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.
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.
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.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
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.
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.
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.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Prostate cancer (PCa) kills one man in forty five and represents the most frequently diagnosed cancer in American men. As is true with cancer, early detection through digital rectal exam and serum ...testing for prostate specific antigen have greatly reduced the number of fatalities yet these same methods sometimes lead to overdiagnosis and overtreatment. Previous studies have highlighted the association between single nucleotide polymorphisms (SNPs) and cancer. In our studies, we sought to find correlations between SNPs on chromosome 8 and PCa. Normal and PCa patient sequencing data was obtained from the Sequence Read Archive and then analysis pipelines were constructed to map the sequences against chromosome 8 followed by indexing and variant calling. Our studies were able to identify four SNPs specific to DNA sequences isolated from prostate cancer tissues but that were absent in normal tissues. We hope that our findings might help improve personalized medicine and possibly reduce the incidences of overdiagnosis and overtreatment of PCa.
Summary
Soybean Glycine max (L.) Merr. is an economically important crop that is grown worldwide. Sudden death syndrome (SDS), caused by Fusarium virguliforme, is one of the top yield‐limiting ...diseases in soybean. However, the genetic basis of SDS resistance, especially with respect to epistatic interactions, is still unclear. To better understand the genetic architecture of soybean SDS resistance, genome‐wide association and epistasis studies were performed using a population of 214 germplasm accessions and 31 914 SNPs from the SoySNP50K Illumina Infinium BeadChip. Twelve loci and 12 SNP–SNP interactions associated with SDS resistance were identified at various time points after inoculation. These additive and epistatic loci together explained 24–52% of the phenotypic variance. Disease‐resistant, pathogenesis‐related and chitin‐ and wound‐responsive genes were identified in the proximity of peak SNPs, including stress‐induced receptor‐like kinase gene 1 (SIK1), which is pinpointed by a trait‐associated SNP and encodes a leucine‐rich repeat‐containing protein. We report that the proportion of phenotypic variance explained by identified loci may be considerably improved by taking epistatic effects into account. This study shows the necessity of considering epistatic effects in soybean SDS resistance breeding using marker‐assisted and genomic selection approaches. Based on our findings, we propose a model for soybean root defense against the SDS pathogen. Our results facilitate identification of the molecular mechanism underlying SDS resistance in soybean, and provide a genetic basis for improvement of soybean SDS resistance through breeding strategies based on additive and epistatic effects.
Significance Statement
We report 12 additive effect loci and 12 epistatic interactions associated with resistance to sudden death syndrome in soybean; and pinpoint a trait‐associated single nucleotide polymorphism in SIK1, encoding a leucine‐rich receptor kinase.
Circular RNAs are new players in regulation of post transcriptional gene expression. Animal genomes express many circular RNAs from diverse genomic locations. A recent study has validated a fairly ...large number of circular RNAs in human, mouse, and nematode. Circular RNAs play a crucial role in fine tuning the level of miRNA mediated regulation of gene expression by sequestering the miRNAs. Their interaction with disease associated miRNAs indicates that circular RNAs are important for disease regulation. In this paper we studied the potential association of circular RNAs (circRNA) with human diseases in two different ways. Firstly, the interactions of circRNAs with disease associated miRNAs were identified, following which the likelihood of a circRNA being associated with a disease was calculated. For the miRNAs associated with individual diseases, we constructed a network of predicted interactions between the miRNAs and protein coding, long non-coding and circular RNA genes. We carried out gene ontology (GO) enrichment analysis on the set of protein coding genes in the miRNA- circRNA interactome of individual diseases to check the enrichment of genes associated with particular biological processes. Secondly, disease associated SNPs were mapped on circRNA loci, and Argonaute (Ago) interaction sites on circular RNAs were identified. We compiled a database of disease-circRNA association in Circ2Traits (http://gyanxet-beta.com/circdb/), the first comprehensive knowledgebase of potential association of circular RNAs with diseases in human.
Single Nucleotide Polymorphisms (SNPs), as the most prevalent type of variation in the human genome, play a pivotal role in influencing human traits. They are extensively utilized in diverse fields ...such as population genetics, forensic science, and genetic medicine. This study focuses on the 'Rita' BeadChip, a custom SNP microarray panel developed using Illumina Infinium HTS technology. Designed for high-throughput genotyping, the panel facilitates the analysis of over 4000 markers efficiently and cost-effectively. After careful clustering performed on a set of 1000 samples, an evaluation of the Rita panel was undertaken, assessing its sensitivity, repeatability, reproducibility, precision, accuracy, and resistance to contamination. The panel’s performance was evaluated in various scenarios, including sex estimation and parental relationship assessment, using GenomeStudio data analysis software. Findings show that over 95 % of the custom BeadChip assay markers were successful, with better performance of transitions over other mutations, and a considerably lower success rate for Y chromosome loci. An exceptional call rate exceeding 99 % was demonstrated for control samples, even with DNA input as low as 0.781 ng. Call rates above 80 % were still obtained with DNA quantities under 0.1 ng, indicating high sensitivity and suitability for forensic applications where DNA quantity is often limited. Repeatability, reproducibility, and precision studies revealed consistency of the panel's performance across different batches and operators, with no significant deviations in call rates or genotyping results. Accuracy assessments, involving comparison with multiple available genetic databases, including the 1000 Genome Project and HapMap, denoted over 99 % concordance, establishing the Rita panel's reliability in genotyping. The contamination study revealed insights into background noise and allowed the definition of thresholds for sample quality evaluation. Multiple metrics for differentiating between negative controls and true samples were highlighted, increasing the reliability of the obtained results. The sex estimation tool in GenomeStudio proved highly effective, correctly assigning sex in all samples with autosomal loci call rates above 97 %. The parental relationship assessment of family trios highlighted the utility of GenomeStudio in identifying genotyping errors or potential Mendelian inconsistencies, promoting the application of arrays such as Rita in kinship testing. Overall, this evaluation confirms the Rita microarray as a robust, high-throughput genotyping tool, underscoring its potential in genetic research and forensic applications. With its custom content and adaptable design, it not only meets current genotyping demands but also opens avenues for further research and application expansion in the field of genetic analysis.
•Illumina custom microarray ‘Rita’ delivers high-quality results for human samples.•Call rate exceeds 90 % with a DNA input as low as 0.195 ng.•Consistently high call rate with a 200 ng input (>99 %), with accuracy beyond 99 %.•High repeatability, reproducibility, and precision across batches and operators.•Rita confirmed as robust method for human genotyping and potential forensic use.
•Ca and P concentrations of 154 walnut genotypes were determined.•A total of 59 SNPs were associated with phenotypic traits.•Putative candidate genes around the SNPs were identified.•The functions of ...the identified candidate genes have been investigated.
Walnut (Juglans regia L.) is a nut species with various applications worldwide and plays a significant role in human nutrition. The walnut kernel contains various essential nutrients crucial for regulating plant physiological functions and maintaining human health. The aim of the current study was to identify SNP markers associated with the accumulations of important macronutrients such as calcium (Ca) and phosphorus (P) in 154 walnut genotypes over two consecutive years (2021–2022) using the GWAS method. Concentrations of Ca and P ranged from 70.83 to 386.67 mg/100g and from 106.17 to 583.08 mg/100g, respectively, over the two-year period. Significant differences between genotypes (p ≤ 0.01) were observed for both macronutrients. High heritability values were obtained for Ca (0.994) and P (0.993) accumulations. The STRUCTURE analysis conducted using a total of 16,473 clean SNP data and 154 walnut genotypes resulted in the population being grouped into three clusters (K=3). The mean fixation index (Fst) and expected heterozygosity values were determined as 0.22 and 0.31, respectively. Using the MLM (Q+K) approach, a total of 59 significant associations (35 for Ca and 24 for P) exceeding the false discovery rate (FDR) threshold were identified (p < 0.01). Among these, 16 SNPs for Ca and 11 SNPs for P were found to be common across both years. One SNP (M14826) was common for Ca-2021, Ca-2022, and P-2022, while two SNPs (M15542 and M576) were common for both macronutrients and both years. Analysis of the 59 SNP sequences using the Genome Data Viewer (GDV) in the NCBI database revealed that 16 SNPs were located in the J. regia genome. For nine SNPs associated with Ca-2021 and Ca-2022 accumulations, a total of 89 candidate genes were identified, while for five SNPs associated with P-2021 and P-2022 accumulations, 64 candidate genes were identified. Additionally, seven candidate genes were identified for one SNP associated with Ca-2021, Ca-2022, and P-2022, and five candidate genes were detected for one SNP associated with accumulations of Ca-2021, Ca-2022, P-2021, and P-2022. The results suggest that SNP markers associated with Ca and P accumulations in walnut kernels can be valuable for facilitating marker-assisted selection (MAS) strategies in future walnut breeding studies and for developing biofortified walnut genotypes.
Pancreatic adenocarcinoma (PA) is one of the most fatal cancers since it shows little to no symptoms until it has metastasized. As is true with most malignancies, an early detection and diagnosis is ...imperative in order to help increase survival rate. Although there are several extant treatments available, their success depends on an early diagnosis. In order to identify genetic loci that may assist in early diagnosis, we analyzed 134 DNA sequences of patients with various stages of PA. NCBI’s Gene Expression Omnibus was used to obtain PA microarray data to identify overexpressed genes. The Sequence Read Archive (SRA) database was then used to provide sequenced data of a PA cohort which was then mapped, indexed and called. With these analyses, we were able to identify single nucleotide polymorphisms (SNPs) that were specific to PA primary, secondary, or metastatic tumors. These results advance our understanding of the development of PA and highlight target sites that could influence PA tumor stages.
In this study, the SNP-TiO2@Cu-MOF composite was prepared successfully by loading non-noble metal modified TiO2 (SNP-TiO2) on the surface of copper metal organic skeleton (Cu-MOF), and compared the ...inactivation efficiency of different photocatalysts to Karenia mikimotoi (K. mikimotoi) under visible light. The obtained photocatalyst had the characteristic crystal faces of Cu-MOF and SNP- TiO2, and contained functional groups such as Cu-O, -COOH, N-O, P-O, etc., which indicated the structural stability of the photocatalyst. The band gap of SNP-TiO2@Cu-MOF composite was 2.82 eV, and it had great light absorption ability in visible light region. It was proved to be a mesoporous adsorption material, which had a huge specific surface area (245 m2/g). Compared with other photocatalysts, SNP-TiO2@Cu-MOF composite showed the strongest photocatalytic activity. When the concentration of composite material was set to 100 mg/L and the exposure time was 6 h, the visible light photocatalytic inactivation efficiency of K. mikimotoi was 93.75 %. By measuring various metabolic indexes of K. mikimotoi under the action of different photocatalysts for 1 h, it was confirmed that cell inactivation was due to the increased membrane permeability and degradation of photosynthetic pigments and main life proteins. This research showed that SNP-TiO2@Cu-MOF composite material was full of great potential and application prospect in controlling the outbreak of eutrophication.
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•Photocatalyst SNP-TiO2@Cu-MOF were prepared and used under visible light.•The inactivation rate of SNP-TiO2@Cu-MOF to algae was 93.75 % in 6 h.•The forbidden band width of the composite was reduced to 2.82 eV.•The inactivation of algal cells was the result of adsorption photocatalysis synergy.
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