that genotype-specific stomatal regulation underpinned the differential yield responses to K fertilization under drought. Full article

Background: The Mediterranean Diet (MedDiet) is a global benchmark for the prevention of cardiometabolic diseases and healthy aging, with Olea europaea L. (O. europaea L.) and Citrus bergamia Risso et Poiteau (bergamot) serving as primary sources of bioactive molecules such as phenols, in particular flavonoids. Recent evidence highlights a paradigm shift from traditional agricultural yield toward a precision-nutrition model, in which the health-promoting potential of these species is increasingly recognized to arise from the interplay between genetic background and environmental factors. Objectives This review summarised current evidence on how genetic variability drives the metabolic fingerprints of olive and bergamot, exploring the integration of genomic, transcriptomic, and metabolomic data to identify cultivars with superior nutraceutical value. Results: Evidence suggests that phytochemical profiles of O. europaea L. and Citrus species, including bergamot, are shaped by the interaction between genetic background and environmental conditions, with genotype contributing significantly to metabolic variability. Specific O. europaea L. and Citrus genotypes display distinct metabolic fingerprints characterized by different bioactive compound profiles, potentially underlying variations in antioxidant, cardioprotective, lipid-lowering, and anti-inflammatory properties. Conclusions: The integration of high-resolution genotyping and metabolic profiling supports the selection of superior genotypes for standardized, evidence-based nutraceuticals. Future advances in precision breeding are expected to further enhance the health-promoting traits of these Mediterranean species. Full article

The Jishen Black pig is a synthetic breed incorporating the genetic backgrounds of Chinese indigenous pigs and Western lean-type pigs. The objective of this study was to characterize phenotypic variation, estimate genetic parameters, and identify genomic loci associated with rib number (NR) and the total number of thoracolumbar vertebrae (NTLV) in Jishen Black pigs. NR, NTLV, and lumbar vertebra number (NLV) were measured in 389 pigs, and genotyping was performed using a 70K SNP chip. Genetic parameters were estimated using HIBLUP, and genome-wide association studies (GWAS) were conducted using the MLM and BLINK models in GAPIT v3.0. The mean values of NR, NTLV, and NLV were 14.88, 20.94, and 6.05, respectively, and their heritability estimates were 0.568, 0.493, and 0.140, respectively. GWAS identified a shared major association peak for NR and NTLV on SSC7 at 91.19–98.15 Mb, centered on VRTN and the adjacent ABCD4-LTBP2-AREL1-PGF linkage region, among which the loci at 96.12 Mb, 96.56 Mb and 97.79 Mb are NR-specific loci. Additional signals included MIB1 on SSC6 and MMRN2 on SSC14 for NTLV, together with NR-specific loci on SSC7 at 111.59 Mb and on SSC8. Database annotation indicated that several significant SNPs overlapped with records for rib number, carcass length, loin muscle area, backfat thickness, or teat number. This study identifies major genomic regions associated with vertebral-number traits in Jishen Black pigs and expands current knowledge of their genetic basis. Full article

Phenolic compounds are critical components that determine the processing quality of wine grapes, and their accumulation is jointly affected by environmental conditions and genotype. However, the respective contributions of production site and cultivar, as well as the response differences in various phenolic components to environmental changes, remain unclear in northern China. In this study, three major red wine grape cultivars (Vitis vinifera L. cvs. Marselan, Cabernet Franc, Cabernet Sauvignon) were sampled from three typical producing areas, including Turpan, the Hexi Corridor, and Huailai in 2024. Botanical characteristics, quantitative agronomic traits, physicochemical indexes, and five phenolic components in berry skins and seeds were determined with three biological replicates. A general linear model (GLM) was used to quantify the effects of production site and genotype on berry quality, and principal component analysis (PCA) and Pearson correlation analysis were performed to explore the relationships between quality indicators. Our results indicate that clear quality differences were observed among the three studied production sites, which were the main source of variation in this dataset, accounting for 65.7% to 82.1% of total variance across most traits. Three distinct regional patterns were observed: grapes from Xinjiang had the highest sugar content, those from Gansu had the highest phenolic levels, and those from Zhangjiakou were richest in anthocyanins. The responsiveness of individual phenolic components to ecological conditions varied markedly, with anthocyanins being the most sensitive, followed by proanthocyanidins, tannins, total phenolics, and flavonoids. Marselan maintained a stable genotypic advantage in proanthocyanidin accumulation across all three sites, with skin levels 12.5–230.5% higher than other cultivars under the same growing conditions. Additionally, a potential tissue-specific association between cluster weight and phenolic components was preliminarily observed: higher cluster weight was associated with lower concentrations of late-accumulating anthocyanins and proanthocyanidins, but did not negatively affect total phenolics and tannins that form in early fruit development. Based on the above results, preliminary suggestions for cultivar–site matching were provided for reference. This study provides preliminary baseline data for cultivar selection and viticultural management in northern China, pending further multi-year validation. Full article

Soybean (Glycine max L.) is a major global source of protein and oil, yet its use in food and feed is constrained by antinutritional factors (ANFs) and allergenic seed proteins. To improve seed nutritional quality, we developed double mutant soybean lines (HBK-WF and HBK-PF) by crossing E16, which lacks the Kunitz trypsin inhibitors KTI-1 and KTI-3, with Lee 2, which is deficient in the α subunit of β conglycinin, a prominent allergen-associated storage protein. One- and two-dimensional gel electrophoresis and immunoblot analyses confirmed the complete absence of these target proteins in both experimental lines. The double mutants exhibited ~50% lower trypsin inhibitor activity relative to wild-type soybean. Tandem mass tag (TMT)-based proteomic analysis quantified 1034 proteins across parental and derived genotypes and revealed extensive proteomic remodeling. Seed composition profiling demonstrated substantial genotypic variation. Lee 2 displayed the highest total protein concentration (44%), while the double mutants exhibited intermediate to elevated levels (39–40%). Oil content in the double mutants (18.4–18.5%) was comparable to E16 and slightly lower than the reference cultivar Maverick. Amino acid profiling further showed that Lee 2 accumulated the highest levels of all measured amino acids, particularly sulfur-containing amino acids, whereas the double mutants displayed intermediate concentrations consistent with additive inheritance. Collectively, these results demonstrate that targeted removal of specific ANFs and an allergen-associated storage protein can improve soybean nutritional quality without compromising seed composition, providing promising germplasm for enhancing the value of soybean-derived food and feed products. Full article

Soil salinization constitutes a major abiotic constraint limiting global crop productivity, and breeding salt-tolerant cultivars represents a pivotal strategy to addressing this challenge. In this study, 50 processing tomato genotypes with diverse genetic backgrounds were cultivated hydroponically in Hoagland nutrient solution and subjected to either 0 (control) or 150 mM NaCl at the four-leaf stage. Nine seedling traits, encompassing plant height, stem diameter, and antioxidant enzyme activities, were measured on the 9th day after treatment initiation. Comprehensive evaluation of salt tolerance was performed using principal component analysis (PCA), fuzzy membership function analysis, and cluster analysis. The coefficients of variation (CVs) for all measured traits ranged from 21.54% to 92.69%, with relative proline content exhibiting the highest CV (92.69%) and relative stem diameter showing the lowest (21.54%). Correlation analysis revealed a highly significant positive correlation between relative plant height and relative stem diameter, and a highly significant negative correlation between relative plant height and relative proline (Pro) content. PCA reduced the nine seedling traits to four principal components, which collectively accounted for 67.529% of the total variance. Based on the combined results of fuzzy membership function and cluster analyses, the 50 genotypes were classified into three distinct categories: highly salt-tolerant (six genotypes), moderately salt-tolerant (26 genotypes), and salt-sensitive (18 genotypes). These findings provide a theoretical foundation and valuable germplasm resources for breeding salt-tolerant processing tomato varieties. Full article

Background: Childhood and adolescent acute lymphoblastic leukemia (ALL) survival outcomes have improved significantly, but treatment-related toxicities (TRTs) remain a major concern affecting dose intensity and quality of life. Germline pharmacogenetic variations contribute to inter-individual differences in chemotherapy response, yet consistent replication of associations has been limited by differences in treatment protocols, ethnic backgrounds, and toxicity definitions. Methods: This systematic review and meta-analysis (PROSPERO CRD42021229748) included 68 studies in the qualitative synthesis, with 42 high-quality studies undergoing structured synthesis and, where appropriate, quantitative meta-analysis. Studies focused on the toxicities of thiopurines, methotrexate, glucocorticoids, vincristine, and asparaginase. Results: Meta-analyses showed strong evidence linking the NUDT15 rs116855232 variant to thiopurine-induced myelosuppression (OR 19.0, 95% CI 1.6–224; I² = 86.5%) and a significant association between the TYMS enhancer repeat polymorphism and osteonecrosis (OR 6.66, 95% CI 3.67–12.11; I² = 0%). In contrast, MTHFR variants and VDR polymorphisms showed no significant associations with methotrexate-induced myelosuppression or osteonecrosis, respectively. Narrative synthesis highlighted clinically actionable associations: TPMT and NUDT15 with thiopurine toxicity; CEP72 with vincristine neuropathy; and HLA haplotypes with asparaginase hypersensitivity. Population allele frequency comparisons (IndiGenomes, gnomAD, UK Biobank) showed strong concordance (r = 0.919–0.997), supporting the broad generalisability of identified variants, which remains to be evaluated prospectively. The main limitations included heterogeneous toxicity definitions, non-uniform genetic models, evolving treatment protocols, population heterogeneity, and a lack of harmonised reporting. Conclusions: The review supports routine TPMT and NUDT15 genotyping and highlights the need for harmonised definitions, multi-ethnic studies, standardised data representation, and prospective validation. A literature-based candidate gene list for future PGx association studies was generated. Full article

Drought is a major constraint limiting maize productivity worldwide, highlighting the need for reliable methods to identify drought-tolerant genotypes. This study evaluated the effectiveness of drought tolerance indices and multivariate analyses for discriminating maize genotypes differing in drought adaptation. In total, 20 maize genotypes were assessed under optimal and water-limited conditions using grain yield under non-stress (Yp) and drought stress (Ys) together with 15 drought tolerance indices. Correlation analysis, principal component analysis (PCA), clustering, and overlay analysis were applied to identify informative indices and characterize genotype responses. Productivity-oriented indices (STI, GMP, HM, MSTI, REI, and YI) were strongly associated with grain yield and consistently identified superior genotypes, whereas SSI, TOL, and SSPI mainly reflected drought susceptibility. PCA separated productivity and stress susceptibility into two complementary components and showed that five variables (Yp, Ys, YI, ATI, and MSTI_K1) retained 99.49% of the variation explained by the complete dataset. Cluster and overlay analyses confirmed stable genotype classification and distinct adaptation strategies. These findings demonstrate that a reduced set of complementary variables provides an efficient framework for drought tolerance assessment and supports the identification of maize germplasm, combining high productivity with stable performance under variable water availability. Full article

Wild almond relatives are valuable reservoirs of allelic variation for crop improvement and conservation, yet Kazakhstan’s wild-almond genetic resources remain poorly characterised. We conducted an exploratory SSR assessment of 80 putative individuals from four taxon-locality groups (20 per group), each representing one sampled population: Prunus ledebouriana, P. tenella, P. petunnikowii, and P. spinosissima. Of 22 nuclear simple sequence repeat loci screened for cross-taxon transferability, 15 generated reproducible profiles and were retained; their even genome-wide distribution was not verified. Across the full dataset, the mean number of alleles was 3.55, the effective number of alleles was 2.62, expected heterozygosity (He) was 0.544, and 95.0% of loci were polymorphic. Missing genotypes ranged from 0.0% to 34.7% among groups, and six loci had at least 20% missing data. AMOVA attributed 76.5% of variation to within-group differences and 23.5% to among-group differences (PhiPT = 0.235, p = 0.001). PCoA, unbiased Nei distances, UPGMA, and descriptive Bayesian clustering separated the four sampled groups. A nine-locus sensitivity analysis that excluded the six high-missing loci retained P. spinosissima as the group with the highest mean He (0.699), whereas P. petunnikowii increased from 0.471 to 0.609. Thus, the low full-panel estimate for P. petunnikowii was not robust to missing data. Because taxon identity was fully confounded with locality and the marker panel was limited, the results are interpreted as a regional marker-transferability and methodological baseline rather than as species-wide or genome-wide inference. Full article

Background/Objectives: Porcine reproductive and respiratory syndrome virus type 2 (PRRSV-2) remains the predominant genotype circulating in China and continues to evolve through mutation and recombination. Although NSP1 is recognized as a multifunctional nonstructural protein involved in immune regulation, its genetic variation among PRRSV-2 strains circulating in China has not been comprehensively characterized. Methods: In this study, 425 complete NSP1 sequences, primarily representing PRRSV-2 strains circulating in China, were analyzed, and 48 representative strains were selected for pairwise percent-identity visualization. Results: Pairwise nucleotide identity among the 48 representative strains was found to range from 80.1% to 100.0%, with the lowest value detected between AHBZ and SD-R, whereas pairwise amino-acid identity ranged from 79.6% to 100.0%, with the lowest value detected between AHBZ and HNhx. Among the 425 aligned amino-acid sequences, 290 variable sites and 93 completely conserved sites were identified. The broad-lineage distribution was composed of Lineage 1 (n = 79), Lineage 3 (n = 4), Lineage 5 (n = 21), and Lineage 8 (n = 321). A global FEL dN/dS of approximately 0.2979 was estimated from 379 non-recombinant unique haplotypes, and seven high-confidence candidate positively selected sites—42, 239, 255, 302, 367, 370, and 378—were supported by MEME, FEL, and FUBAR. A descriptive lineage-biased pattern concentrated in Lineage 5 was observed for NSP1β Val19Ile, corresponding to full-length NSP1 V199I. Eight candidate recombination events were identified using RDP4, and six representative events were further examined using SimPlot. Conclusions: Overall, NSP1 was found to be under predominant purifying selection while retaining localized variability, lineage-biased residue patterns, and candidate recombination signals that should be interpreted cautiously and validated experimentally. Full article

Fusarium ear rot (FER), caused by Fusarium verticillioides (F. verticillioides), is a major disease of maize that reduces grain yield and quality globally. However, few major loci for FER have been verified and cloned. Resistance to FER is a quantitative trait influenced by environmental conditions, and maize genotypes completely resistant to the pathogen remain unknown. To gain a comprehensive understanding of the genetic basis of natural variation in FER resistance, a recombinant inbred line (RIL) population consisting of 257 progenies was developed by crossing the resistant line BT with the susceptible line Xi502. This population was genotyped using a set of 6807 high-density single nucleotide polymorphism (SNP) markers developed in this study. As a result, a total of five QTLs were identified by linkage mapping across three years, located on five chromosomes, and explaining 4.38–13.13% of the phenotypic variation. Among these was a major QTL, qFER5-2. Located on chromosome 5 within the interval 185568562–185574073, qFER5-2 explained 13.13% of the total phenotypic variance. The two candidate genes within qFER5-2 exhibited distinct expression profiles between the BT and Xi502 inbred lines, suggesting their potential association with FER resistance. Collectively, these findings provide candidate genetic resources for further investigation and offer potentially useful materials for maize disease resistance breeding. Full article

The Eghoria goat constitutes the major indigenous goat population in Greece and represents an important genetic resource. Despite its significance, genomic information remains scarce. This study aimed to investigate coding variation in the Eghoria goat using whole-genome sequencing (WGS), with particular focus on missense single nucleotide polymorphisms (SNPs) and coding insertions/deletions (indels). Whole-genome sequencing was performed on Eghoria goats (n = 6), followed by bioinformatic processing and variant filtering. Functional characterization was conducted through Gene Ontology (GO) and KEGG pathway analyses (FDR < 0.05). Normalized variant density metrics identified highly polymorphic genes. Selected missense SNPs were validated in an independent population (n = 54) using MassARRAY genotyping. Whole-genome analysis identified 10,796,211 SNPs and 1,022,779 indels. After prioritization, 15,949 missense SNPs and 861 indels were retained. Functional enrichment analyses highlighted pathways related to metabolism, ion transport, calcium signaling, immune function, transcriptional regulation, and environmental adaptation. Genes exhibiting elevated polymorphism density included olfactory receptor family members, and loci associated with metabolic regulation. Validation analyses confirmed the presence of selected variants in the Eghoria goat population. The study expands current knowledge of genomic diversity in the indigenous Eghoria goat and provides valuable resources for future genetic improvement, conservation, and breeding programs. Full article

Photosynthetic phenotypic parameters of winter wheat are important indicators of canopy physiological status, photosynthetic function, and crop growth. However, canopy-scale hyperspectral estimation of these parameters remains affected by canopy structural heterogeneity, environmental variation, and mixed spectral signals. This study evaluated the contribution of visible (VIS), near-infrared (NIR), and shortwave infrared (SWIR) regions and their combinations to estimating photosynthetic phenotypic parameters of winter wheat. Field experiments were conducted under three nitrogen application levels and 65 winter wheat genotypes, and a total of 507 valid canopy-level samples were used for model development and validation. Competitive adaptive reweighted sampling (CARS) was used to select characteristic wavelengths, and partial least squares regression (PLSR), Bayesian ridge regression (BR), and backpropagation neural network (BPNN) were applied to construct estimation models. Model performance was assessed using R², RMSE, and RPD. Results showed that NIR-based models achieved the best overall performance, with the highest validation R² of 0.828 for photosynthetic rate. The VIS + NIR combination showed stable predictive ability across multiple parameters, whereas SWIR-only models showed limited performance, with R² values below 0.5 for most parameters. Photosynthetic rate, intercellular CO₂ concentration, performance index on an absorption basis, and chlorophyll a content were predicted more accurately than the other traits. These findings indicate that canopy hyperspectral data can support quantitative monitoring of photosynthetic phenotypic parameters, and that NIR-related structural and scattering information plays a key role in winter wheat canopy phenotyping. Full article