Search Results (643)

Lonicera japonica Thunb. is a traditional Chinese medicinal herb whose floral buds are the primary source of pharmacological compounds that require manual harvesting. As a result, its floral bud duration, determined by the opening time, is a key determinant of both quality and economic value. However, the genetic mechanisms controlling floral bud duration remain poorly understood. In this study, we employed population structure analysis and molecular experiments to identify candidate genes associated with this trait. The improved cultivar Beihua No. 1 (BH1) opens its floral buds significantly later than the landrace Damaohua (DMH). Exogenous application of methyl jasmonate (MeJA) to BH1 indicated that jasmonate acts as a negative regulator of floral bud duration by accelerating floral bud opening. A genome-wide selection scan across 35 germplasms with varying floral bud durations identified the transcription factor LjWRKY50 as the causative gene influencing this trait. The dual-luciferase reporter assay and qRT-PCR experiments showed that LjWRKY50 activates the expression of the jasmonate biosynthesis gene, LjAOS. A functional variant within LjWRKY50 (Chr7:24636061) was further developed into a derived cleaved amplified polymorphic sequence (dCAPS) marker. These findings provide valuable insights into the jasmonate-mediated regulation of floral bud duration, offering genetic and marker resources for molecular breeding in L. japonica. Full article

Corn smut, caused by Ustilago maydis, significantly threatens maize production. This study evaluated 199 maize inbred lines at the seedling stage under greenhouse conditions for resistance to U. maydis, identifying 39 highly resistant lines. A genome-wide association study (GWAS) using the mrMLM model detected 19 significant single-nucleotide polymorphism (SNP) loci. Based on a linkage disequilibrium (LD) decay distance of 260 kb, 226 candidate genes were identified. Utilizing the significant loci chr1_244281660 and chr5_220156746, two kompetitive allele-specific PCR (KASP) markers were successfully developed. A PCR-based sequence-specific oligonucleotide probe hybridization technique applied to the 199 experimental lines and 60 validation lines confirmed polymorphism for both markers, with selection efficiencies of 48.12% and 43.33%, respectively. The tested materials were derived from foundational inbred lines of domestic and foreign origin. Analysis of 39 highly resistant lines showed that the advantageous alleles carrying thymine/cytosine (T/C) predominated at frequencies of 94.87% and 53.84%, respectively. The genotype TTCC conferred high resistance, while CCTT was highly susceptible. The resistance exhibited high heritability and significant gene-by-environment interaction. This work systematically dissects the genetic basis of common smut resistance in maize, identifies favorable alleles, and provides a novel KASP marker-based strategy for developing disease-resistant germplasm. Full article

Nitrogen use efficiency remains the primary bottleneck for sustainable maize production. This study elucidates the functional mechanisms of the amino acid transporter ZmAAP1 in nitrogen absorption and stress resilience. Through systematic evolutionary analysis of 55 maize inbred lines, we discovered that the ZmAAP1 gene family exhibits distinct chromosomal localization (Chr7 and Chr9) and functional domain diversification (e.g., group 10-specific motifs 11/12), indicating species-specific adaptive evolution. Integrative analysis of promoter cis-elements and multi-omics data confirmed the root-preferential expression of ZmAAP1 under drought stress, mediated via the ABA-DRE signaling pathway. To validate its biological role, we generated transgenic maize lines expressing Arabidopsis thaliana AtAAP1 via Agrobacterium-mediated transformation. Three generations of genetic stability screening confirmed the stable genomic integration and root-specific accumulation of the AtAAP1 protein (Southern blot/Western blot). Field trials demonstrated that low-N conditions enhanced the following transgenic traits: the chlorophyll content increased by 13.5%, and the aboveground biomass improved by 7.2%. Under high-N regimes, the gene-pyramided hybrid ZD958 (AAP1 + AAP1) achieved a 12.3% yield advantage over conventional varieties. Our findings reveal ZmAAP1’s dual role in root development and long-distance nitrogen transport, establishing it as a pivotal target for molecular breeding. This study provides actionable genetic resources for enhancing NUE in maize production systems. Full article

Background: Medullary thyroid carcinoma (MTC) has a high rate of local and distant metastases. In particular, the RET protooncogene appears to be the predominant driver mutation for oncogenesis. The German S3 thyroid carcinoma guidelines recommend molecular genetic analysis of the tumour without specifying the site of the tissue sampling. Whether there is difference in RET protooncogene between the primary tumour, lymph node, and distant metastasis has not yet been investigated. However, differences could be important with regard to biopsy localization, and also, thus, the choice of single- or multi-tyrosine-kinase-inhibitor therapy. Methods: In a case of sporadic MTC, Cancer Hotspot panel diagnostics were performed on the primary tumour, lymph node metastasis, and distant metastasis. Mutations were classified using different gene databases, and the different stages of metastasis were compared. Results: RET protooncogene (chr10:43609933, c.1886_1891delTGTGCG, p.Leu629_Asp631delinsHis) was found to be present in the MTC tissue of the primary tumour, lymph node, and distant metastasis in the Cancer Hotspot Panel diagnostic, while the other investigated therapy-relevant mutational profiles were not consistently found. Conclusions: Further longitudinal studies in larger patient cohorts are required to elucidate the role of the RET protooncogene in the metastatic progression of MTC and to determine its impact on the selection of biopsy sites and the subsequent decision-making regarding single- versus multi-tyrosine kinase inhibitor therapy. Full article

Long- or post-COVID-19 syndrome, which is also designated by WHO as Post COVID-19 Condition (PCC), is characterized by the persistent symptoms that remain after recovery from SARS-CoV-2 infection. A worldwide consortium of Long COVID-19 Host Genetics Initiative (Long COVID-19 HGI) identified an SNP rs9367106 (G>C; chr6:41,515,652, GRCh38, p = 1.76 × 10⁻¹⁰, OR = 1.63, 95% CI: 1.40–1.89) that is associated with PCC. Unraveling the functional significance of this SNP is of prime importance to understanding the development of the PCC phenotypes and their therapy. Here, in Silico, I explored how the risk allele of this SNP alters the functional mechanisms and molecular pathways leading to the development of PCC phenotypes. Bioinformatic methods include physical interactions using HI-C and Chia-PET analysis, Transcription Factors (TFs) binding ability, RNA structure modeling, epigenetic, and pathway analysis. This SNP resides within two long RNA genes, LINC01276 and FOXP4-AS1, and is located at ~31 kb upstream of a transcription factor FOXP4. This DNA region, including this SNP, physically interacts with FOXP4-AS1 and FOXP4, implying that this regulatory SNP could alter the normal cellular function of FOXP4-AS1 and FOXP4. Furthermore, rs9367106 is in eQTL with the FOXP4 gene in lung tissue. rs9367106 carrying DNA sequences act as distant enhancers and bind with several transcription factors (TFs) including YY1, PPAR-α, IK-1, GR-α, and AP2αA. The G>C transition extensively modifies the RNA structure that may affect the TF bindings and enhancer functions to alter the interactions and functions of these RNA molecules. This SNP also includes an ALU/SINE sequence and alteration of which by the G>C transition may prevent IFIH1/MDA5 activation, leading to suppression of host innate immune responses. LINC01276 targets the MED20 gene that expresses mostly in brain tissues, associated with sleep disorders and basal ganglia abnormalities similar to some of the symptoms of PCC phenotypes. Taken together, G>C transition of rs9367601 may likely alter the function of all three genes to explain the molecular basis of developing the long-term symptomatic abnormalities in the lungs and brain observed after COVID-19 recovery. Full article

Plant protein phosphatase 2C (PP2C) represents the largest and most functionally diverse group of protein phosphatases in plants, playing pivotal roles in regulating metabolic processes, hormone signaling, stress responses, and growth regulation. Despite its significance, a comprehensive genome-wide analysis of the PP2C gene family in oat (Avena sativa L.) has remained unexplored. Leveraging the recently published oat genome, we identified 194 AsaPP2C genes, which were unevenly distributed across all 21 chromosomes. A phylogenetic analysis of PP2C classified these genes into 13 distinct subfamilies (A-L), with conserved motif compositions and exon-intron structures within each subfamily, suggesting evolutionary functional specialization. Notably, a promoter analysis revealed an abundance of stress-responsive cis-regulatory elements (e.g., MYB, MYC, ARE, and MBS), implicating AsaPP2Cs in hormones and biotic stress adaptation. To elucidate their stress-responsive roles, we analyzed transcriptomic data and identified seven differentially expressed AsaPP2C (Asa_chr6Dg00217, Asa_chr6Ag01950, Asa_chr3Ag01998, Asa_chr5Ag00079, Asa_chr4Cg03270, Asa_chr6Cg02197, and Asa_chr7Dg02992) genes, which were validated via qRT-PCR. Intriguingly, these genes exhibited dynamic expression patterns under varying stress conditions, with their transcriptional responses being both time-dependent and stress-dependent, highlighting their regulatory roles in oat stress adaptation. Collectively, this study provides the first comprehensive genomic and functional characterization of the PP2C family in oat, offering valuable insights into their evolutionary diversification and functional specialization. Full article

Growth traits are the most important economic traits in red tilapia (Oreochromis spp.) production, and are the main targets for its genetic improvement. Increasing salinity levels in the environment are affecting the growth, development, and molecular processes of aquatic animals. Red tilapia tolerates saline water to some degree. However, few credible genetic markers or potential genes are available for choosing fast-growth traits in salt-tolerant red tilapia. This work used genome-wide association study (GWAS) and RNA-sequencing (RNA-seq) to discover genes related to four growth traits in red tilapia cultured in saline water. Through genotyping, it was determined that 22 chromosomes have 12,776,921 high-quality single-nucleotide polymorphisms (SNPs). One significant SNP and eight suggestive SNPs were obtained, explaining 0.0019% to 0.3873% of phenotypic variance. A significant SNP peak associated with red tilapia growth traits was located on chr7 (chr7-47464467), and plxnb2 was identified as the candidate gene in this region. A total of 501 differentially expressed genes (DEGs) were found in the muscle of fast-growing individuals compared to those of slow-growing ones, according to a transcriptome analysis. Combining the findings of the GWAS and RNA-seq analysis, 11 candidate genes were identified, namely galnt9, esrrg, map7, mtfr2, kcnj8, fhit, dnm1, cald1, plxnb2, nuak1, and bpgm. These genes were involved in ‘other types of O-glycan biosynthesis’, ‘glycine, serine and threonine metabolism’, ‘glycolysis/gluconeogenesis’, ‘mucin-type O-glycan biosynthesis’ and ‘purine metabolism signaling’ pathways. We have developed molecular markers to genetically breed red tilapia that grow quickly in salty water. Our study lays the foundation for the future marker-assisted selection of growth traits in salt-tolerant red tilapia. Full article

The El Tor biotype of Vibrio cholerae caused the seventh cholera pandemic (7CP). Although V. cholerae variants of this biotype frequently emerge, studies on their microevolution and spatiotemporal transmission in epidemics caused by a single clone are limited. During the cholera outbreak in Sichuan Province, China, in the 1990s, strains belonging to phage type 6 (PT6) but resistant to typing phage VP5 due to a deletion mutation in ompW, which is the gene associated with the VP5 receptor were identified. In this study, we analyzed PT6 strains using genome sequencing to reveal the genomic and transmission characteristics of such a transient phage type in China’s cholera epidemic history. The findings revealed that the PT6 strains formed an independent clone during the four-year epidemic and emerged in wave 2. Most of them carried multiple CTX^classΦ genome copies on chromosome 2 (Chr. 2) and two copies each of RS1^ET and RS1-4** on chromosome 1 (Chr. 1). Frequent cross-regional transmission and local outbreaks within Sichuan Province, China, were revealed for this clone. A variety of spontaneous mutations in the ompW gene, conferring resistance to the VP5 phage, were observed under VP5 infection pressure, showing the incident mutation of OmpW for the survival adaptation of V. cholerae to phage pressure. Therefore, this genomic epidemiological revisit of these distinct phage-resistant phenotype strains reveals their clonal genetic structure, improves our understanding of the spread of V. cholerae by tracking their variation, and assists in epidemic source tracing and disease control. Full article

Peters anomaly (PA) is a rare congenital disorder within the anterior segment dysgenesis (ASD) spectrum, characterized by corneal opacity, iridocorneal adhesions, and potential systemic involvement. The genetic basis of PA and related syndromes are complex and incompletely understood. This study investigates novel genetic variants and their clinical impact in two unrelated individuals diagnosed with PA spectrum disorder. Whole-exome sequencing (WES), long-range PCR, and breakpoint analysis were applied to identify pathogenic variants. In the first patient, a heterozygous ~1.6 Mb deletion was detected, spanning the genes PEX2 and ZFHX4 (GRCh37 chr8:g.76760782_78342600del). The second patient carried a heterozygous FOXC1 variant (NM_001453.3:c.310A>G), classified as likely pathogenic. Both variants were confirmed by Sanger sequencing and considered de novo, as they were not present in the biological parents. Clinical evaluations revealed phenotypic variability, with the first patient displaying both ocular and systemic anomalies as in a Peters plus-like syndrome phenotype, while the second patient had isolated ocular manifestations as in a PA type 1 phenotype. These findings expand the genetic landscape of PA, underscoring the importance of comprehensive genomic analysis in subclassifying ASD disorders. Further studies are needed to elucidate the functional consequences of these variants and improve diagnostic and therapeutic strategies. Full article

This paper presents an analysis of the time-dependent response of a spherical container to internal pressure that increases over time. The wall of the container is relatively thin, in the sense that the wall thickness is negligible in comparison to the container’s radius. The wall is composed of three layers. The two surface layers of the wall are identical, i.e., they are made from the same material and have the same thickness. One of the most important features regarding the response of the wall layers is the non-linear creep. The stresses and strains are determined, and their relationships with the parameters of the layers are studied. Full article

A pipe subjected to an evenly distributed internal pressure is investigated in this theoretical paper. The pipe has a thin wall that is built-up by a functionally graded engineering material. The circumferential stresses and strains in the pipe wall are investigated. In essence, the current investigation is non-linear since the wall behaves as a non-linear elastic body with non-linearly distributed properties through the wall thickness. The different stages of the work of the wall are investigated and the corresponding parameters of stressed and strained state are derived. The dependence of the pressure on the material and geometrical parameters are studied. Full article

Advances in spinning technology have increased the demand for upland cotton (Gossypium hirsutum L.) cultivars with superior fiber quality. However, progress in breeding for traits such as fiber length is constrained by limited phenotypic and genetic diversity within upland cotton. Introgression from Gossypium barbadense, a closely related species known for its superior fiber traits, offers a promising strategy. Sealand 883 is an obsolete upland germplasm developed through G. barbadense introgression and is known for its long and fine fibers. Previous studies have identified a fiber length quantitative trait locus (QTL) on Chromosome 25, designated qFL-Chr.25, in Sealand 883, conferred by an allele introgressed from G. barbadense. This study evaluated the effect of qFL-Chr.25 in near-isogenic introgression lines (NIILs) using Advanced Fiber Information System (AFIS) measurements. Across four genetic backgrounds, NIILs carrying qFL-Chr.25 consistently exhibited longer fibers, as reflected in multiple length parameters, including UHML, L(n), L(w), UQL(w), and L5%. Newly developed TaqMan SNP diagnostic markers flanking the QTL enable automated, reproducible, and scalable screening of large populations typical in commercial breeding programs. These markers will facilitate the incorporation of qFL-Chr.25 into commercial breeding pipelines, accelerating fiber quality improvement and enhancing the competitiveness of cotton against synthetic fibers. Full article

Autosomal trisomy, a genetic disorder characterized by the presence of an extra autosome, is a rare but important chromosomal abnormality in horses, often associated with infertility, developmental abnormalities, and reduced life expectancy. This study represents the largest population-level screening for autosomal trisomy in horses; the analysis used single nucleotide polymorphism (SNP) panel genotype intensity data from 17,078 horses, 6601 of which were juveniles (i.e., ≤12 months of age) when genotyped. Using methodologies adapted from similar screening studies in cattle, the only aneuploidy detected was trisomy 27 in two juvenile male Irish Sport Horses (ISH) (0.03% prevalence among juveniles or 0.01% prevalence in the overall population). One ISH colt was cytogenetically confirmed and displayed no overt external phenotypic abnormalities, while cytogenetics was not undertaken on the other ISH colt, nor was it phenotypically assessed. Parentage analysis revealed that one ISH colt inherited two different copies of chr27 from the sire, demonstrating heterodisomy, likely due to a nondisjunction event during meiosis I in the sire. The other ISH colt inherited two different copies of chr27 from the dam, also indicating heterodisomy; the dam was 23 years of age when the colt was born. Based on the observed prevalence of autosomal trisomy, it can be estimated that at least 3 foals per 10,000 live births are likely to have autosomal trisomy. Though, given that only 74 (i.e., 0.004%) of horses were genotyped within a month of birth, this is likely an underestimate. The economic consequence of undiagnosed trisomy in high-value breeding horses that are potentially infertile could be substantial. As horse genotyping for parentage verification and discovery is transitioning to medium-density single nucleotide polymorphism panels, routine genomic screening for autosomal aneuploidy could be readily undertaken and potentially should form a standard screening prerequisite along with other genetic defects at horse sales. Currently, thoroughbred horses registered for racing are not genotyped, and only a limited number of sport horse studbooks are using SNP genotyping. This highlights an opportunity for those already genotyping to expand their support for breeders through low-cost, high-value chromosomal screening at the time of registration rather than incurring additional costs over the horse’s life cycle to determine the root cause of certain phenotypes owing to the undiagnosed trisomy. Full article

Plant U-box (PUB) E3 ubiquitin ligases have undergone significant expansion compared to their fungal and animal counterparts. These E3 ligases play critical roles in diverse biological processes, including responses to biotic and abiotic stresses. However, systematic identification of PUB genes in cucumber (Cucumis sativus L.) has been lacking, and their expression and functional characterization remain largely unexplored. Leveraging the recently released near-complete cucumber genome, we identified 53 putative PUB proteins classified into eight distinct groups based on domain architecture. The molecular weights of CsPUBs range from 26 to 166 kilodaltons (kDa). Exon numbers in CsPUB genes vary substantially, with CsPUB48 containing a maximum of 17 exons, while 18 CsPUB genes harbor only a single exon. Chromosomal distribution of CsPUBs is uneven, with Chr 3 harboring the highest density (12 genes) and Chr 7 the lowest (1 gene). Notably, tandem duplications (e.g., CsPUB29-CsPUB36 and CsPUB18-CsPUB49) and seven collinear gene pairs were identified, suggesting evolutionary diversification. Promoter regions of CsPUBs are enriched with cis-regulatory elements linked to plant growth and development, phytohormone, stress responses, light, and so on, implying their regulatory roles in various biological processes. Expression profiling revealed tissue-specific patterns and differential regulation of multiple CsPUBs under stress conditions. Subcellular localization studies demonstrated that CsPUBs target diverse organelles, with some localizing to punctate structures potentially representing uncharacterized compartments. Collectively, this systematic analysis establishes a comprehensive framework for understanding particular CsPUB functions. Full article

Grain size is a crucial agronomic trait that significantly impacts yield potential in sorghum (Sorghum bicolor), making it a key focus for genetic improvement. In this study, we investigated the genetic basis of grain size variation using two contrasting sorghum accessions, PI302232 (small grain, Sg) and PI563512 (large grain, Lg). The 1000-grain weight, grain length, and grain width of Lg were 3.63-fold, 1.22-fold, and 1.65-fold higher than Sg, respectively. The 1000-grain weight in the F₂ segregating population derived from the cross Sg and Lg parents exhibited the highest phenotypic variation and followed a normal distribution in the three traits. Using bulked segregant analysis sequencing (BSA-seq) with small- and large-grain bulks from the F₂ population, two major quantitative trait loci (QTLs) for grain size were identified on chromosomes 1 and 3. Fine mapping with SSR markers narrowed the qGS1 locus to a 1.03 Mb region on chromosome 1 (Chr01: 22,001,448–23,035,593), containing 49 candidate genes. To narrow down potential candidate genes, transcriptome analysis of spike tissues from Sg and Lg at 0 and 14 days after heading revealed 3719 differentially expressed genes (DEGs), primarily enriched in “starch and sucrose metabolism” and “phenylpropanoid biosynthesis” pathways. Integrating fine mapping intervals and RNA-seq data, 6 DEGs were identified within the qGS1 region. Quantitative real-time PCR confirmed that 6 genes exhibited different expression at two stages. The expression and bioinformatics analysis showed Sobic.001G230700 was the most likely candidate gene for the qGS1 locus. This study provides new insights into the genetic regulation of grain size and a new target to improve grain size in sorghum. Full article