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294 results for “SNPs”
Identification of candidate SNPs in the encoding region of two sugarcane cultivars as to resistance to water stress
<p>Identification of candidate SNPs in the encoding region of two sugarcane cultivars as to resistance to water stress</p>
Copy number variants outperform SNPs to reveal genotype-temperature association in a marine species
<p>Copy number variants (CNVs) are a major component of genotypic and phenotypic variation in genomes. To date, our knowledge of genotypic variation and evolution has largely been acquired by means of single nucleotide polymorphism (SNPs) analyses. Until recently, the adaptive role of structural variants (SVs) and particularly that of CNVs has been overlooked in wild populations, partly due to their challenging identification. Here, we document the usefulness of Rapture, a derived reduced‐representation shotgun sequencing approach, to detect and investigate copy number variants (CNVs) alongside SNPs in American lobster (<i>Homarus americanus</i>) populations. We conducted a comparative study to examine the potential role of SNPs and CNVs in local adaptation by sequencing 1,141 lobsters from 21 sampling sites within the southern Gulf of St. Lawrence, which experiences the highest yearly thermal variance of the Canadian marine coastal waters. Our results demonstrated that CNVs account for higher genetic differentiation than SNP markers. Contrary to SNPs, for which no significant genetic–environment association was found, 48 CNV candidates were significantly associated with the annual variance of sea surface temperature, leading to the genetic clustering of sampling locations despite their geographic separation. Altogether, we provide a strong empirical case that CNVs putatively contribute to local adaptation in marine species and unveil stronger spatial signal of population structure than SNPs. Our study provides the means to study CNVs in nonmodel species and highlights the importance of considering structural variants alongside SNPs to enhance our understanding of ecological and evolutionary processes shaping adaptive population structure.</p>
A genomic data set of single‐nucleotide polymorphisms (SNPs) generated by ddRAD tag sequencing in Q. petraea (Matt.) Liebl. populations from Central-Eastern Europe and Balkan Peninsula
<p>This genomic dataset provides highly variable single-nucleotide polymorphism (SNP) markers from georeferenced natural <em>Quercus petraea</em> (Matt.) Liebl. populations collected in Bulgaria, Hungary, Romania, Serbia, Bosnia and Herzegovina, Kosovo and Albania. These SNP loci can be used to assess genetic diversity, differentiation, population structure, and can also be used to detect signatures of selection and local adaptation.</p>
Data from: "Discovery and characterization of 80 SNPs and 1,624 SSRs in the transcriptome of Atlantic mackerel (Scomber scombrus, L)" in Genomic Resources Notes Accepted 1 June 2015 to 31 July 2015
This paper reports on SNP discovery in the Atlantic mackerel transcriptome, using next generation sequencing technologies and applying developed methodology already proven successful for the European anchovy. A total of 9,966 high quality transcriptome contigs were assembled, from which 951 putative SNPs were discovered. In all, 479 putative SNPs and 1,624 simple sequence repeats (SSRs) suitable for genotyping were identified. A subset of 96 was selected for genotyping; from these, 80 SNPs were considered polymorphic and reliably scored after genotyping of 105 individuals from three locations in the Eastern Atlantic Ocean. These markers will be valuable for future studies on population genetic structure assessment and for product tracing.
Data from: SNPs across time and space: population genomic signatures of founder events and epizootics in the House Finch (Haemorhous mexicanus)
Identifying genomic signatures of natural selection can be challenging against a background of demographic changes such as bottlenecks and population expansions. Here, we disentangle the effects of demography from selection in the House Finch (Haemorhous mexicanus) using samples collected before and after a pathogen-induced selection event. Using ddRADseq, we genotyped over 18,000 SNPs across the genome in native pre-epizootic western US birds, introduced birds from Hawaii and the eastern United States, post-epizootic eastern birds, and western birds sampled across a similar time span. We found 14% and 7% reductions in nucleotide diversity, respectively, in Hawaiian and pre-epizootic eastern birds relative to pre-epizootic western birds, as well as elevated levels of linkage disequilibrium and other signatures of founder events. Despite finding numerous significant frequency shifts (outlier loci) between pre-epizootic native and introduced populations, we found no signal of reduced genetic diversity, elevated linkage disequilibrium, or outlier loci as a result of the epizootic. Simulations demonstrate that the proportion of outliers associated with founder events could be explained by genetic drift. This rare view of genetic evolution across time in an invasive species provides direct evidence that demographic shifts like founder events have genetic consequences more widespread across the genome than natural selection.
Genetic differentiation at methylation array probe SNPs leads to spurious results in meQTL discovery
<p>Data Associated with Figures 1 and 2 in Communications Biology Matters Arising: Genetic differentiation at methylation array probe SNPs leads to spurious results in meQTL discovery. Original data arising from B. Li et al. <i>Communications Biology</i> <a href="https://doi.org/10.1038/s42003-022-03353-5">https://doi.org/10.1038/s42003-022-03353-5</a> (2022)</p>
Genotypes and geographic positions of 5797 European white oaks from 636 locations genotyped at 355 nuclear SNPs and 28 maternally inherited SNPs of the chloroplast and mitochondria
<p class="MsoNormal"><span>The data set is the result of genetic inventory on 5797 white oaks collected at 636 locations all over Europe. The oaks trees were assigned in forest inventories as <em>Quercus robur</em> </span><em>L.</em> <span>(3342), <em>Quercus petraea </em></span><em>Matt</em>. <span>(2090), <em>Quercus pubescens </em></span><em>Willd</em>. <span>(170) or as unspecified <em>Quercus</em>. spp. (195). The sampling had a focus on central and east Europe as well as the Black Sea and Caucasus region. All individuals were genotyped at 355 nuclear SNPs and 28 maternally inherited SNPs of the chloroplast and mitochondria. The combination of the maternally inherited SNPs resulted in 26 different haplotypes. </span></p> <p class="MsoNormal"><span>The genotype of each individual is one row in the csv-file "genotypes". The genotypes at the nuclear markers are diploid and represented by two columns per gene marker. The genetic information at the organelle genome is haploid. For each of these gene markers one column is used. Genotypes are coded by Arabic numbers. The meaning of the numbers is explained in the table "coding genotypes" in a second csv-file. Each Individual has a unique "Genotype_ID" and a "Thuenen_Sample_ID". The "Thuenen_Sample_ID" is a unique ID that serves to identify the sample in our depository at the Thuenen Institute of Forest Genetics. Each individual has data on the geographic origin given as "Longitude" and "Latitude" in decimal degrees. For each individual the putative oak species ("Putative species") as it has been assigned in the forest inventories is given. The numbers of the "Haplotype" represent the multilocus combination of the mitochondrial and chloroplast SNPs of that individual.</span></p>
Varieties SNPs-based sequencies
<p>This is not a consensus sequencing. SNPs for one sample per file were used. Pinot noir was used as a reference.</p>
Varieties SNPs-based sequencies (3)
Open the record for dataset details and reuse information.
Data from: Distances and their visualization in studies of spatial-temporal genetic variation using single nucleotide polymorphisms (SNPs)
<p>Distance measures are widely used for examining genetic structure in datasets that comprise many individuals scored for a very large number of attributes. Genotype datasets composed of single nucleotide polymorphisms (SNPs) typically contain bi-allelic scores for tens of thousands if not hundreds of thousands of loci.</p> <p>We examine the application of distance measures to SNP genotypes and sequence tag presence-absences (SilicoDArT) and use real datasets and simulated data to illustrate pitfalls in the application of genetic distances and their visualization.</p> <p>The datasets used to illustrate points in the associated review are provided here together with the R script used to analyse the data. Data are either simulated internal to this script or are SNP data generated as part of other studies and included as compressed binary files readily accessable by reading into R using R base function readRDS(). Refer to the analysis script for examples.</p>
South-east Australian Feral Pig SNPs
<p>Methods: During feral pig control programs, either tissue or blood samples were collected from culled pigs for genetic analysis. Tissue biopsies were collected in tissue sampling unit (TSU) buffer (Allflex) or 80% ethanol. Blood sampling was undertaken using the GenoTube swab system (Thermo Fisher). Samples were extracted using the sbeadex Livestock DNA Purification Kit (Biosearch Technologies) on the Kingfisher Flex Purification System (ThermoFisher) under manufacturer’s instructions for tissue or blood extractions. SNP genotyping was conducted using the Porcine SNP60 BeadChip (v2 and v3, Illumina) containing 61,565 (v2) or 75,753 (v3) SNPs, according to the manufacturer’s protocol. After genotyping, individuals were filtered to exclude samples with less than a 99% call rate. SNPs were filtered to exclude sites with a call-rate of less than 99% (which also excluded SNPs that were only found on the v3 BeadChip), minor allele frequency of < 0.01, all unmapped SNPs and those on sex chromosomes.</p>
Seychelles warbler whole genome SNPs
<p>1) SNPs for 2018 low coverage whole-genome sequenced Seychelles warblers that have been imputed by STITCH to fill in missing genotype data.</p> <p>2) The chromosome-level Seychelles warbler reference genome.</p> <p>Please email for access: kgllee1@sheffield.ac.uk</p>
The application of short and highly polymorphic microhaplotypes based on nonbinary-SNPs in kinship testing of extremely degraded samples
<p>Kinship testing becomes more difficult in extremely degraded samples. But commonly used genetic markers cannot completely solved this problem. Microhaplotype combining the advantages of STR and SNP may be a promising genetic marker for kinship testing in extremely degraded samples. Therefore, in this study, 36 short and highly polymorphism microhaplotype loci with length smaller than 100 bp and Ae greater than 3.0 were developed, of which 29 loci met the Hardy-Weinberg and linkage equilibrium. The CPD and CPE of these 29 loci were 0.99999999999999999999999997036 and 0.9999999945, respectively. Allele dropout of these loci was not observed in extremely degraded samples. Through simulated kinship analysis, the effectiveness of paternity testing reached 98.39% at threshold of 4/-4, and effectiveness of full-sibling testing reached 93.01% at threshold of 2/-2, which were greater than that of 15 STR loci. After combining with other 50 short and highly polymorphic microhaplotype loci, the effectiveness of half-sibling testing also reached 82.42% at the threshold of 2/-2. Our developed short and highly polymorphic microhaplotype loci may be useful for paternity testing and full-sibling testing in extremely degraded samples, and after combining with other short and highly polymorphic microhaplotype loci, may be helpful to analyze the more distant kinship relationship.</p>
De novo assembly of SNPs in VCF format for 112 individualss of Campylorhynchus in western Ecuador
<p>Climate variability has a significant impact on the evolution of biodiversity, which results in genetic and phenotypic diversity within species. A balance between gene flow and selection maintains changes in the frequency of genetic and phenotypic variants that occur along an environmental gradient. Here, we investigate a hybrid zone in western Ecuador involving C. zonatus, C. fasciatus, and admixed populations. We hypothesized that different ecological preferences and geographical distances result in limited dispersal between populations along the precipitation gradient in western Ecuador.</p> <p>In the context of testing IBE and IBD shaping distributions of C. zonatus, C. fasciatus, and potential hybrids, we asked (1) Is there evidence of genetic admixture and introgression between these taxa in Western Ecuador? And (2) What is the relative contribution of IBE and IBD on patterns of genetic differentiation and admixture patterns? We analyzed 4409 SNPs from the blood of 112 individuals sequenced using ddRadSeq. The most likely clusters ranged from K=2-4, corresponding to categories defined by geographic origins, known phylogenetics, and physical or ecological constraints. Evidence for IBE was weak but stronger for IBD. We observed gradual changes in genetic admixture between C. f. pallescens and C. zonatus along the environmental gradient. Genetic differentiation of the two populations of C. f. pallescens could be driven by a previously undescribed potential physical barrier near the center of western Ecuador. Lowland habitats in this region may be limited due to the proximity of the Andes to the coastline, limiting dispersal and gene flow, particularly among dry-habitat specialists.</p>
Single Nucleotide Polymorphisms (SNPs) identified from the whole genome sequences of hilsa shad (Tenualosa ilisha) of the Bay of Bengal
<p>The data file contains 792,939 isolated SNPs identified by discoSnp++ v2.3.x (Uricaru et al., 2015) from the whole genome sequence of T. ilisha of the Bay of Bengal. The central sequence of length 2k-1 is seen in upper case, while the flanking sequences are seen in lower case. SNP_higher/lower: one of the two alleles. id: id of the SNP (each SNP has a unique id).</p> <p>FOR SNPs:</p> <p>P_i:pos_Alt1/Alt2: Information about a ith SNP (If more than a unique SNP is found, the following format is used: P_1:pos_Alt1/Alt2,P_2:pos_Alt1/Alt2,...</p> <p>pos: position of the SNP with respect to the starting position of the bubble, i.e. the starting of the upper case sequence.</p> <p>Alt1: One of the two alleles</p> <p>Alt2: the other</p> <p>FOR INDELs:</p> <p>P_1:pos_size_repeatSize</p> <p>pos: predicted position of the indel with respect to the starting position of the bubble, i.e. the starting of the upper case sequence.</p> <p>size: predicted size of the indel</p> <p>repeatSize: Size of the longest sequence both prefix of the indel and prefix of the sequence located just after the insertion.</p> <p>high/low: sequence complexity. If the sequence if of low complexity (e.g. ATATATATATATATAT) this variable would be low</p> <p>nb_pol: number of polymorphism.</p> <p>left_unitig_length: size of the full left extension.</p> <p>right_unitig_length: size of the right extension.</p> <p>left_contig_length: size of the full left extension.</p> <p>right_contig_length: size of the right extension.</p> <p>C1: number of reads mapping the central upper case sequence from the first read set.</p> <p>C2: number of reads mapping the central upper case sequence from the second read set.</p> <p>Q1 [if reads were given in fastq]: average phred quality of the central nucleotide from the mapped reads from the first read set.</p> <p>Q2 [if reads were given in fastq]: average phred quality of the central nucleotide from the mapped reads from the second read set.</p> <p>G1: Genotype of the variant in the first read set.</p> <p>G2: Genotype of the variant in the second read set.</p> <p>rank: ranks the predictions according to their read coverage in each condition favoring SNPs that are discriminant between conditions.</p>
Prakriti differentiating significant SNPs annotation
<p>List of Prakriti differentiating significant (p<0.05) SNPs in North (North India) & Vadu (Western India) cohorts</p>
Replication of significant Genes & SNPs between North & Vadu cohorts
<p>List of Prakriti differentiating significant Genes (with or without replicated SNP) & SNPs (with or without replicated profiles) between North & Vadu cohorts</p>
PHEWAS LD SNPs
<p>List of SNPs associated with multiple phenotypes in PHEWAS catalog in strong LD (r^2 > 0.8) with <em>Prakriti d</em>ifferentiating SNPs in North and Vadu cohorts </p>
GWAS LD SNPs
<p>List of SNPs associated with disease/traits in GWAS catalog1.0.2 in strong LD (r^2 > 0.8) with Prakriti Differentiating SNPs in North and Vadu cohorts</p>
Crown morphology in Norway spruce (Picea abies [Karst.] L.) as adaptation to mountainous environments is associated with single nucleotide polymorphisms (SNPs) in genes regulating seasonal growth rhythm
Trees growing at high altitude or latitude have to be adapted, amongst others, to the lower temperatures, a shorter vegetation period, heavier snow load and frost desiccation. Association between molecular genetic markers and climatic variables may provide evidence for the genetic control of climatic adaptation. With increasing genomic resources, several genes with importance to climatic adaptation are identified over a wide range of tree species. Commonly, circadian clock genes are linked to the adaptation to lower temperatures and especially to a shortened vegetation period, as they are regulating metabolic and phenological processes in the day-night shift and seasonal change. Potentially adaptive "candidate" genes associated with latitudinal and elevational gradients were identified in several Picea spp. Before molecular markers became available to study climatic adaptation, phenotypic traits measured in natural populations and/or common garden studies were used to search for their association with climate variables. In Norway spruce, the crown architecture is the most noticeable trait associated with altitude and the related environment. The mountainous narrow-crowned morphotype is characterised by superior resistance to snow breakage in regions with heavy snow fall. In total, the crown shape was assessed in 765 individual trees from mountainous regions in the Thuringian Forest, the Ore Mountains (Saxony) and Harz Mountains (Lower-Saxony/Saxony-Anhalt), and they were genotyped at 44 single nucleotide polymorphisms (SNPs) in 24 adaptive trait related candidate genes. Six SNPs in three genes, APETALA 2-like 3 (AP2L3), GIGANTEA (GI), and mitochondrial transcription termination factor (mTERF) were associated with variation in crown shape. GI has previously been identified in angiosperms and gymnosperms to be associated with temperature and growth cessation. Our results showed that crown morphology in Norway spruce is associated with genetic markers which are putatively involved in the complex process of genetic adaptation to climatic conditions at high altitudes.
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OpenNeuro
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