Search Results (1,127)

This study measured eight key phenotypic traits across 259 fresh maize inbred lines, including plant height and spike length. A total of 82 single nucleotide polymorphisms (SNPs) significantly associated with these phenotypes were identified by applying a mixed linear model to calculate the best linear unbiased prediction (BLUP) values and integrating genome-wide genotypic data through genome-wide association analysis (GWAS). A further analysis of significant SNPs contributed to the identification of 63 candidate genes with functional annotations. Notably, 11 major candidate genes were identified from multi-trait association loci, all of which exhibited highly significant P-values (<0.0001) and explained between 7.21% and 12.78% of phenotypic variation. These 11 genes, located on chromosomes 1, 3, 4, 5, 6, and 9, were functionally involved in signaling, metabolic regulation, structural maintenance, and stress response, and are likely to play crucial roles in the growth and physiological processes of fresh maize inbred lines. The functional genes identified in this study have significant implications for the development of molecular markers, the optimization of breeding strategies, and the enhancement of quality in fresh maize. Full article

Background/Objectives: Optical genome mapping (OGM) has recently emerged as a new technology in the clinical cytogenomics laboratories. This methodology has the ability to detect balanced and unbalanced structural rearrangements using ultra-high molecular weight DNA. This article discusses the uses of this new technology in both constitutional and somatic settings, its advantages as well as opportunity for improvements. Methods: We reviewed the medical and scientific literature for methodology and current clinical uses of OGM. Results: OGM is a recent addition to the methods used in cytogenomics laboratories and can detect a wide range of structural and copy number variations across a plethora of diseases. Conclusions: Clinical cytogenomics is an important laboratory specialty for which various technologies have been validated over the last several decades to improve detection of copy number and structural variations and their association to human disease. OGM has proven to be a powerful tool in the arsenal of clinical laboratories and provides a unified workflow for the detection of chromosomal aberrations across a wide range of diseases. Full article

Background: Neurodevelopmental disorders (NDDs), including autism spectrum disorder (ASD), are genetically complex and often linked to structural genomic variations such as copy number variants (CNVs). Current diagnostic strategies face challenges in interpreting the clinical significance of such variants. Methods: We developed a customized, gene-oriented chromosomal microarray (CMA) targeting 6026 genes relevant to neurodevelopment, aiming to improve diagnostic yield and candidate gene prioritization. A total of 39 patients with unexplained developmental delay, intellectual disability, and/or ASD were analyzed using this custom platform. Systems biology approaches were employed for downstream interpretation, including protein–protein interaction networks, centrality measures, and tissue-specific functional module analysis. Results: Pathogenic or likely pathogenic CNVs were identified in 31% of cases (9/29). Network analyses revealed candidate genes with key topological properties, including central “hubs” (e.g., NPEPPS, PSMG1, DOCK8) and regulatory “bottlenecks” (e.g., SLC15A4, GLT1D1, TMEM132C). Tissue- and cell-type-specific network modeling demonstrated widespread gene involvement in both prenatal and postnatal developmental modules, with glial and astrocytic networks showing notable enrichment. Several novel CNV regions with high pathogenic potential were identified and linked to neurodevelopmental phenotypes in individual patient cases. Conclusions: Customized CMA offers enhanced detection of clinically relevant CNVs and provides a framework for prioritizing novel candidate genes based on biological network integration. This approach improves diagnostic accuracy in NDDs and identifies new targets for future functional and translational studies, highlighting the importance of glial involvement and immune-related pathways in neurodevelopmental pathology. Full article

Background/Objectives: Miscarriage is an increasingly common event worldwide arising from various factors, and identifying its etiology is important for planning and managing any future pregnancies. It is estimated that about half of early pregnancy loss cases are caused by genetic abnormalities, while a significantly lower rate is found in late pregnancy loss. Multiplex ligation-dependent probe amplification (MLPA) can detect small changes within a gene with precise breakpoints at the level of a single exon. The aim of our study was to identify the rate of copy number variations (CNVs) in spontaneous pregnancy loss samples after having previously tested them via quantitative fluorescence PCR (QF-PCR), with no abnormal findings. Methods: DNA was extracted from product-of-conception tissue samples, followed by the use of an MLPA kit for the detection of 31 microdeletion/microduplication syndromes (SALSA^® MLPA^® Probemix P245 Microdeletion Syndromes-1A, MRC-Holland, Amsterdam, The Netherlands). Results: A total of 11 (13.1%) out of the 84 successfully tested samples showed CNVs. Duplications accounted for 9.5% of the analyzed samples (eight cases), while heterozygous or hemizygous deletions were present in three cases (3.6%). Among all the detected CNVs, only three were certainly pathogenic (3.6%), with two deletions associated with DiGeorge-2 syndrome and Rett syndrome, respectively, and a 2q23.1 microduplication syndrome, all detected in early pregnancy loss samples. For the remaining cases, additional genetic tests (e.g., aCGH/SNP microarray) are required to establish CNV size and gene content and therefore their pathogenicity. Conclusions: MLPA assays seem to have limited value in detecting supplementary chromosomal abnormalities in miscarriages. Full article

Background: Fanconi Anemia (FA) is a rare disorder, characterized by chromosomal instability, congenital abnormalities, progressive bone marrow failure, and predisposition to cancer. FA is caused by pathogenic variants in any of the 23 (FANCA-FANCY) linked genes. Procedure: Retrospective analysis of 13 FA patients with a causative variant was performed. Patients (6 boys and 7 girls) aged from 9 to 26 years old, (mean age of 7.3 years), at diagnosis. Results: Phenotype evaluation demonstrated in 11/13 patients’ congenital anomalies, with pigmentary changes and short stature, present in 90% of cases. Hematological abnormalities were present in 10/11 patients, with thrombocytopenia being the prominent finding. Genetic analysis for the most common complementation group FA-A revealed that 12/13 patients belonged to this group and only one patient was found to be FA-E. Exon deletions, single nucleotide variations, and duplications were identified. Familial patterns, due to consanguinity, were evident in one case. Twelve patients underwent hematopoietic stem cell transplantation (HSCT), with variable pre-HSCT supportive treatments. Post-HSCT data showed that 9 out of 10 patients for whom follow up data was available, survived for a median time of 5.4 years. Complications like acute graft-versus-host disease were noted. Conclusions: Our study highlights the importance of genotype towards tailored monitoring for children and families with FA. Full article

Fusarium root rot, caused by Fusarium equiseti, poses a significant threat to soybean production. This study aimed to explore the genetic basis of resistance to Fusarium equiseti root rot (FERR) by evaluating the resistance phenotype of 346 soybean germplasms and conducting a genome-wide association study (GWAS) using 698,949 SNP markers obtained from soybean germplasm resequencing data. GWAS analysis identified 101 SNPs significantly associated with FERR resistance, distributed across nine chromosomes, with the highest number of SNPs on chromosomes 13 and 20. Further gene-based association and allele variation analyses identified candidate genes whose mutations are closely related to FERR resistance. To accelerate soybean FERR resistance breeding screening, we developed CAPS markers S13_14464319-CAPS1 and S15_9215524-CAPS2, targeting these SNP sites, and KASP markers based on the S15_9205620-G/A, providing an effective tool for marker-assisted selection (MAS). This study offers a valuable theoretical foundation and molecular marker resources for the functional validation of FERR resistance genes and soybean disease resistance breeding. Full article

Fruit size is an important agronomic trait affecting the yield and commercial value of melon and a key trait selected for during domestication. In this study, two respective melon accessions (large-fruited M202008 and small-fruited M202009) were crossed, and developed biparental mapping populations of the F₂ generation (160 and 382 plants) were checked across two subsequent experimental years (2023 and 2024). The phenotypic characterization and genetic inheritance analysis showed that melon fruit size is modulated by quantitative genetics. Bulked segregant sequencing analysis (BSA-seq) identified a stable and effective quantitative trait locus (QTL, named Cmfs) controlling fruit size, localized to a 3.75 Mb region on chromosome 9. To better delineate the main-effect Cmfs locus, co-dominant polymorphic molecular markers were developed in this genetic interval, and genotyping was performed within the F₂ mapping populations grown across two years. QTL analysis of the phenotypic and genotypic datasets delimited the major-effect Cmfs locus interval for fruit length [2023: logarithm of odds (LOD) value = 6.16, 16.20% phenotypic variation explained (PVE); 2024: LOD = 5.44, 6.35% PVE] and fruit diameter (2023: LOD value = 5.48, 14.59% PVE; 2024: LOD = 6.22, 7.22% PVE) to 1.88 and 2.20 Mb intervals, respectively. The annotation analysis across the melon genome and comparison of resequencing data from the two parental lines led to the preliminary identification of MELO3C021600.1 (annotated as cytochrome P450 724B1) as a candidate gene related to melon fruit size. These results provide a better understanding for further fine mapping and functional gene analysis related to melon fruit size. Full article

Polyploidy in plants can enhance stress resistance and secondary metabolite production, offering potential benefits for Clausena lansium (L.) Skeel, a medicinally valuable species. However, systematic studies of polyploidy-induced morphological, anatomical, and metabolic changes in this species are lacking. This study aimed to induce and characterize polyploid C. lansium lines, assess ploidy-dependent variations, and evaluate their impact on bioactive metabolite accumulation. Three cultivars were hybridized, treated with colchicine, and bred, yielding 13 stable polyploid lines confirmed by flow cytometry and chromosome counting. The polyploids exhibited distinct traits, including larger pollen grains, altered leaf margins, increased leaflet numbers, enlarged guard cells with reduced stomatal density, and thicker leaf tissues. Metabolomic analysis revealed that tetraploids accumulated significantly higher levels of flavonoids, alkaloids, and phenolic acids compared to diploids, while triploids showed moderate increases. These findings demonstrate that polyploidization, particularly tetraploidy, enhances C. lansium’s medicinal potential by boosting pharmacologically active compounds. The study expands germplasm resources and supports the development of high-quality cultivars for pharmaceutical applications. Full article

Salt stress severely limits the growth and ornamental value of pecan (Carya illinoinensis) in salinized regions, yet the transcriptional mechanisms underlying its stress adaptation remain unclear. In this study, a comprehensive genomic analysis of the GRAS transcription factor family identified 58 CiGRAS genes in pecan. These genes were classified into 11 subfamilies and showed conserved motifs and gene structures, with variation in promoter cis-elements suggesting diverse regulatory functions. Chromosomal distribution and duplication analysis indicated that whole-genome and dispersed duplication events were the main drivers of CiGRAS expansion. Transcriptome data revealed tissue-specific expression and strong responsiveness to salt and other stresses. Under 0.6% NaCl treatment, several CiGRAS genes were significantly upregulated, especially at 48 h. Gene co-expression analysis further highlighted GRAS-enriched modules associated with redox regulation and stress signaling. qRT-PCR validation confirmed time-specific induction of seven CiGRAS genes under salt stress. These findings provide insights into the evolutionary dynamics and stress-related roles of CiGRAS genes and offer candidate regulators for improving pecan salt tolerance in ecological greening and landscape applications. Full article

Microcystis is a genus of cyanobacteria responsible for harmful algal blooms (HABs) in freshwater ecosystems, posing significant ecological and public health risks. Despite its importance, current genomic resources are heavily biased toward Microcystis aeruginosa, limiting comprehensive understanding of genomic diversity within the genus. In this study, we present the first complete genome sequences of two morphospecies, M. ichthyoblabe FBCC-A1114 and M. protocystis FBCC-A270. Using long-read sequencing, both genomes were assembled into single circular chromosomes of 5.84 Mb and 5.76 Mb, respectively. Phylogenetic analyses placed both strains within genospecies G, alongside M. aeruginosa and M. viridis. Comparative analysis of biosynthetic gene clusters revealed that, while most genospecies G members harbor aeruginosin, cyanobactin, and microviridin gene clusters, the two newly sequenced strains lack cyanobactin and microcystin clusters but retain the microginin cluster. Synteny analysis demonstrated high structural conservation between the two genomes, while notable structural variations were observed when compared with M. aeruginosa NIES-298. These findings reveal both functional and structural plasticity within the genospecies, suggesting ecotype diversification driven by environmental adaptation. The newly assembled genomes provide critical resources to refine classification frameworks and advance our understanding of Microcystis genomic diversity. Full article

In farmed animals, body color is not only an ecological trait but also an important trait that influences the commercial value of the animals. Melanin plays an important role in the formation of body color in animals, while the tyrosinase (TYR) gene family is a group of key enzymes that regulate melanogenesis. The Chinese soft-shelled turtle (Pelodiscus sinensis) is one of the most important reptiles in freshwater aquaculture. However, the potential role of the TYR gene family in the body color formation of P. sinensis remains unclear. This study aimed to investigate the expression and conservation of the TYR gene family in relation to body color variation in P. sinensis. Three core members of this gene family were identified from the P. sinensis genome. Following identification, the genomic features were analyzed. They shared similar physicochemical properties and conserved domains. Chromosome mapping showed that the three genes of P. sinensis were all located on the autosomes, while phylogenetic and collinearity analysis suggested that the protein functions of the three genes in the studied species were highly conserved. Amino acid sequence alignment indicated high conservation among the three TYR gene family proteins (TYR, TYRP1, and DCT) in multiple critical regions, particularly in their hydrophobic N-/C-terminal regions and cysteine/histidine-rich conserved domains. The qRT-PCR revealed that the TYR and DCT genes were highly expressed in the eyes of individuals with different body colors. The expression levels of TYR and TYRP1 genes in the skin were significantly higher in dark-colored individuals than in light-colored ones (p < 0.05). These results will lay the groundwork for functional studies and breeding programs targeting color traits in aquaculture. Full article

Soybean (Glycine max) peptide lunasin exhibits significant cancer-preventive, antioxidant, and hypocholesterolemic effects. This study aimed to identify quantitative trait nucleotides (QTNs) associated with lunasin content and to annotate the candidate genes in the soybean genome. The mapping panel of 144 accessions was gathered from the USDA Soybean Germplasm Collection, encompassing diverse geographical origins and genetic backgrounds, and was genotyped using SoySNP50K iSelect Beadchips. The lunasin content in soybean seeds was measured using the enzyme-linked immunosorbent assay (ELISA) method, with lipid-adjusted soybean flour prepared from seeds obtained from the Germplasm Resource Information Network (GRIN) of USDA-ARS in 2003 and from North Carolina in 2021, respectively. QTNs significantly related to lunasin content in soybean seeds were detected on 15 chromosomes, with LOD scores greater than 3.0, explaining various phenotypic variations identified using the R package mrMLM (v4.0). Significant QTNs on chromosomes 3, 13, 16, 18, and 20 were consistently identified across multiple models as being significantly associated with soybean lunasin content, based on assessment data from two years. Twenty-nine candidate genes were found, with 12 identified in seeds from 2003 and 17 from 2021. Our study is an important effort to understand the genetic basis and functional genes for lunasin production in soybean seeds. Full article

Branching is a critical agronomic trait in flowering Chinese cabbage (Brassica rapa subsp. chinensis), influencing plant architecture and yield. In this study, there was a highly significant difference between CX010 (single primary rosette branches) and BCT18 (multiple primary rosette branches). Phenotypic analysis revealed significant differences in primary rosette branch numbers, with BCT18 showing up to 15 branches and CX010 displaying only one main stem branch. Genetic analysis indicated that branching was controlled by quantitative trait loci (QTL) with a normal distribution of branch numbers. Using bulked segregant analysis coupled with sequencing (BSA-seq), we identified a candidate interval of approximately 2.96 Mb on chromosome A07 linked to branching. Fine mapping narrowed this to a 172 kb region containing 29 genes, with BraA07g032600.3C (BrTCP1) as the most likely candidate. cDNA cloning of the BrTCP1 gene revealed several variations in BCT18 compared to CX010, including a 6 bp insertion, 10 SNPs, and two single-nucleotide deletions. Expression analysis indicated that BrTCP1 was highly expressed in the rosette stems of CX010 compared to BCT18, consistent with its role as a branching suppressor. The heterologous mutants in Arabidopsis confirmed the conserved role of BrTCP1 in branch inhibition. These findings reveal that BrTCP1 might be a key regulator of branching in flowering Chinese cabbage, providing insights into the molecular mechanisms underlying this trait and offering a framework for genetic improvement in Brassica crops. Full article

Immune checkpoints such as PD-1/PD-L1, CTLA-4, LAG-3, TIM-3, and TIGIT play critical roles in regulating anti-tumor immunity and are exploited by hematological malignancies to evade immune surveillance. While classic Hodgkin lymphoma (HL) demonstrates notable responsiveness to immune checkpoint inhibitors (ICIs), which is attributed to genetic alterations like chromosome 9p24.1 amplification, the responsiveness of non-Hodgkin lymphoma (NHL), acute myeloid leukemia (AML), and multiple myeloma (MM) remain inconsistent and generally modest. In NHL, the heterogeneous immune microenvironment, particularly variations in tumor-infiltrating lymphocytes and PD-L1 expression, drives differential ICI outcomes. AML shows limited responsiveness to monotherapy, but the combination of monotherapy with hypomethylating agents yield encouraging results, particularly in selected patient subsets. Conversely, MM trials have largely failed, potentially due to genetic polymorphisms influencing checkpoint signaling pathways and the inherently immunosuppressive bone marrow microenvironment. Both intrinsic tumor factors (low tumor mutational burden, impaired antigen presentation, IFN-γ pathway alterations) and extrinsic factors (immunosuppressive cells and alternative checkpoint upregulation) contribute significantly to primary and acquired resistance mechanisms. Future strategies to overcome resistance emphasize combination therapies, such as dual checkpoint blockade, epigenetic modulation, and reprogramming the tumor microenvironment, as well as biomarker-driven patient selection, aiming for precision-based, tailored immunotherapy across hematological malignancies. Full article

Production scheduling and machine tool intermittent state control separately influence a workshop’s machining and intermittent energy consumption. Effective scheduling decisions and intermittent state control are crucial for optimizing the overall energy consumption in the workshop. However, the scheduling scheme determines the machine tool intermittent durations, which imposes strong constraints on the decision-making process for intermittent state control. This makes it difficult for intermittent state control to be used in providing feedback and optimizing scheduling decisions, significantly limiting the overall energy-saving potential of the workshop. To this end, a workshop energy-saving scheduling method is proposed integrating machine tool intermittent state control. Firstly, the variation characteristics of workshop machining energy consumption, machine tool intermittent durations, and intermittent energy consumption are analyzed, and an energy-saving optimization strategy is designed. Secondly, by incorporating variables such as intermittent durations, intermittent energy consumption, and variable operation start time, a multi-objective integrated optimization model is established. Thirdly, the energy-saving optimization strategy is integrated into chromosome encoding, and multiple crossover and mutation genetic operator strategies, along with a low-level selection strategy, are introduced to improve the NSGA-II algorithm. Finally, the effectiveness of the proposed method is verified through a machining case. Results show that the generated Gantt chart reflects both production scheduling and intermittent state control decision outcomes, resulting in a 1.51% reduction in makespan, and 3.90% reduction in total energy consumption. Full article