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74 results for “genotyping-by-sequencing”
Genotyping-by-sequencing (GBS) dataset for genome wide associations of growth, phenology and plasticity traits in willow (Salix viminalis (L.))
<p>These vcf-files constitute underlying raw data material for the manuscript "Genome wide associations of growth, phenology and plasticity traits in willow (Salix viminalis (L.))". For more detailed information please consult the README file in the repository.</p>
Genomic characterization and gene bank curation of Aegilops using genotyping-by-sequencing
<p>In this study, genotyping-by-sequencing (GBS) was performed on 1041 <em>Aegilops</em> accessions, representing 23 different species. These accessions have been maintained by the Wheat Genetics and Resource Center (WGRC) at Kansas State University. The GBS FASTQ files have been uploaded to the NCBI SRA public repository under the BioProject accession number # PRJNA985892. We have provided other files related to data analysis, such as the barcode key file, SNP matrices, and taxonomic information of the accessions in this Dryad repository, which can be accessed through the provided link. The aim of the study was to explore the genetic and genomic characteristics of wild wheat relatives, <em>Aegilops,</em> using a larger number of SNP markers. Here, we also curated the WGRC gene bank <em>Aegilops</em> collection via the identification of misclassified accessions and genetically identical redundant accessions. Further, we explored the genomic relationship between wheat and the different <em>Aegilops</em> species. </p>
Genomic characterization and gene bank curation of Aegilops using genotyping-by-sequencing
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Data from: RapidRat: development, validation and application of a genotyping-by-sequencing panel for rapid biosecurity and invasive species management
<p>Invasive alien species (IAS) are among the main causes of global biodiversity loss. Invasive brown (Rattus norvegicus) and black (R. rattus) rats, in particular, are leading drivers of extinction on islands, especially in the case of seabirds where >50% of all extinctions have been attributed to rat predation. Eradication is the primary form of invasive rat management, yet this strategy has resulted in a ~10-38% failure rate on islands globally. Genetic tools can help inform IAS management, but such applications to date have been largely reactive, time-consuming, and costly. Here, we developed a Genotyping-in-Thousands by sequencing (GT-seq) panel for rapid species identification and population assignment of invasive brown and black rats (RapidRat) in Haida Gwaii, an archipelago comprising ~150 islands off the central coast of British Columbia, Canada. We constructed an optimized panel of 443 single nucleotide polymorphisms (SNPs) using previously generated double-digest restriction-site associated DNA (ddRAD) genotypic data (27,686 SNPs) from brown (n=295) and black rats (n=241) sampled throughout Haida Gwaii. The informativeness of this panel for identifying individuals to species and island of origin was validated relative to the ddRAD results; in all comparisons, admixture coefficients and population assignments estimated using RapidRat were consistent. To demonstrate application, 20 individuals from novel invasions of three islands (Agglomerate, Hotspring, Ramsay) were genotyped using RapidRat, all of which were confidently assigned (>98.5% probability) to Faraday and Murchison Islands as putative source populations. These results indicated that a previous eradication on Hotspring Island was conducted at an inappropriate geographic scale; future management should expand the eradication unit to include neighboring islands to prevent re-invasion. Overall, we demonstrated that RapidRat is an effective tool for managing invasive rat populations in Haida Gwaii and provided a clear framework for GT-seq panel development for informing biodiversity conservation in other systems.</p>
Genotyping-by-sequencing of Canada's Apple Biodiversity Collection
<p><span>Canada's Apple Biodiversity Collection (ABC) is one of the most diverse collections of apples in the world, which was designed to enable genetic mapping. The ABC is located at the Agriculture and Agri-Food Canada (AAFC) Kentville Research and Development Centre in Nova Scotia, Canada. </span>In addition to phenotypic descriptions of the ABC, sequencing the accessions in the collection provides a valuable resource not only for researchers working on the collection, but for those studying apples more broadly. With this in mind, we report and make publicly available genotyping-by-sequencing (GBS) data for over 1,000 apple accessions from the ABC. By<span> using three SNP callers and imputation, we were able to genotype 278,231 SNPs from 1,175 diverse apple accessions from the ABC.</span></p>
Data from: Targeted genotyping-by-sequencing of potato and data analysis with R/polyBreedR
<p>"Mid-density" targeted genotyping-by-sequencing (GBS) combines trait-specific markers with thousands of genomic markers at an attractive price for linkage mapping and genomic selection. A 2.5K targeted GBS assay for potato was developed using the DArTag<sup>TM</sup> technology and later expanded to 4K targets. Genomic markers were selected from the potato Infinium<sup>TM</sup> SNP array to maximize genome coverage and polymorphism rates. The DArTag and SNP array platforms produced equivalent dendrograms in a test set of 298 tetraploid samples, and 83% of the common markers showed good quantitative agreement, with RMSE (root-mean-squared-error) less than 0.5. DArTag is suited for genomic selection candidates in the clonal evaluation trial, coupled with imputation to a higher-density platform for the training population. Using the software polyBreedR, an R package for the manipulation and analysis of polyploid marker data, the RMSE for imputation by linkage analysis was 0.15 in a small half-diallel population (N=85), which was significantly lower than the RMSE of 0.42 with the Random Forest method. Regarding high-value traits, the DArTag markers for resistance to potato virus Y, golden cyst nematode, and potato wart appeared to track their targets successfully, as did multi-allelic markers for maturity and tuber shape. In summary, the potato DArTag assay is a transformative and publicly available technology for potato breeding and genetics.</p>
Alfalfa genotyping-by-sequencing (GBS) data
<p>Alfalfa (<i>Medicago</i> <i>sativa</i> L.) quantitative trait loci (QTL) mapping population (184 F<sub>1</sub>) derived from cultivars 3010 (cold-tolerant) as female parent and CW 100 (cold-sensitive) as male parent were genotyped using genotyping-by-sequencing (GBS). Polymorphic SNPs unique to either 3010 (AB x AA) or CW 1010 (AA x AB) were identified as single dose allele (SDA) markers and used to generate the genetic linkage maps. Two sets of linkage maps, a set for each parent, were used to map the traits and the QTL were identified. With the genotyping and phenotyping informations we were able to map various alfalfa traits such as fall dormancy, winter-hardiness, freezing tolerance, flowering time, yield and leaf-rust resistance. The raw sequence data were deposited at NCBI SRA with the accession number SRP150116. This study identified several genomic regions and associated markers that can be further utilized in marker-assisted breeding to improve the alfalfa. </p>
Data from: A comparison of non-destructive visceral swab and tissue biopsy sampling methods for genotyping-by-sequencing in the freshwater mussel Fusconaia askewi
<p>Limiting harm to organisms via genetic sampling is an important consideration for rare species. Nondestructive sampling techniques have been developed to address this issue in freshwater mussels. Two methods, visceral swabbing and tissue biopsies, have proven to be effective for DNA sampling, though it is unclear as to which method is preferable for genotyping-by-sequencing (GBS). Tissue biopsies may cause undue stress and damage to organisms, while visceral swabbing potentially reduces the chance of such harm. Our study compared the efficacy of these two DNA sampling methods for generating GBS data for the Unionid freshwater mussel, Texas Pigtoe (<em>Fusconaia askewi</em>). Our results find both methods generate quality sequence data, though some considerations are in order. Tissue biopsies produced significantly higher DNA concentrations and larger numbers of reads when compared to swabs, though there was no significant association between starting DNA concentration and number of reads generated. Swabbing produced greater sequence depth (more reads per sequence) while tissue biopsies revealed greater coverage across the genome (at lower sequence depth). Patterns of genomic variation as characterized in principal component analyses were similar regardless of the sampling method, suggesting that the less invasive swabbing is a viable option for producing quality GBS data in these organisms.</p>
Alfalfa genotyping-by-sequencing (GBS) data
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Colonization history of the Canary Islands endemic Lavatera acerifolia, (Malvaceae) unveiled with Genotyping-by-Sequencing data and niche modeling
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GBS SNP datasets from "Genotyping-by-sequencing resolves relationships in Polygonaceae tribe Eriogoneae", TAXON
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Data from: Targeted genotyping-by-sequencing of potato and data analysis with R/polyBreedR
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Data from: RapidRat: development, validation and application of a genotyping-by-sequencing panel for rapid biosecurity and invasive species management
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Data from: A comparison of non-destructive visceral swab and tissue biopsy sampling methods for genotyping-by-sequencing in the freshwater mussel Fusconaia askewi
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Genotyping-by-sequencing Single-nucleotide Polymorphism Dataset for Corynorhinus rafinesquii (CORA) and Myotis austroriparius (MYAU)
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Genotyping-by-sequencing of Canada’s Apple Biodiversity Collection
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Assigning the sex-specific markers via genotyping-by-sequencing onto the Y chromosome for a torrent frog Amolops mantzorum
<p><span>We use a genotyping-by-sequencing (GBS) approach to identify sex-linked markers in a torrent frog (<i>Amolops mantzorum</i>) using wild-caught individuals of 21 males and 19 females from the same population. A total of 141 putatively sex-linked markers were screened from 1,015,964 GBS tags through three approaches, respectively based on sex differences in allele frequencies, sex difference in heterozygosity, and sex-limited occurrence. With validations, 69 sex-linked markers were confirmed, all of which point to male heterogamety. The male specificity of eight sex markers was further verified by PCR amplifications with a large number of additional individuals covering the whole geographic distribution of the species. Y chromosome (No. 5) was microdissected under a light microscope, amplified by whole-genome amplification, and assembled a draft Y genome. 55 out of 69 sex-linked markers could be mapped to the Y chromosome assembly (i.e 79.7 %). Thus the chromosome 5 could be added as candidate chromosomes that particularly favored to recruit for sex determination than others among frogs. Three sex-linked markers that mapped on Y chromosome were aligned to three different promoter regions of <i>Rana rugosa</i> CYP19A1 gene, which might be considered as a candidate gene to trigger sex determination in <i>A</i>.<i> mantzorum</i>.</span></p>
The 49,890 SNPgenotype derived from genotyping-by-sequencing strategy for the NIP/9311 backcross inbred lines population
<p>Transmission ratio distortion (TRD) refers to a widespread phenomenon in which one allele is transmitted by heterozygotes more frequently to the progeny than the opposite allele. TRD is considered as a mark suggesting the presence of reproductive barrier. However, the genetic and molecular mechanisms underlying TRD in rice remain largely unknown. In the present study, a population of backcross inbred lines (BILs) derived from the cross of a japonica cultivar Nipponbare and an indica variety 9311 was utilized to study the genetic base of TRD. A total of eighteen genomic regions were identified for TRD in the BILs. Among them, twelve and six regions showed indica (9311) and japonica (Nipponbare) alleles with preferential transmission, respectively. A series of F2 populations were used to confirm the TRD effects, including six genomic regions that were confirmed by chromosome segment substitution line (CSSL)-derived F2 populations from inter-subspecific allelic combinations. However, none of the regions was confirmed by the CSSL-derived populations from intra-subspecific allelic combination. Furthermore, significant epistatic interaction was found between TRD1.3 and TRD8.1 suggesting that TRD could positively contribute to breaking inter-subspecific reproductive barriers. Our results have laid the foundation for identifying the TRD genes and provide an effective strategy to breakdown TRD for breeding wide-compatible lines, which will be further utilized in the inter-subspecific hybrid breeding programs.</p>
Data from: Genotyping-by-sequencing for Populus population genomics: an assessment of genome sampling patterns and filtering approaches
Continuing advances in nucleotide sequencing technology are inspiring a suite of genomic approaches in studies of natural populations. Researchers are faced with data management and analytical scales that are increasing by orders of magnitude. With such dramatic advances comes a need to understand biases and error rates, which can be propagated and magnified in large-scale data acquisition and processing. Here we assess genomic sampling biases and the effects of various population-level data filtering strategies in a genotyping-by-sequencing (GBS) protocol. We focus on data from two species of Populus, because this genus has a relatively small genome and is emerging as a target for population genomic studies. We estimate the proportions and patterns of genomic sampling by examining the Populus trichocarpa genome (Nisqually-1), and demonstrate a pronounced bias towards coding regions when using the methylation-sensitive ApeKI restriction enzyme in this species. Using population-level data from a closely related species (P. tremuloides), we also investigate various approaches for filtering GBS data to retain high-depth, informative SNPs that can be used for population genetic analyses. We find a data filter that includes the designation of ambiguous alleles resulted in metrics of population structure and Hardy-Weinberg equilibrium that were most consistent with previous studies of the same populations based on other genetic markers. Analyses of the filtered data (27,910 SNPs) also resulted in patterns of heterozygosity and population structure similar to a previous study using microsatellites. Our application demonstrates that technically and analytically simple approaches can readily be developed for population genomics of natural populations.
Data from: Identification and characterization of sex-associated loci in sockeye salmon using genotyping-by-sequencing and comparison with a sex-determining assay based on the sdY gene
Loci that can be used to screen for sex in salmon can provide important information for study of both wild and cultured populations. Here, we tested for associations between sex and genotypes at thousands of loci available from a genotyping-by-sequencing (GBS) dataset to discover sex-associated loci in sockeye salmon (Oncorhynchus nerka). We discovered seven sex-associated loci, developed high-throughput assays for two loci, and tested the utility of these two assays in eight collections of sockeye salmon sampled throughout North America. We also screened an existing assay based on the master sex-determining gene in salmon (sdY) in these collections. The ability of GBS-derived loci to assign fish to their phenotypic sex varied substantially among collections suggesting that recombination between the loci that we discovered and the sex-determining gene has occurred. Assignment accuracy to phenotypic sex was much higher with the sdY assay but was still less than 100%. Alignment of sequences from GBS-derived loci to draft genomes for two salmonids provided strong evidence that many of these loci are found on the chromosome orthologous to the known sex chromosome in sockeye salmon. Our study is the first to describe the approximate location of the sex-determining region in sockeye salmon and indicates that sdY is also the master sex-determining gene in this species. However, discordances between sdY genotypes and phenotypic sex and the variable performance of GBS-derived loci warrant more research.
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Allen Brain Atlas
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International Brain Laboratory public data
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OpenNeuro
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