Search Results (1,991)

Background: Chromosomal aneuploidy, characterized by an abnormal number of chromosomes, represents a significant cause of genetic disorders. While karyotyping and chromosomal microarray analysis (CMA) are established diagnostic approaches, they are limited by cost and extended turnaround times. Advances in exome sequencing (ES) bioinformatics enable detection of chromosomal aneuploidy alongside single-nucleotide variant analysis. This study explores the utility of clinical ES for the detection of aneuploidies. Method: We analyzed exome sequencing data (2023–2024) from samples positive for Trisomy 21 (n = 27), Trisomy 18 (n = 4), Turner syndrome (n = 3), and Klinefelter syndrome (n = 2) from our clinical ES cohort (n = 10,000). Results: The results obtained were concordant with copy number variants (CNVs) identified by clinical testing. Conclusion: In conclusion, our findings suggest that exome sequencing offers a rapid and viable approach for the detection of chromosomal aneuploidy, potentially reducing turnaround time and associated costs. Full article

Background/Objective: Prenatal cytogenetic testing is essential for pregnant women who are at high risk of having a child with a chromosomal abnormality. While conventional karyotyping detects large aneuploidies and structural rearrangements (>5–10 Mb), chromosomal microarray analysis (CMA) identifies smaller copy number variants (CNVs), increasing the diagnostic yield by approximately 5%. CMA is now recommended as the first-line test for evaluating fetal structural anomalies that are detected by ultrasound. Method: From March 2023 to September 2024, we analyzed 344 prenatal samples using conventional karyotyping and SNP-based CMA. Karyotyping was performed via flask culture, and CMA was conducted using the Infinium Global Screening Array Cyto (GSA-Cyto) on the Illumina iScan platform. We interpreted the CNVs using NxClinical v6.0 and curated databases including ClinVar, DECIPHER, OMIM, and ClinGen, among others. Our results aligned with the GRCh37/hg19 reference genome. Results: Chromosomal abnormalities were identified in 57/344 cases (16.5%). Of these, 39 cases were numerical chromosomal anomalies, and 18 cases were pathogenic or likely pathogenic CNVs. Notably, 11 CNVs (3.2%) were undetectable by conventional karyotyping, emphasizing the added value of CMA. Conclusions: CMA enhances the prenatal diagnostic accuracy by detecting submicroscopic CNVs that are not visible with conventional methods, supporting the routine use of this analysis in prenatal genetic evaluation. Full article

Background: The Dirigent (DIR) gene family is pivotal for lignin polymerization and stress adaptation in plants, yet its systematic characterization in Sorghum bicolor (S. bicolor), a critical bioenergy crop, remains underexplored. Methods: Leveraging the S. bicolor genome database, we conducted a genome-wide identification, phylogenetic classification, and expression profiling of the DIR gene family. Evolutionary dynamics, gene structure variations, promoter cis-regulatory elements, and spatiotemporal transcriptome patterns were analyzed using bioinformatics and experimental validation (RT-qPCR). Results: A total of 53 SbDIR genes were systematically identified, exhibiting uneven chromosomal distribution. Phylogenetic analysis clustered them into five clades (DIR-a, DIR-b/d, DIR-c, DIR-e, DIR-f), with subfamily-specific exon number variations suggesting functional divergence. Evolutionary studies revealed tandem duplication (TD) as the primary driver of family expansion, accompanied by strong purifying selection. Promoter analysis highlighted abundant hormone- and stress-responsive cis-elements. Tissue-specific RNA-seq data revealed root-enriched expression of SbDIR2/4/18/39/44/53, implicating their roles in root development. Notably, SbDIR39 and SbDIR53 were significantly upregulated (2.8- and 5-fold, respectively) under 150 mM NaCl stress, underscoring their stress-responsive functions. Conclusions: This study provides the first comprehensive atlas of the DIR gene family in S. bicolor, elucidating its evolutionary mechanisms and tissue-specific/stress-induced expression profiles. Key candidates (SbDIR39/53) were identified as promising targets for molecular breeding or CRISPR-based editing to enhance stress resilience in S. bicolor. These findings lay a foundation for translating genomic insights into agronomic improvements. Full article

PR/SET domain 2 (PRDM2)/RIZ is a member of the histone/protein methyltransferases (PRDMs) superfamily. Discovered to have the ability to bind retinoblastoma in the mid-1990s, PRDM2 was assumed to play a role in neuronal development. Like other family members characterized by a conserved N-terminal PR structural domain and a classical C2H2 zinc-finger array at the C-terminus, PRDM2 encodes two major protein types, the RIZ1 and RIZ2 isoforms. The two subtypes differ in the presence or absence of the PR domain: the RIZ1 subtype has the PR domain, whereas the RIZ2 subtype lacks it. The PR domain exhibits varying conservation levels across species and shares structural and functional similarities with the catalytic SET domain, defining histone methyltransferases. Functioning as an SET domain, the PR domain possesses protein-binding interfaces and acts as a lysine methyltransferase. The variable number of classic C2H2 zinc fingers at the C-terminus may mediate protein–protein, protein–RNA, or protein–DNA interactions. An imbalance in the RIZ1/RIZ2 mechanism may be an essential cause of malignant tumors, where PR-positive isoforms are usually lost or downregulated. Conversely, PR-negative isoforms are always present at higher levels in cancer cells. RIZ1 isoforms are also important targets for estradiol interaction with hormone receptors. PRDM2 can regulate gene transcription and expression combined with transcription factors and plays a role in the development of several systemic diseases through mRNA expression deletion, code-shift mutation, chromosomal deletion, and missense mutation occurrence. Thus, PRDM2 is a key indicator for disease diagnosis, but it lacks systematic summaries to serve as a reference for study. Therefore, this paper describes the structure and biological function of PRDM2 from the perspective of its role in various systemic diseases. It also organizes and categorizes its latest research progress to provide a systematic theoretical basis for a more in-depth investigation of the molecular mechanism of PRDM2’s involvement in disease progression and clinical practice. Full article

Background and Clinical Significance: The 45,X0/46,XY mosaic karyotype is categorized as a disorder of sex development and can lead to atypical sexual development. Latent mosaicism involving Y chromosomal segments may be much more prevalent than previously assumed, according to a growing number of findings. This primarily depends on how sensitive cytogenetic methods are—such as traditional karyotype screening, FISH methods, or molecular analyses. Case Presentation: We present the case of a 10-week-old infant with hermaphroditic external genitalia. During pregnancy, ultrasonography revealed severe fetal development difficulties, including severe widespread edema. An abnormal 45,X0/46,XY mosaic karyotype was discovered during a genetic amniocentesis conducted during the 16th week of pregnancy. The infant was born in average general condition at 39 + 6 weeks of gestation. Physical examination of the infant revealed features of facial dysmorphia, webbed neck, and hermaphroditic external genitalia. The testicle was palpable on the left side, but the gonad was absent on the right. Laboratory tests revealed a typical hormonal profile of the mini-puberty period in boys. Moreover, a hormone panel and thyroid ultrasound were performed; congenital hypothyroidism was diagnosed. Three separate independent sources of biological material were used in cytogenetic analysis to determine the karyotype: skin fibroblasts (to confirm tissue mosaicism), oral epithelial cells (FISH), and peripheral blood lymphocytes. It showed that a mosaic occurred very early in embryogenesis by confirming the existence of karyotypes 45,X and 46,XY in various tissues (mosaic tissue distribution). Conclusions: Tissue mosaicism should be compared to the analysis of tissues from other embryonic origins, including blood and oral tissue. Support for gender identity and treatment decisions, including the prediction of the future risk of gonadoblastoma, as well as multidisciplinary care, is necessary. Full article

Leaf morphology significantly impacts rice (Oryza sativa L.) plant architecture and yield. Here, we identified and characterized a novel narrow-leaf mutant, nal25, derived from indica rice cultivar ‘Huazhan’ using EMS mutagenesis. Phenotypic analyses revealed that nal25 exhibited significantly narrower leaves, reduced plant height, increased tiller number, and notably decreased grain size, seed setting rate, and thousand-grain weight compared to the wild type. Genetic analyses demonstrated that the narrow-leaf phenotype is controlled by a single recessive nuclear gene. Through precise localization analysis, the NAL25 gene was located within a region of approximately 103 kb on the long arm of rice chromosome 7. The sequencing results showed that the mutant nal25 had a T to C mutation at position 173 of the heat-shock protein gene LOC_Os07g09450 encoding the DnaJ domain in this interval, resulting in a change in amino acid 58 from leucine to proline. The qRT-PCR results showed that the expression level of NAL25 gene decreased in the mutant. The nal25 mutant obtained in this study exhibits stable mutant phenotypes, including dwarfism and excessive tillering, traits typically unfavorable for rice production. Nevertheless, it serves as valuable genetic material for forward genetics approaches to identify yield-related genes regulating leaf morphology and culm height. Thus, research on the nal25 mutant advances the development of rice varieties with ideal plant architecture, thereby stabilizing yield increases and safeguarding global food security. Full article

In this study, we performed whole-genome resequencing (WGS) to investigate genomic variation and functional divergence among four wild Cymbidium species—C. ensifolium, C. sinense, C. kanran, and C. floribundum—collected from Fujian Province, China. A total of 350.58 Gbp of high-quality sequencing data was obtained from 13 samples, enabling comprehensive identification of SNPs and InDels. Genomic variants were unevenly distributed, with lower variation in gene-rich regions and higher levels in non-coding areas. Circos plots and variant density heatmaps revealed significant regional differences across chromosomes, with longer chromosomes exhibiting greater variant enrichment in 1 Mb windows. C. floribundum harbored the highest number of nonsynonymous SNPs and InDel-associated genes, whereas C. sinense and C. kanran had fewer mutations. KEGG pathway enrichment analysis revealed species-specific functional divergence, particularly in metabolism, stress response, and secondary metabolite biosynthesis. Population structure analysis and principal component analysis (PCA) indicated genetic differentiation among these species Notably, C. kanran exhibited high within-population genetic diversity. These findings provide essential genomic resources for the conservation and functional studies of wild Cymbidium species in subtropical China. Full article

As a key tropical economic tree species, the girth of the rubber tree (Hevea brasiliensis) not only reflects its growth rate and timber yield but also determines tapping schedules and non-productive periods. This trait critically influences both the species’ economic value and latex production potential. Despite recent advances in genetic analyses of girth driven by genomic technologies, the number of identified key genes remains insufficient to support molecular breeding programs. This study focuses on 138 samples of rubber tree natural accessions, integrating phenotypic data analysis, population genetic structure analysis, and genome-wide association analysis (GWAS) to identify genetic loci and candidate genes associated with girth. Population stratification divides the tested accessions into four genetic groups: Groups Ⅰ and Ⅳ exhibit high genetic purity, while Groups Ⅱ and Ⅲ display hybrid characteristics. GWAS based on a mixed linear model detects 7 and 23 SNPs significantly associated with girth at p = 4.4 × 10⁻⁸ and p = 2.22 × 10⁻⁷, respectively. The most significant SNP is located at position 44994744 on chromosome CM021229.1. Under the highly significant association threshold, 27 candidate genes were identified, 4 of which are directly related to girth. Gene Ontology (GO) annotation of these 27 candidate genes reveals their primary involvement in metabolic regulation, signal transduction, and cell component construction. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis shows they are primarily enriched in the “aminoacyl-tRNA biosynthesis” and “glycolysis/gluconeogenesis” pathways. These findings provide significant theoretical support for genetic enhancement and mechanistic analysis of rubber tree growth traits. They reveal novel SNP markers and genes that complement existing genetic resources, refining breeding strategies for elite genotype selection and ultimately contributing to enhanced rubber production. Full article

In this paper, we propose a crossover operator for genetic algorithms with binary chromosomes populations based on the cellular automata ($\mathit{CGACell}$). After presenting the fundamental elements regarding cellular automata with specific examples for one- and two- dimensional cases, the the most widely used crossover operators in applications with genetic algorithms are described, and the crossover operator based on cellular automata is defined. Specific forms of the crossover operator based on the ECA and 2D CA cases are described and exemplified. The $\mathit{CGACell}$ crossover operator is used in the genetic structure to improved the KNN algorithm in terms of the parameter represented by the number of nearest neighbors selected by the data classification method. Validity and practical performance testing are performed on image data classification problems by optimizing the nearest-neighbors-based algorithm. The experimental study on the proposed crossover operator, by comparing a GA algorithm based on $\mathit{CGACell}$ with GA algorithms based on other crossover methods, including classical GAs and permutation-based, heuristic, and hybrid methods, attests to good qualitative performance in terms of correctness percentages in the recognition of new images, as well as in classification and recognition applications of facial image classes corresponding to several persons. Full article

Chimonanthus praecox, a traditional ornamental plant in China, is admired for its ability to bloom during the cold winter season and is recognized as an outstanding woody cut flower. MADS-box genes encode transcription factors essential for plant growth and development, with key functions in regulating flowering time and the formation of floral organs. In this study, 74 MADS-box genes (CpMADS1–CpMADS74) were identified and mapped across 11 chromosomes, with chromosome 1 harboring the highest number (13 genes) and chromosome 3 the fewest (3 genes). Physicochemical property analysis revealed that all CpMADS proteins are hydrophilic and predominantly nuclear-localized. Phylogenetic analysis classified these genes into Type I and Type II subfamilies, highlighting a clear divergence in domain structure. Eighty simple sequence repeat (SSR) loci were detected, with dinucleotide repeats being the most abundant, and the majority located in Type II MADS genes. From 23 C. praecox samples, 10 polymorphic SSR markers were successfully developed and PCR-validated, enabling a cluster analysis that grouped these cultivars into three distinct clusters. This study offers significant insights into the regulation of flowering, floral organ development, genetic linkage map construction, and the application of marker-assisted selection in C. praecox. Full article

Genomes of animals harbor not only homozygous (ROH) but also HRR segments of chromosomes. In the current study, the HRRs in Holstein cattle were analyzed using a 50K array. On average, 366 Holstein cows from six herds had 439 ± 7 and 111 ± 3 HRRs per cow when HRRs with a minimum length of 50 kb and 250 kb were detected, respectively. The average HRRs values did not differ between herds. Removal of SNP with an MAF less than 0.01 leads to a noticeable increase in the number of HRRs. The distribution of HRRs in the chromosomes of cows is not uniform and depends on the scanned lengths of the HRR segments. No clear correlations were found between interchromosomal HRR specific density and the occurrence of HRRIs. When HRR segments with a length of 50 kb or more have been detected, the significant HRRIs were located on BTA1, BTA10, BTA20, and BTA21(first set); for HRR segments with a length of 250 kb or more, significant islands were found on BTA9, BTA11, and BTA29 (second set). According to the Tajima D test, the islands on the BTA of the first set have maximum values of 3.47–2.82, while the islands on the BTA of the second set have values of less than 2.49. The genes in the HRRIs are involved in immune response, oogenesis, and reproduction but are not related to milk production traits. These results show that the recognition of HRRIs strongly depends on the length of the scanned HRR segments. No single “mechanism” was identified as the main cause of HRRIs. Full article

Rubus magurensis Wolanin, M. Nobis & Oklej. (Rosaceae), a new species from the Northern Carpathians, described and illustrated here, is a tetraploid (2n = 28) belonging to the subgenus Rubus series Micantes. Among the most characteristic features of this species are first-year stems that are almost glabrous, leaflets most often arched downward, and inflorescences leafy to the apex with a few simple oval leaves in the upper part, which make this species easy to recognise. This species resembles R. tabanimontanus Figert, from which it differs in having smaller primocane prickles, digitate to subpedate leaves, larger flowers, and inflorescences leafy to the apex. Rubus magurensis is currently known from 11 populations located in southeastern Poland (7 ATPOL 2 × 2 km units). Most of them were found in the central part of the Low Beskid Mts., with two populations located in the northwestern part of the Strzyżów Foothills. Full article

More than 5.9 million plant germplasm accessions currently conserved in over 850 national genebanks worldwide will accumulate deleterious mutations over long-term conservation. However, little is known about how mutations accumulate in germplasm under long-term conservation. An attempt was made using seed-based RNA-Seq analysis to identify and characterize deleterious genetic variants in 190 diverse soybean accessions that were conserved since 1972 and were regenerated up to 10 cycles. The analysis identified 588 deleterious variants, which were widely distributed across 20 soybean chromosomes, mostly present in 10 or fewer samples, associated with diverse biological processes, and largely predicted to be weakly and mildly detrimental. Significant differences in estimates of three mutation burdens (total, heterozygous, and homozygous) were found among the samples, including sample groups representing different countries of origin. Total and heterozygous mutation burden estimates were found to increase significantly with the number of conservation years since accession acquisition and the number of germplasm regenerations, but homozygous mutation burden estimates were not correlated with these two conservation-related accession features. Total mutation burden estimates were negatively correlated with expressed gene counts and RNA integrity numbers (RINs) and marginally positively associated with averaged gene expression levels. Correlations were also found among expressed gene count, averaged gene expression level, and RIN value. No significant differences were detected between seed-based and leaf-based estimates of total mutation burden, expressed gene count, averaged expression level, and RIN. These findings provide the first empirical evidence that total mutation burden increased primarily through the accumulation of heterozygous, rather than homozygous, deleterious mutations over successive soybean germplasm regenerations. This insight is useful for conducting informative assessments of deleterious mutation accumulation and enhancing the management and conservation of plant germplasm. Full article

Artificial gynogenesis is an essential technique for aquaculture breeding. Fertile offspring of the WuLi carp (Cyprinus carpio var. Quanzhounensis, 2n = 100, WLC) were successfully produced via gynogenesis using ultraviolet-irradiated sperm from the blunt snout bream (Megalobrama amblycephala, 2n = 48, BSB). As anticipated, gonadal section examination confirmed that all gynogenetic WuLi carp (2n = 100, GWB) were female. To investigate whether paternal DNA fragments from BSB were integrated into the GWB genome, comparative analyses of morphological traits, DNA content, chromosomal numbers, 5S rDNA sequences, microsatellite DNA markers, fluorescence in situ hybridization (FISH), growth performance and nutritional composition were systematically conducted between GWB and maternal WLC. The results revealed pronounced maternal inheritance patterns across morphological characteristics, DNA quantification, chromosomal configurations, 5S rDNA sequences and FISH signals, while microsatellite detection unequivocally confirmed paternal BSB DNA fragment integration into the GWB genome. Remarkably, GWB demonstrated significantly superior growth performance and elevated unsaturated fatty acid content relative to the maternal line. This approach not only addressed germplasm degradation in WLC but also provided valuable theoretical foundations for breeding programs in this commercially significant species. Full article

Potato (Solanum tuberosum L.) crop yields may be reduced by nitrogen deficiency stress tolerance. An evaluation of 144 tetraploid potato genotypes was carried out during two consecutive seasons (2019 and 2020), with the objective of characterizing their variability in key physiological and agronomic parameters. Physiological parameters included chlorophyll content and fluorescence, stomatal conductance, NDVI, leaf area, and perimeter, while agronomic characteristics such as yield, tuber fresh weight, tuber number, starch content, dry matter, and reducing sugars were evaluated. To genotype the population, the GGP V3 Potato array was used, generating 18,259 high-quality SNP markers. Marker–trait association analysis was conducted using the GWASpoly package in R, applying Q + K linear mixed models to enhance precision. This methodology enabled the identification of 18 SNP markers that exhibited statistically significant associations with the traits analyzed in both trials and periods, relating them to genes whose functional implication has already been described. Genetic loci associated with chlorophyll content and tuber number were detected across non-stress and stress treatments, while markers linked to leaf area and leaf perimeter were identified specifically under nitrogen deficiency stress. The genomic distribution of these markers revealed that genetic markers or single-nucleotide polymorphisms (SNPs) correlated with phenotypic traits under non-stress conditions were predominantly located on chromosome 11, whereas SNPs linked to stress responses were mainly identified on chromosomes 2 and 3. These findings contribute to understanding the genetic mechanisms underlying potato tolerance to nitrogen deficiency stress, offering valuable insights for the development of future marker-assisted selection programs aimed at improving nitrogen use efficiency and stress resilience in potato breeding. Full article