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Background To date, genome-scale analyses in the domestic horse have been limited by suboptimal single nucleotide polymorphism (SNP) density and uneven genomic coverage of the current SNP genotyping arrays. The recent availability of whole genome sequences has created the opportunity to develop a next generation, high-density equine SNP array. Results Using whole genome sequence from 153 individuals representing 24 distinct breeds collated by the equine genomics community, we cataloged over 23 million de novo discovered genetic variants. Leveraging genotype data from individuals with both whole genome sequence, and genotypes from lower-density, legacy SNP arrays, a subset of ~5 million high-quality, high-density array candidate SNPs were selected based on breed representation and uniform spacing across the genome. Considering probe design recommendations from a commercial vendor (Affymetrix, now Thermo Fisher Scientific) a set of ~2 million SNPs were selected for a next-generation high-density SNP chip (MNEc2M). Genotype data were generated using the MNEc2M array from a cohort of 332 horses from 20 breeds and a lower-density array, consisting of ~670 thousand SNPs (MNEc670k), was designed for genotype imputation. Conclusions Here, we document the steps taken to design both the MNEc2M and MNEc670k arrays, report genomic and technical properties of these genotyping platforms, and demonstrate the imputation capabilities of these tools for the domestic horse.

We used whole genome resequencing of pooled individuals to develop a high‐density single‐nucleotide polymorphism (SNP) chip for Eucalyptus. Genomes of 240 trees of 12 species were sequenced at 3.5× each, and 46 997 586 raw SNP variants were subject to multivariable filtering metrics toward a multispecies, genome‐wide distributed chip content. Of the 60 904 SNPs on the chip, 59 222 were genotyped and 51 204 were polymorphic across 14 Eucalyptus species, providing a 96% genome‐wide coverage with 1 SNP/12–20 kb, and 47 069 SNPs at ≤ 10 kb from 30 444 of the 33 917 genes in the Eucalyptus genome. Given the EUChip60K multi‐species genotyping flexibility, we show that both the sample size and taxonomic composition of cluster files impact heterozygous call specificity and sensitivity by benchmarking against ‘gold standard’ genotypes derived from deeply sequenced individual tree genomes. Thousands of SNPs were shared across species, likely representing ancient variants arisen before the split of these taxa, hinting to a recent eucalypt radiation. We show that the variable SNP filtering constraints allowed coverage of the entire site frequency spectrum, mitigating SNP ascertainment bias. The EUChip60K represents an outstanding tool with which to address population genomics questions in Eucalyptus and to empower genomic selection, GWAS and the broader study of complex trait variation in eucalypts.

Background Black point is a serious threat to wheat production and can be managed by host resistance. Marker-assisted selection (MAS) has the potential to accelerate genetic improvement of black point resistance in wheat breeding. We performed a genome-wide association study (GWAS) using the high-density wheat 90 K and 660 K single nucleotide polymorphism (SNP) assays to better understand the genetic basis of black point resistance and identify associated molecular markers. Results Black point reactions were evaluated in 166 elite wheat cultivars in five environments. Twenty-five unique loci were identified on chromosomes 2A, 2B, 3A, 3B (2), 3D, 4B (2), 5A (3), 5B (3), 6A, 6B, 6D, 7A (5), 7B and 7D (2), respectively, explaining phenotypic variation ranging from 7.9 to 18.0%. The highest number of loci was detected in the A genome (11), followed by the B (10) and D (4) genomes. Among these, 13 were identified in two or more environments. Seven loci coincided with known genes or quantitative trait locus (QTL), whereas the other 18 were potentially novel loci. Linear regression showed a clear dependence of black point scores on the number of favorable alleles, suggesting that QTL pyramiding will be an effective approach to increase resistance. In silico analysis of sequences of resistance-associated SNPs identified 6 genes possibly involved in oxidase, signal transduction and stress resistance as candidate genes involved in black point reaction. Conclusion SNP markers significantly associated with black point resistance and accessions with a larger number of resistance alleles can be used to further enhance black point resistance in breeding. This study provides new insights into the genetic architecture of black point reaction.

Background Comparing mutation patterns and population-specific genetic signatures, such as single-nucleotide polymorphisms (SNPs), is of fundamental importance in genetic and genomic studies today. The problem is challenging because it falls into the category of NP-hard problems, meaning that the computational time increases exponentially, or even faster, as the problem size grows. Additionally, existing approaches often fails to account for the exact number of SNPs per gene (gene-SNP abundance) nor their distribution across populations, hindering the detection of genes that are uniquely or richly mutated in specific groups. Results To bridge this gap, by harnessing gene-SNP abundance and distribution information as well as their heterogeneity across individuals and populations, we develop the SnpC (SNP comparison) method (framework) for detecting genes with unique or enriched SNPs, referred to as unique genes (UGs) and enriched genes (EGs) for specific population. The power of SnpC lies in two novel metrics: Gene-SNP Heterogeneity (GSH), which identifies genes with unique or enriched number of SNPs in one population compared to others, and Population Gene-SNP Diversity (PGSD), which measures the population-level diversity of gene mutations including SNP. These metrics are coupled with robust permutation tests to provide statistical significance. Conclusions We demonstrate SnpC on data from the 1000 Genomes Project, where it successfully catalogs population-specific (unique/enriched) genes and quantifies their inter-population mutation diversity pattern. SnpC delivers a unique, actionable output for gene prioritization in association studies and comparative population genomic analysis. It is easily extended to other variation types, and the R code is provided in the article's supplements.

Gao et al. have proposed a facile method of silica nanoparticle synthesis called the solvent varying technique (SVT). Silica nanoparticles (SNPs) have been synthesized using the SVT. The diameters of the SNPs produced by these recipes are sensitive to drying temperature especially when they are used to form photonic crystal films on the surface of textiles. The colour appearance of the coated fabrics can be affected by unused reactants from the colloidal suspensions. These form a thin layer on the surface of the SNPs, which can adversely affect the constructive interference of light from the photonic crystal. In this paper, the original SNP solutions have been processed using a centrifuge and solvent replacement technique in order to reduce this problem. A TEM was used to record the morphology of the surface of the original and centrifuged particles. The resultant images show that there were fewer impurities present on the surface of the centrifuged SNPs than that of the original SNPs. DLS was used to measure the diameters and dispersion of the original and the centrifuged particles. A spectrophotometer was used to measure the reflectance of the samples. The chromaticities of the coated fabrics using both the original and centrifuged SNPs dried at a range of temperatures (40 °C, 60 °C, 80 °C and 100 °C) have been compared. It was determined that the centrifuged SNPs could be dried at higher temperatures than previously reported with little effect on the colour appearance of the photonic crystals.

Starch is affected by several limitations, e.g., retro-gradation, high viscosity even at low concentrations, handling issues, poor freeze–thaw stability, low process tolerance, and gel opacity. In this context, physical, chemical, and enzymatic methods have been investigated for addressing such limitations or adding new attributes. Thus, the creation of biomaterial-based nanoparticles has sparked curiosity. Because of that, single nucleotide polymorphisms are gaining a lot of interest in food packaging technology. This is due to their ability to increase the mechanical and water vapor resistance of the matrix, as well as hide its re-crystallization during storage in high-humidity atmospheres and enhance the mechanical properties of films when binding in paper machines and paper coating. In medicine, single nucleotide polymorphisms (SNPs) are suitable as carriers in the field of drug delivery for immobilized bioactive or therapeutic agents, as well as wastewater treatments as an alternative to expensive activated carbons. Starch nanoparticle preparations can be performed by hydrolysis via acid hydrolysis of the amorphous part of a starch molecule, the use of enzymes such as pullulanase or isoamylase, or a combination of two regeneration and mechanical treatments with the employment of extrusion, irradiation, ultrasound, or precipitation. The possibility of obtaining cheap and easy-to-use methods for starch and starch derivative nanoparticles is of fundamental importance. Nano-precipitation and ultra-sonication are rather simple and reliable methods for nanoparticle production. The process involves the addition of a diluted starch solution into a non-solvent, and ultra-sonication aims to reduce the size by breaking the covalent bonds in polymeric material due to intense shear forces or mechanical effects associated with the collapsing of micro-bubbles by sound waves. The current study focuses on starch nanoparticle manufacturing, characterization, and emerging applications.

[This corrects the article DOI: 10.3389/fimmu.2025.1725218.].

The solvent varying technique (SVT) provides a simple method for the production of uniform batches of silica nanoparticles (SNPs) of a target average diameter. SNPs synthesized using the SVT have been observed to agglomerate over increasing storage times leading to an increase in average particle diameter. Since the particle diameters of the SNPs produced using the SVT may vary over increasing storage durations, the previous model, suggested by Gao et al., which is based on the diameter of the original SNPs, is unreliable when predicting a target particle diameter using the initial volume of ethanol. A centrifuge and replacement of solvent method has been applied in this investigation to the SNP solutions created using the SV technique. This reduces the amount of unused reactants in the centrifuged colloidal suspensions, which further improves the quality of the SNPs and hence any subsequent photonic crystals. Post centrifuge and replace, the morphology of the centrifuged particles is more uniform than that of the original particles, which has been evaluated using SEM micrographs. The face-centered cubic (FCC) structures observed on the surface of the photonic crystal films have also been imaged using a SEM. A linear equation for the prediction of the SNP diameters for a given initial amount of ethanol is proposed based on the centrifuged SNP diameters. The particle diameter measurements for the new equation were recorded using a DLS instrument. The dispersion of the SNPs was also recorded using DLS. The morphology of the surface of the particles has been confirmed using TEM micrographs.

Background Single nucleotide polymorphisms (SNPs) have emerged as the marker of choice in breeding and genetics, particularly in non-model organisms such as black pepper ( Piper nigrum L.), a globally recognized spice crop. This study presents a comprehensive catalog of SNPs in the black pepper genome using data from 30 samples obtained from RNA sequencing and restriction site-associated DNA sequencing, retrieved from the Sequence Read Archive, and their consequences at the sequence level. Results Three SNP calling and filtering pipelines, namely BCFtools, Genome Analysis Toolkit (GATK)-soft filtering, and GATK-hard filtering, were employed. Results revealed 498,128, 396,003, and 312,153 SNPs respectively identified by these pipelines, with 260,026 SNPs commonly detected across all methods. Analysis of SNP distribution across the 45 scaffolds of the black pepper genome showed varying densities, with pseudo-chromosomes Pn25 (0.86 SNPs/kb), Pn8 (0.74 SNPs/kb), and Pn7 (0.72 SNPs/kb) exhibiting the highest densities. Conversely, scaffolds Pn27 to Pn43 exhibited minimal SNP distribution, except Pn45. Approximately 34.80% of SNPs exhibited stronger genetic linkage ( r 2   >  0.7). Moreover, SNPs predominately mapped to downstream (≈ 32.54%), upstream (≈ 22.52%), and exonic (≈ 16.20%) regions of genes. Transition substitution accounted for the majority (≈ 57.42%) of identified SNPs, resulting in an average transition-to-transversion ratio of 1.36. Notably, 56.09% of SNPs were non-synonymous, with a significant proportion (≈ 53.59%) being missense mutations. Additionally, 12,491 SNPs with high or moderate impacts were identified, particularly in genes associated with secondary metabolism and alkaloid biosynthesis pathways. Furthermore, the expression of 675 genes was potentially influenced by local (cis-acting) SNPs, while 554 genes were affected by distal (trans-acting) SNPs. Conclusion The findings of the present study underscore the utility of identified SNPs and their targets, especially those impacting important pathways, for future genetic investigations and crop improvement efforts in black pepper. The characterization of SNPs in genes related to secondary metabolism and alkaloid biosynthesis highlights their potential for targeted breeding aimed at enhancing the yield, quality, and resilience of this economically important crop in diverse environmental conditions.

β-Carotene intake and tissue/blood concentrations have been associated with reduced incidence of several chronic diseases. Further bioactive carotenoid-metabolites can modulate the expression of specific genes mainly via the nuclear hormone receptors: retinoic acid receptor- and retinoid X receptor-mediated signalling. To better understand the metabolic conversion of β-carotene, inter-individual differences regarding β-carotene bioavailability and bioactivity are key steps that determine its further metabolism and bioactivation and mediated signalling. Major carotenoid metabolites, the retinoids, can be stored as esters or further oxidised and excreted via phase 2 metabolism pathways. In this review, we aim to highlight the major critical control points that determine the fate of β-carotene in the human body, with a special emphasis on β-carotene oxygenase 1. The hypothesis that higher dietary β-carotene intake and serum level results in higher β-carotene-mediated signalling is partly questioned. Alternative autoregulatory mechanisms in β-carotene / retinoid-mediated signalling are highlighted to better predict and optimise nutritional strategies involving β-carotene-related health beneficial mediated effects.