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2,785 results for “genotyping”
Data for: Plasticity and co-variation of root traits govern phosphorus acquisition among 20 wheat genotypes
<p>Trait plasticity (variation of a trait under environmental variability or gradients) and trait integration are both crucial for plant adaption to environmental change. Variations in different suite of root traits such as biomass allocation, morphology and physiology underlie diverse phosphorus (P) acquisition strategies among plants. Yet, how the intraspecific plasticity and integration of root traits influence plant adaptation to different P supply remains obscure. To characterize diverse adaptive strategies in relation to plant P acquisition, eight root traits were assessed in 20 wheat (<em>Triticum aestivum</em> L.) genotypes grown in a culture room with low and high P supply. High P supply increased shoot P accumulation and biomass of all wheat genotypes. The shoot P accumulation in genotypes with high P sensitivity (PS: calculated as shoot P content at low P / shoot P content at high P supply) was higher with high P supply and lower with low P supply compared with that in the genotypes with low PS. The high-PS genotypes exhibited larger variation in root length, root/shoot ratio and rhizosphere pH across P supplies than the low-PS genotypes, suggesting an integrated response at the whole-plant level. At low P supply, the high-PS genotypes had greater root length and specific root length, but lower acid phosphatase activity than the low-PS genotypes, which suggests contrasting P-acquisition strategies across the genotypes. Strong co-variation of root traits occurred across low-PS genotypes regardless of P supply; conversely, the high-PS genotypes only exhibited strong trait integration at low P supply, whereas high P supply sharply reduced root trait co-variation. Our findings suggest that P stress may strengthen root trait integration in wheat plants, and that both plasticity and integration of root traits drive plant adaptive strategies and tolerance to P-deficiency stress.</p>
Life-history genotype explains variation in migration activity in Atlantic salmon (Salmo salar)
<p>Data and R-script used in the paper titled in the title.</p>
Western redcedar single nucleotide polymorphism (SNP) genotyping data for genomic selection and population genetics
<p>Western redcedar (<em>Thuja plicata</em>) Single Nucleotide Polymorphism (SNP) data in Variant Call Format (VCF) for genomic selection training and target populations, genomic selection parents, and self-fertilized (selfing) lines, comprising 4,833 trees.</p> <p>Targeted sequencing-based genotyping was done by Capture-Seq methodology at Rapid Genomics (Neves est al. 2013). A set of 57,000 probes as designed for initial marker discovery, from which a panel of 20,858 probes was selected for genotyping. A set of transcriptomes (Shalev et al. 2018) (PRJNA704616) was aligned to the reference genome to identify SNPs. Candidate probes (120 nt) were initially designed in silico and 57,000 selected by removing candidates with poor base composition for hybridization (GC content <0.2 and >0.6, high G content >0.2 and long homopolymers >7), followed by removing probes aligning to more than one position on the reference genome (≥90% identity and length). The 57,000 probes represent 14,517 scaffolds (average 3.9 probes/scaffold), with 37,275 targeting at least one SNP and 19,725 mapping to intergenic regions not containing pre-identified SNPs. A set of 128 individuals were selected to validate the 57,000 probe panel and associated polymorphisms. Genomic DNA (0.5 ug) was fragmented (mean size 300 bp), followed by repair of ends, phosphorylation, adenylation, ligation of Illumina compatible adapters containing 8bp indexes and 5’ T-overhang, and 10 cycles PCR amplification with universal primers to produce sequencing-ready libraries. Libraries were quantified using PicoGreen. Libraries from 16 samples were pooled, hybridized to the 120 nt RNA probes following Agilent’s SureSelect Target Enrichment System (Agilent Technologies) and sequenced on an Illumina HiSeq X machine with paired-end 150bp cycle for an average sequencing depth per sample of 15X. Sequence data were aligned to the reference genome with BWA-MEM (http://arxiv.org/abs/1303.3997) and sets of four samples were combined to increase sequencing depth for identifying markers. Putative SNPs were identified using Freebayes (http://arxiv.org/abs/1207.3907) in 150bp on either side of the 57,000 probes and filtered probes that had more than 17 SNPs per 420 bp target region (150bp + 120bp + 150bp). The sequencing depth of the probes was used to select the final set of 20,885 probes, removing probes on both sides of the distribution (low and high sequencing depth), for Capture-Seq on the remainder of the samples.</p>
Genotype data for: Population genetics reveals divergent lineages and ongoing hybridization in a declining migratory fish species complex
<p>Deciphering the effects of historical and recent demographic processes responsible for the spatial patterns of genetic diversity and structure is a key objective in evolutionary and conservation biology. Using population genetic analyses, we investigated the demographic history, the contemporary genetic diversity and structure, and the occurrence of hybridization and introgression of two species of anadromous fish with contrasting life history strategies and which have undergone recent demographic declines, the allis shad (<em>Alosa alosa</em>) and the twaite shad (<em>Alosa fallax</em>). We genotyped 706 individuals from 20 rivers and 5 sites at sea in Southern Europe at thirteen microsatellite markers. Genetic structure between populations was lower for the nearly semelparous species <em>A. alosa</em>, which disperses greater distances compared to the iteroparous species, <em>A. fallax</em>. Individuals caught at sea were assigned at the river level for <em>A. fallax</em> and at the region level for A. alosa. Using an approximate Bayesian computation framework, we inferred that the most likely long term historical divergence scenario between both species and lineages involved historical separation followed by secondary contact accompanied by strong population size decline. Accordingly, we found evidence for contemporary hybridization and bidirectional introgression due to gene flow between both species and lineages. Moreover, our results support the existence of at least one distinct species in the Mediterrannean sea: <em>A. agone</em> in Golfe du Lion area, and another divergent lineage in Corsica. Overall, our results shed light on the interplay between historical and recent demographic processes and life history strategies in shaping population genetic diversity and structure of closely related species. The recent demographic decline of these species' populations and their hybridization should be carefully considered while implementing conservation programs.</p>
Raw Data Survival, Development and Reproduction of Gonipterus platensis on Eucalyptus genotypes
<p>Data used in the paper "The survival, development, and reproduction of <em>Gonipterus platensis </em>(Coleoptera: Curculionidae) on the main <em>Eucalyptus </em>(Myrtaceae) genotypes planted in Brazil"</p>
Data from: An integrated genotyping-by-sequencing polymorphism map for over 10,000 sorghum genotypes
[No abstract entered]
Data from: Stepwise Threshold Clustering: a new method for genotyping MHC loci using next-generation sequencing technology
Genes of the vertebrate major histocompatibility complex (MHC) are of great interest to biologists because of their important role in immunity and disease, and their extremely high levels of genetic diversity. Next generation sequencing (NGS) technologies are quickly becoming the method of choice for high-throughput genotyping of multi-locus templates like MHC in non-model organisms. Previous approaches to genotyping MHC genes using NGS technologies suffer from two problems: 1) a "gray zone" where low frequency alleles and high frequency artifacts can be difficult to disentangle and 2) a similar sequence problem, where very similar alleles can be difficult to distinguish as two distinct alleles. Here were present a new method for genotyping MHC loci – Stepwise Threshold Clustering (STC) – that addresses these problems by taking full advantage of the increase in sequence data provided by NGS technologies. Unlike previous approaches for genotyping MHC with NGS data that attempt to classify individual sequences as alleles or artifacts, STC uses a quasi-Dirichlet clustering algorithm to cluster similar sequences at increasing levels of sequence similarity. By applying frequency and similarity based criteria to clusters rather than individual sequences, STC is able to successfully identify clusters of sequences that correspond to individual or similar alleles present in the genomes of individual samples. Furthermore, STC does not require duplicate runs of all samples, increasing the number of samples that can be genotyped in a given project. We show how the STC method works using a single sample library. We then apply STC to 295 threespine stickleback (Gasterosteus aculeatus) samples from four populations and show that neighboring populations differ significantly in MHC allele pools. We show that STC is a reliable, accurate, efficient, and flexible method for genotyping MHC that will be of use to biologists interested in a variety of downstream applications.
Spatiotemporal monitoring of the rare Northern dragonhead, Dracocephalum ruyschiana (Lamiaceae): SNP genotyping and environmental niche modelling herbarium specimens
<p><strong>Aim: </strong>We have studied spatiotemporal genetic change in the Northern dragonhead, a plant species that has experienced a drastic population decline and habitat loss in Europe. We add a temporal perspective to the monitoring of dragonhead in Norway by genotyping herbarium specimens up to 200 years old. We also assess whether dragonhead has achieved its potential distribution in Norway. Location: Europe (mainly Norway)</p> <p><strong>Methods:</strong> We have applied a microfluidic array consisting of 96 SNP markers on 130 herbarium specimens collected from 1820 to 2008, mainly from Norway (83) but also beyond (47). We have compared our new genotype data with existing data from modern samples. We have modelled the species' environmental niche and potential distribution in Norway using sample metadata and observational records.</p> <p><strong>Results: </strong>The SNP array successfully genotyped all included herbarium specimens. The captured genetic diversity was negatively correlated with distance from Norway. The historical-modern comparison revealed similar genetic structure and diversity across space and limited genetic change through time in Norway. The ENM suggests that dragonhead is anchored in warmer and drier habitats.</p> <p><strong>Main conclusions: </strong>With appropriate design procedures, the SNP array technology is promising for genotyping old herbarium specimens. We found no signs of any regional bottleneck. The regional areas in Norway have remained genetically divergent, however, both from each other and more so from populations outside of Norway, rendering continued protection of the species in Norway relevant. The ENM suggests that dragonhead has not fully achieved its potential distribution in Norway.</p>
Data from: Nitrogen availability and plant-plant interactions drive leaf silicon concentration in wheat genotypes
<p><span>Estimating plasticity of leaf silicon (Si) in response to abiotic and biotic factors underpins our comprehension of plant defences and stress resistance in natural and agroecosystems. However, how nitrogen (N) addition and intraspecific plant-plant interactions affect Si accumulation remains unclear. </span></p> <p><span>We grew 19 durum wheat genotypes (<em>Triticum turgidum</em> ssp. durum) in pots, either alone, or in intra- or intergenotypic cultures of two individuals, and with or without N. </span><span>Aboveground biomass, plant height and leaf [Si] were quantified at the beginning of the flowering stage.</span></p> <p><span>Nitrogen addition</span> <span>decreased leaf</span> <span>[Si] for most genotypes, proportionally to the biomass increase. Si plasticity to plant-plant interactions varied significantly among genotypes, with both increases and decreases in </span><span>leaf</span> <span>[Si] when mixed with a neighbour, regardless of the mixture type (intra-/intergenotype). Besides, increased leaf [Si] in response to plant-plant interactions was associated with increased plant height.</span></p> <p><span>Our results suggest the occurrence of </span><span>both facilitation and competition for Si uptake from the rhizosphere in wheat mixtures. Future research should identify which leaf and root traits characterize facilitating neighbours for Si acquisition. We also show that Si could be involved in height gain in response to intraspecific competition, possibly for increasing light capture. This important finding opens up new research directions on Si and plant-plant interactions in both natural ecosystems and agroecosystems. More generally,</span> <span>o</span><span>ur results stress the need to explore leaf Si plasticity in responses to both abiotic and biotic factors to understand plant stress resistance.</span></p>
Genotyping-by-sequencing-based identification of Arabidopsis pattern recognition receptor RLP32 recognizing proteobacterial translation initiation factor IF1
<p>Activation of plant pattern-triggered immunity (PTI) relies on the recognition of microbe-derived structures, termed patterns, through plant-encoded surface-resident pattern recognition receptors (PRRs). We show that proteobacterial translation initiation factor 1 (IF1) triggers PTI in <em>Arabidopsis thaliana</em> and related Brassicaceae species. Unlike for most other immunogenic patterns, IF1 elicitor activity cannot be assigned to a small peptide epitope, suggesting that tertiary fold features are required for IF1 receptor activation. We have deployed natural variation in IF1 sensitivity to identify <em>Arabidopsis</em> leucine-rich repeat (LRR) receptor-like protein 32 (RLP32) as IF1 receptor using a restriction site-associated DNA sequencing approach. RLP32 confers IF1 sensitivity to rlp32 mutants, IF1-insensitive <em>Arabidopsis</em> accessions and IF1-insensitive <em>Nicotiana benthamiana</em>, binds IF1 specifically and forms complexes with LRR receptor kinases SOBIR1 and BAK1 to mediate signaling. Similar to other PRRs, RLP32 confers resistance to <em>Pseudomonas syringae</em>, highlighting an unexpectedly complex array of bacterial pattern sensors within a single plant species.</p>
Local adaptation to hosts and parasitoids shape Hamiltonella defensa genotypes across aphid species - Datasets and scripts
<p>Datasets and scripts from "Local adaptation to hosts and parasitoids shape <em>Hamiltonella defensa</em> genotypes across aphid species"</p>
Data from: Detecting macroevolutionary genotype-phenotype associations using error-corrected rates of protein convergence
<p><span>On macroevolutionary timescales, extensive mutations and phylogenetic uncertainty mask the signals of genotype-phenotype associations underlying convergent evolution. To overcome this problem, we extended the widely used framework of nonsynonymous-to-synonymous substitution rate ratios and developed the novel metric <em>ω<sub>C</sub></em>, which measures the error-corrected convergence rate of protein evolution. While </span><span><em>ω<sub>C</sub></em></span><span> distinguishes natural selection from genetic noise and phylogenetic errors in simulation and real examples, its accuracy allows an exploratory genome-wide search of adaptive molecular convergence without phenotypic hypothesis or candidate genes. Using gene expression data, we explored over 20 million branch combinations in vertebrate genes and identified the joint convergence of expression patterns and protein sequences with amino acid substitutions in functionally important sites, providing hypotheses on undiscovered phenotypes. We further extended our method with a heuristic algorithm to detect highly repetitive convergence among computationally nontrivial higher-order phylogenetic combinations. Our approach allows bidirectional searches for genotype-phenotype associations, even in lineages that diverged for hundreds of millions of years.</span></p>
Genomic Selection Paves Way for the Identification of Rust Disease Resistant Genotypes in Bread Wheat (Triticum aestivum).
<p><span>In the last two decades, genomic prediction (GP) or Genomic Selection (GS) methods have been widely adopted in various plant and animal breeding programs globally. GP/GS is a promising method that employs genomic markers to calculate genomic-estimated breeding values (GEBVs) to select best individuals. To evaluate the performance of different genomic selection (GS) models, we examined six different models namely, ridge regression (RR), least absolute shrinkage and selection operator (LASSO), genomic best linear unbiased prediction (GBLUP), elastic net (EN), reproducing kernel Hilbert spacing (RKHS), and random forest (RF) models, for seedling and adult plant resistance to leaf, stem and stripe rust of wheat using a panel of 347 wheat germplasm accessions. The GBLUP and RF models performed noticeably better than the other GS models, with mean predictive abilities of 0.5 and 0.4 for seedling resistance and 0.4 and 0.3 for adult plant resistance (APR) for leaf and stem rust, respectively. Unfortunately, except for a few environments, the performance of GP models in the current study is quite low for stripe rust for both seedling and APR. The outcomes of this study revealed the capability of GP to be applied for breeding initiatives aimed at developing wheat varieties resistant to rust diseases. </span><span>Moreover, based on favorable allele analysis we also identified a total of 2 lines (CRP-165/42, HGP1-470) that showed resistance to most of the pathotypes at seedling and adult plant stage to all three rusts.<strong><span> </span></strong>These lines can serve as valuable resources for future breeding programs focused on rust resistance.</span></p> <p><strong><span>Keywords: </span></strong><span>GS;</span><strong><span> </span></strong><span>GEBVs; leaf rust; stem rust; stripe rust; seedling resistance; APR</span></p>
Genotyping of 180 feathers of Golden eagle from french mountain massifs
<p><span>Two batches of 90 feathers of Golden eagle were genotyped. The first batch included 90 feathers collected during four consecutive years in four golden eagle territories of the Massif Central. Of these feathers, 19 were directly sampled from individuals (adults and chicks, see appendix A) and 71 were collected from nests. </span></p> <p><span>A second batch of 90 feather samples collected from nests or directly from individuals in five different French mountainous regions was performed: Drôme (N=13), Vanoise (N=4), Hautes-Alpes (N=22), Massif Central (N=40) and Pyrenees (N=11). </span></p> <p><span>These two batches of feathers were genotyped on 17 microsatellite markers divided into two multiplexes: A (8 markers) and B (9 markers). These markers were selected from several past studies (Gautschi et al. 2000; Hailer et al. 2005; Martinez-Cruz et al. 2005; Bourke and Dawson 2006; Bielikova et al. 2010). </span></p>
SSR and SNP profiles obtained for 40 non-redundant grapevine genotypes found in the living collection of Ain Taoujdate (Morocco)
<p>This dataset includes the genetic profiles (13 SSR and 240 SNP markers) of 40 grapevine genotypes identified in the living collection of Ain Taoujdate (Morocco)</p>
The Performance Growth and Yield of Genotypes Sweet Corn (Zea Mays Saccharata Sturt) by Silica Fertilizer Application
<p>This material has presented on 2nd International Conference on Advance Research in Agriculture and Food 2023 in October 25, 2023.</p>
Phased genotype data for FILET's analysis of introgression in D. simulans and D. sechellia
<p>This dataset contains all genotype files prepared for Schrider et al.'s analysis of introgression between D. simulans and D. sechellia. For more information see https://www.biorxiv.org/content/early/2017/09/25/170670</p>
High Density Sheep Genotypes used for Aseasonal GWAS
<p>Illumina Ovine HD genotypes of 257 ewes used for an out of season lambing GWAS</p>
Dataset specialist generalist genotype of Two-Spotted Spider Mite across various species of Lonicera and Euonymus europaeus.
<p>A map containing the Excel sheets, tables, figures, SPSS scripts and figures and an explanation of what is to find in all maps in the repository. </p>
Genotype data of 14 nuclear microsatellite loci for 18 Quercus chenii populations in China
<p>This dataset includes genotype data of 14 nuclear microsatellite loci for 419 individuals of Quercus chenii from 18 natural populations in China.</p>
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
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DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.