Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
183
datasets available to search
ShareScore release 0.9.0
Dataset results
183 results for “association mapping”
Data from: Genome wide association mapping of floral traits in cultivated sunflower (Helianthus annuus)
Floral morphology and pigmentation are both charismatic and economically relevant traits associated with cultivated sunflower (Helianthus annuus L.). Recent work has linked floral morphology and pigmentation to pollinator efficiency and seed yield. Understanding the genetic architecture of such traits is essential for crop improvement, and gives insight into the role of genetic constraints in shaping floral diversity. A diversity panel of 288 sunflower genotypes was phenotyped for a variety of morphological, phenological, and color traits in both a greenhouse and a field setting. Association mapping was performed using 5788 SNP markers using a mixed linear model approach. Several dozen markers across ten linkage groups were significantly associated with variation in morphological and color trait variation. Substantial trait plasticity was observed between greenhouse and field phenotyping, and associations differed between environments. Color traits mapped more strongly than morphology in both settings, with markers together explaining 16% of petal carotenoid content in the greenhouse, and 17% and 24% of variation in disc anthocyanin presence in the field and greenhouse, respectively. Morphological traits like disc size mapped more strongly in the field, with markers together explaining up to 19% of disc size variation. Loci identified here through association mapping within cultivated germplasm differ from those identified through biparental crosses between modern cultivated sunflower and either its wild progenitor or domesticated landraces. Several loci lie within genomic regions involved in domestication. Differences between phenotype expression under greenhouse and field conditions highlight the importance of plasticity in determining floral morphology and pigmentation.
Data from: Admixture mapping in a hybrid zone reveals loci associated with avian feather coloration
Identifying the genetic bases for color patterns has provided important insights into the control and expression of pigmentation and how these characteristics influence fitness. However, much more is known about the genetic bases for traits based on melanin pigments than for traits based on another major class of pigments, carotenoids. Here we use natural admixture in a hybrid zone between Audubon's and myrtle warblers (Setophaga coronata auduboni / S. c. coronata) to identify genomic regions associated with both types of pigmentation. Warblers are known for rapid speciation and dramatic differences in plumage. For each of five plumage coloration traits, we found highly significant associations with multiple SNPs across the genome and these were clustered in discrete regions. Regions near significantly associated SNPs were enriched for genes associated with keratin filaments, fibrils that makeup feathers. A carotenoid-based trait that differs between the taxa—throat color—had more than a dozen genomic regions of association. One cluster of SNPs for this trait overlaps the Scavenger Receptor Class F Member 2 (SCARF2) gene. Other scavenger receptors are presumed to be expressed at target tissues and involved in the selective movement of carotenoids into the target cells, making SCARF2 a plausible new candidate for carotenoid processing. In addition, two melanin-based plumage traits—colors of the eye line and eye spot—show very strong associations with a single genomic region mapping to chromosome 20 in the zebra finch. These findings indicate that only a subset of the genomic regions differentiated between these two warblers are associated with the plumage differences between them and demonstrate the utility of reduced-representation genomic scans in hybrid zones.
Genome-wide association mapping for component traits of drought and heat tolerance in wheat
<p>The study material in GWAS panel with 282 advanced breeding line of bread wheat genotypes from IARI stress breeding program was selected to map the genomic regions responsible for Drought and heat tolerance component traits.</p> <p>Phenotypic data:</p> <p>The GWAS panel was evaluated at multiple locations namely, IARI, New Delhi - DL (28.6550° N, 77.1888° E, MSL 228.61 m), ARI, Pune - PUNE (18.5204° N, 73.8567° E, MSL 560m), IIWBR, Karnal - IIWBR (29.6857° N, 76.9905°E, MSL 243m), IARI, Jharkhand - JR (24.1929° N, 85.3756° E, MSL 580m) and IARI RS, Indore - IND (22.7196° N, 75.8577° E, MSL 553 m) with augmented RCBD design. Three tratments viz, IR (Irrigated), RI (Restricted irrigated) and LS (Late sown) were imposed for control, drought and heat stress, respectively. Data was collected on traits like Days to heading (DH), Days to maturity (DM), Normalized Difference Vegetation Index (NDVI) at anthesis and grain filling stage, chlorophyll content (SPAD) of flag leaf at post anthesis stage, Plant height (PH), Canopy temperature (CT), Grain weight per spike (GWPS), Thousand Grain weight (TGW), Plot Yield (PLTY) and Biomass.</p> <p>Genotypic data:</p> <p>Genomic DNA of the GWAS panel was extracted from the leaves of seedlings by Cetyl Trimethyl Ammonium Bromide (CTAB) method. The panel was genotyped using Axiom Wheat Breeder's Genotyping Array (Affymetrix, Santa Clara, CA, United States) having 35,143 genome-wide SNPs. The monomorphic, markers with minor allele frequency (MAF) of <5%, missing data of >20%, and heterozygote frequency >25% were removed from the analysis. The remaining set of 10546 high-quality SNPs was used in GWAS analysis.</p> <p>The detailed information of the methods and software used, data analysis and GWAS is provided at doi: 10.3389/fpls.2022.943033</p>
Code and data associated with the paper 'Large-scale calcium imaging reveals a systematic V4 map for encoding natural scenes'
<p>Code and data associated with the paper 'Large-scale calcium imaging reveals a systematic V4 map for encoding natural scenes'.</p> <p>See Readme.pdf for data and code details.</p>
MAP 1 in Synopsis of Miridae (Hemiptera: Heteroptera) in Atlantic Forest Dominion, Espírito Santo State, Brazil: keys, diagnoses, new species, plant associations, and geographic distribution. Part I: Bryocorinae, Cylapinae and Deraeocorinae.
MAP 1. Vegetation types of Espírito Santo with inset showing location within Brazil (Based on Wikipedia 2023).
FIGURE 1. Map showing collection localities. A in Two new sponge-associated Branchiosyllis (Annelida: Syllidae: Syllinae) from Northeastern Brazil
FIGURE 1. Map showing collection localities. A, the two oceanic islands and a coastal region in Northeastern Brazil; B, Fernando de Noronha Island, 1: Buraco da Raquel; C, Rocas Atoll, 2 and 3: Canal da Barretinha and Piscina das Tartarugas, respectively; D, Todos os Santos Bay, 4: Ilha dos Frades. Colors of numbers and circles are just for a better view.
DMGAT: Predicting ncRNA-Drug resistance associations based on diffusion map and heterogeneous graph attention network
<p>Dataset for the paper: DMGAT: Predicting ncRNA-Drug resistance associations based on diffusion map and heterogeneous graph attention network</p>
Data from: Genome-wide association mapping of date palm fruit traits
Date palms (Phoenix dactylifera) are an important fruit crop of arid regions of the Middle East and North Africa. Despite its importance, few genomic resources exist for date palms, hampering evolutionary genomic studies of this perennial crop species. Here we report an improved long-read genome assembly for P. dactylifera that is 772.3 Mb in length, with contig N50 of 897.2 Kb, and use this to perform GWAS mapping of the sex determining region and 21 fruit traits. We find a fruit color GWAS at the R2R3-MYB transcription factor (VIRESCENS) gene and identify functional alleles that include a retrotransposon insertion and start codon mutation. We also find a GWAS peak for sugar composition spanning deletion polymorphisms in multiple linked invertase genes. MYB transcription factors and invertase are implicated in fruit color and sugar composition in other crop species, demonstrating the importance of parallel evolution in the evolutionary diversification of domesticated species.
Figure 2. Map showing the 10 in Arthropods associated with nests of Cacicus sp. and Psarocolius sp. (Passerida: Icteridae) in varzea forest near the meeting of the rivers Negro and Solimões (Central Amazonia, Brazil) at high water
Figure 2. Map showing the 10 sampling points, municipality of Iranduba, Amazonas State, Brazil. Note: modified from Kunth (1995).
Data from: Chromosome-scale reference genome and RAD-based genetic map of yellow starthistle (Centaurea solstitialis) reveal putative structural variation and QTLs associated with invader traits
<p>The data directory here includes all of the data and scripts necessary to recreate the results and plots for the manuscript titled "Chromosome-scale reference genome and RAD-based genetic map of yellow starthistle (Centaurea solstitialis) reveal putative structural variation and QTLs associated with invader traits". These data include a genetic map, QTL analysis, paleolog analysis, gene synteny analysis, and assembly validation for yellow starthistle (Centaurea solstitialis).</p>
Factors associated with the gender gap in the STEM sector: Comparison of theoretical and empirical concept maps and qualitative SWOT analysis
<p>Word tree STEM</p>
Factors associated with the gender gap in the STEM sector: Comparison of theoretical and empirical concept maps and qualitative SWOT analysis
<p>Word tree gender</p>
Factors associated with the gender gap in the STEM sector: Comparison of theoretical and empirical concept maps and qualitative SWOT analysis
<p>Word tree gap</p>
Factors associated with the gender gap in the STEM sector: Comparison of theoretical and empirical concept maps and qualitative SWOT analysis
<p>Word tree rights</p>
Factors associated with the gender gap in the STEM sector: Comparison of theoretical and empirical concept maps and qualitative SWOT analysis
<p>Empirical conceptual map</p>
Factors associated with the gender gap in the STEM sector: Comparison of theoretical and empirical concept maps and qualitative SWOT analysis
<p>Theoretical concept map</p>
Data from: Admixture mapping in a hybrid zone reveals loci associated with avian feather coloration
Open the record for dataset details and reuse information.
Data from: Genome wide association mapping of floral traits in cultivated sunflower (Helianthus annuus)
Open the record for dataset details and reuse information.
Data from: Genome-wide association mapping of resistance to Septoria nodorum leaf blotch in a Nordic spring wheat collection
Open the record for dataset details and reuse information.
Data from: Genome-wide association mapping of date palm fruit traits
Open the record for dataset details and reuse information.
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
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.