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Single nucleotide polymorphisms

Tìm thấy 20+ kết quả cho từ khóa "Single nucleotide polymorphisms"

Absence of single nucleotide polymorphisms (SNPs) in the open reading frame (ORF) of the prion protein gene (PRNP) in a large sampling of various chicken breeds

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The funding bodies played no role in the design of the study and collection, analysis, and interpretation of data and in writing the manuscript.. 1 Distribution of the single nucleotide polymorphisms (SNPs) at coding region of the prion protein gene ( PRNP ) in various species. Brain tissue samples from 298 chickens, including 3 chicken breeds (100 Ross, 100 Korean native chickens and 98 Ogolgye), were obtained from slaughter houses in the Republic of Korea.

Benchmarking hybrid assembly approaches for genomic analyses of bacterial pathogens using Illumina and Oxford Nanopore sequencing

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Numbers of single nucleotide polymorphisms (SNPs) in the hybrid assemblies of bacterial strains with real Illumina short reads and Oxford Nanopore long reads using MaSuRCA, SPAdes, and Unicycler, as determined by aligning to their corresponding reference genomes and expressed as SNPs per 1 million bp of the reference genome..

Population analysis of the Korean native duck using whole-genome sequencing data

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Specifically, we sequenced the whole genomes of 20 KDs, collected whole- genome sequencing data of 14 phenotypically diverse duck breeds (Additional file 1: Table S1), and discovered single nucleotide polymorphisms (SNPs) for 15 duck breed popu- lations including KD.

Genome-wide association analyses identify known and novel loci for teat number in Duroc pigs using single-locus and multilocus models

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Previous genome-wide association studies (GWAS) in a cross between Landrace and Ko- rean pigs [3], Duroc pigs [4], Erhualian pigs [5], and Large White pigs [7] found that several single nucleotide polymorphisms (SNPs) near or within the Vertebrae De- velopment Associated ( VRTN ) gene on Sus scrofa chromosome 7 (SSC7) were associated with teat number.. [12] showed that the 291 bp insertion of VRTN has associations with ver- tebral number, carcass length, and teat number in Chin- ese indigenous Erhualian

Comparing low-pass sequencing and genotyping for trait mapping in pharmacogenetics

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At common single nucleotide polymorphisms (SNPs), the mean imputation r 2 from the genotyping array was 0.90, which was comparable to the imputation r 2 from 0.4x coverage sequencing, while the mean imputation r 2 from 1x sequencing data was 0.96..

Population structure, genetic diversity, and selective signature of Chaka sheep revealed by whole genome sequencing

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A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain

Genome-wide association screening and verification of potential genes associated with root architectural traits in maize (Zea mays L.) at multiple seedling stages

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GWAS use millions of single nucleotide polymorphisms (SNPs) markers to determine alleles associated with multiple traits in crops and identify genes controlling. In this analysis, a total of 1,490,007 consistent SNP markers were distributed among the ten maize chromosomes to directly mine SNPs and genes putatively associated with seven root architectural traits viz.

Novel genomic resources for shelled pteropods: A draft genome and target capture probes for Limacina bulimoides, tested for cross-species relevance

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Indeed, from the four non-focal pteropod species, most of the recovered targets had low diversity, containing only a single SNP (Fig. 3 Density of single nucleotide polymorphisms (SNPs, present in 80% of individuals) plotted against coverage for each of the five pteropod species (a: Limacina bulimoides , b: L. levels of gene flow in the focal species.

A phenomics-based approach for the detection and interpretation of shared genetic influences on 29 biochemical indices in southern Chinese men

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Result: A total of 1999 subjects with 29 biochemical indices and 709,211 single nucleotide polymorphisms (SNPs) were subjected to phenomics analysis. The results showed that 29 biochemical indices were from a network. IgA, IgG, IgE, IgM, HCY, AFP and B12 were in the central community of 29 biochemical indices. Key genes and loci associated with metabolism traits were further identified, and shared genetics analysis showed that 29 SNPs ( P <. 10 − 4 ) were associated with three or more traits.

Fine dissection of limber pine resistance to Cronartium ribicola using targeted sequencing of the NLR family

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Keywords: Cronartium ribicola, Limber pine (Pinus flexilis), NGS-based bulked segregation analysis (BSA), Resistance gene analog (RGA), Single nucleotide polymorphisms (SNPs), Targeted genomic sequencing (TS). S2), indicating that a large part of the limber pine R gene families were highly polymorphic in the seed family LJ-112. ribicola , since limber pine was not previously exposed to WPBR prior to the last century..

Genomic variation between PRSV resistant transgenic SunUp and its progenitor cultivar Sunset

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Results: In this study, a total of more than 74 million Illumina reads for progenitor ‘ Sunset ’ were mapped onto transgenic papaya ‘ SunUp ’ reference genome. 310,364 single nucleotide polymorphisms (SNPs) and 34,071 small Inserts/deletions (InDels) were detected between ‘ Sunset ’ and ‘ SunUp. Among all nuclear organelle DNA (norgDNA) junction sites, 96% of junction sites were shared by ‘ SunUp ’ and ‘ Sunset.

Multi-trait GWAS using imputed highdensity genotypes from whole-genome sequencing identifies genes associated with body traits in Nile tilapia

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Some of the lead single nucleotide polymorphisms (SNPs) were found within important functional candidate genes previously associated with growth-related traits in other terrestrial species. Conclusions: The high-resolution mtGWAS presented here allowed the identification of significant SNPs, linked to strong functional candidate genes, associated with body traits in Nile tilapia. The most important body traits in Nile tilapia are body weight measured at a spe- cific age (e.g.

Prevalence, antibiotic resistance, virulence and genetic diversity of Staphylococcus aureus isolated from bulk tank milk samples of U.S. dairy herds

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Phylogenetic analysis of Staphylococcus aureus isolates Single nucleotide polymorphisms (SNP) were identified from the trimmed reads with Snippy v. 4.1 [59] using ref- erence genome Staphylococcus aureus NCTC 8325 (NC_. MRSA: Methicillin Resistant Staphylococcus aureus;. https://doi.. org/10.1016/S . https://doi.org/10.1038/nrmicro1289..

Genome-wide association analysis of canine T zone lymphoma identifies link to hypothyroidism and a shared association with mast-cell tumors

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A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118

Whole-genome sequencing of Puccinia striiformis f. sp. tritici mutant isolates identifies avirulence gene candidates

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Of the single nucleotide polymorphisms (SNPs) caused by EMS, C/G to T/A transitions were most frequent in various organisms, including Arabidop- sis thaliana [11, 12], Caenorhabditis elegans [13, 14], Lotus japonicus [15], Oryza sativa [12, 16] and Saccharo- myces cerevisiae [17]. Identifying and cloning avirulence genes are based on the gene-for-gene hypothesis proposed by Flor [22], which states that host R genes confer resistance to the cognate Avr genes in the pathogen.

Imprints of independent allopolyploid formations on patterns of gene expression in two sibling yarrow species (Achillea, Asteraceae)

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This made it easy to identify homeologous gene copies in the allotetraploid species using the single nucleotide polymorphisms (SNPs) between the two diploid species. asiatica apart were chosen, and clean reads in the allotetraploids exhibiting parental SNPs were parsed into homeolog-specific bins using custom perl scripts so that reads in the tetraploids were desig- nated as of A.

Luận án Tiến sĩ Nông nghiệp: Nghiên cứu hệ gen phiên mã (Transcriptome) của tôm sú (Penaeus monodon) nhằm sàng lọc các chỉ thị phân tử phục vụ công tác chọn giống

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. "Prediction of nonsynonymous single nucleotide polymorphisms in human disease-associated genes.". "Antimicrobial peptides discovered in the black tiger shrimp Penaeus monodon using the EST approach.". "Identification of immune-related genes in hemocytes of black tiger shrimp (Penaeus monodon).". "Characterization of candidate genes involved in growth of black tiger shrimp Penaeus monodon.". "Hypervariability of simple sequences as a general source for polymorphic

Stratified reconstruction of ancestral Escherichia coli diversification

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On the other hand, molecular polymorphism hallmark (mPH) based on detecting con- served single nucleotide polymorphisms in the different lin- eages selected in different times.. An initial limitation, found during the first stages in the de- velopment of this work, was that around 90% of the se- quenced E. 1% of the total number of sequenced E. On the contrary, the proposed phylogroup H [17] (based on one single gen- ome) still represents an ‘undetectable’ fraction in the population.

Cruxome: A powerful tool for annotating, interpreting and reporting genetic variants

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A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila. org/10.4161/fly.19695.. https://doi.org hg0720s76.. https://doi.org/10.1093/nar/gky1016.. org/10.1016/j.ajhg . doi.org S15-S7.. https://doi.org/10.1371/journal.pone.0075504.. Kohler S, Carmody L, Vasilevsky N, Jacobsen JOB, Danis D, Gourdine JP, et al..

Combining information from genome-wide association and multi-tissue gene expression studies to elucidate factors underlying genetic variation for residual feed intake in Australian Angus cattle

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Candidate genes and single nucleotide polymorphisms associated with variation in residual feed intake in beef cattle. Transcriptome profiling of the rumen epithelium of beef cattle differing in residual feed intake. Role of Deltex-1 as a transcriptional regulator downstream of the notch receptor. A region on BTA14 that includes the positional candidate genes LYPLA1, XKR4 and TMEM68 is associated with feed intake and growth phenotypes in cattle 1.