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28 results for “Marker Map”
Point, polygon, or marker? In search of the best geographic entity for mapping Cultural Ecosystem Services using the online PPGIS tool, "My Green Place."
<p>Excel files include the raw database and the processed data that led to the quadrat analyses. The "Matrix_raw data" file includes the raw data as downloaded from the server. This data was cleaned and organized for its posterior use. "Quadrat analyzes "file includes all the quadrat analyses resulting in each research question in the paper except question four. Question 4 can be seen in the file "Water analysis_Blaarmeersen." All excel files come with a "CODE" tab that describes each of the codes used, their meaning, and ways that were calculated where necessary. Two zip files include all the GIS files. The first one includes the GIS files from which "Matrix_raw data" was built from. The second folder includes the resulting maps from the quadrat analyses. In order to visualize them as in the paper, configure the symbology tab at the GIS software in quantile and the categories number, as shown in the paper.</p> <p>The production of the files in the "GIS_Processed data" folder was done via a repetitive line of commands in ArcGIS pro. The same process was followed for each one of the quadrat analysis described in the paper. Refer to "<a href="https://zenodo.org/api/files/72403e0b-78a9-4bbf-8dca-ed9b8702e3ae/Reproduction%20commands%20and%20parameters.pdf">Reproduction commands and parameters.pdf</a>" for further information.</p>
Mapping of the QTLs governing grain micronutrients and thousand kernel weight in wheat (Triticum aestivum L.) using high density SNP markers
<p>The mapping population consists of 166 recombinant inbred lines (RILs) derived from a cross between HD3086 and HI1500.</p> <p><strong>Phenotypic data</strong><br>The RILs population along with parents were evaluated under four conditions namely timely sown irrigation (TSIR) taken as control, timely sown restricted irrigation (TSRI), late sown irrigation (LSIR), and late sown restricted irrigation (LSRI) conditions at Delhi, and under restricted irrigation condition at Indore. From each plot, 20 random spikes were harvested and spikes from each plot were threshed separately. While cleaning, care was taken to prevent metal and dust contamination. The grain iron concentration (GFeC) and grain zinc concentration (GZnC) were measured using Energy Dispersive X-ray Fluorescence (ED-XRF) machine (model X-Supreme 8000 M/s Oxford Inc, USA). The thousand kernel weight (TKW) was recorded by counting 1000 grains manually and weighted with an electronic balance.</p> <p><strong>Genotypic data</strong><br>DNA was extracted from 21 days old seedlings using CTAB method (Murray and Thompson, 1980). Genomic DNA quality was determined using 0.8% agarose gel electrophoresis with λ DNA as the standard and quantified using nanodrop. The 35K SNP Axiom breeders' array was used for genotyping of parents and the RILs population.</p>
SNP markers used for QTL mapping in the inbred lines
<p><span>Young leaves of the 175 inbred lines and their seven parents were collected from seedlings grown in a greenhouse. </span><span>About 200 mg bulk leaf sample from three plants of a line was placed in 2 ml safe-lock </span><span>Eppendorf tube and stored at ‒80 </span><span>˚C for one night prior to crushing using a Mixer Mill (TissueLyser II, Qiagen, Germany). Genomic DNA was extracted using SIGMA DNA extraction kit (Sigma-Aldrich, St. Louis, MO, USA) following the manufacturer's instruction. DNA concentration and purity of the samples were assessed using a NanoDrop 2000c spectrophotometer (Thermo Scientific, Wilmington, DE, USA). The samples were processed and sequenced using tunable genotyping-by-sequencing (tGBS®) method by Data2Bio (Ames, IW, USA). Genomic DNA was digested using two restriction enzymes NSpI (5′-RCATG^Y-3′) and BfuCI/Sau3AI (5′-^GATC-3′) which created 3´and 5´overhangs, respectively. Two single-stranded oligos, one containing a sample-specific internal barcode and the other a universal oligo, were ligated to the complementary 3´ and 5´ overhangs, respectively. </span>All 175 inbred lines' and seven parents' treated DNA was pooled for construction of the tGBS library and sequencing. The raw sequence data were demultiplexed by barcode, which was subsequently removed bioinformatically from each sequence. The barcode-trimmed sequence reads of genotype were further trimmed using the trimming software, Lucy (Chou & Holmes, 2001; Li & Chou 2004) to remove low-quality reads based on Phred quality scores of Q15.</p>
Coverage data in males and females, and genetic markers used for genetic mapping of the guppy LG12 (sex chromosome pair)
<p>The study used genetic mapping and coverage data in genome sequences of multiple male and female individuals of <i>M. picta</i> from multiple natural populations to investigate genetic degeneration of the Y chromosome, and quantify gene loss from the Y. The files include coverage results from the sex chromosome that were (i) used for sexing the sequenced individuals, and (ii) combined with autosomal results to analyze M/F, M/A and F/A depth of coverage ratios. Genetic mapping was also used to validate sex linkage, and the data set includes files with genotypes of genetic markers.</p>
SNP markers used for QTL mapping in the inbred lines
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Coverage data in males and females, and genetic markers used for genetic mapping of the guppy LG12 (sex chromosome pair)
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Mapping of the QTLs governing grain micronutrients and thousand kernel weight in wheat (Triticum aestivum L.) using high density SNP markers
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QTL mapping and marker development for tolerance to sulfur phytotoxicity in melon (Cucumis Melo)
<p><span>Elemental sulfur is an effective, inexpensive fungicide for many foliar pathogens, but severe phytotoxicity prohibits its use on many melon varieties. Sulfur phytotoxicity causes chlorosis and necrosis of leaf tissue, leading to plant death in the most sensitive lines, while other varieties have little to no damage. A high-density, genotyping-by-sequencing (GBS)-based genetic map of a recombinant inbred line (RIL) population segregating for sulfur tolerance was used for a quantitative trait loci (QTL) mapping study of sulfur phytotoxicity in melon. One major (qSulf-1) and two minor (qSulf-8 and qSulf-12) QTL were associated with sulfur tolerance in the population. <a name="_Hlk40443716">The development of Kompetitive Allele-Specific PCR (KASP) markers developed across qSulf-1 decreased the QTL interval from 239 kb (cotyledons) and 157 kb (leaves) to 97 kb (both tissues). </a>The markers were validated for linkage to sulfur tolerance in a set of melon cultivars. These KASP markers can be incorporated into melon breeding programs for introgression of sulfur tolerance into elite melon germplasm.</span></p> <p> </p> <p> </p>
Construction of genetic linkage map based on SNP markers, QTL mapping and detection of candidate genes of growth-related traits in Pacific abalone using genotyping-by-sequencing
<p><a name="_Hlk72585736"><span>Pacific abalone (<i>Haliotis discus hannai</i>) is a commercially important high valued molluscan species. Its wild population has decreased in recent years. Pacific abalone is widely cultured in Korea. Traditional breeding programs have been implemented for hatchery production of abalone seeds. To obtain more genetic information for the molecular breeding program, a high-density linkage map and quantitative trait locus (QTL) for three growth-related traits was constructed for Pacific abalone. F1 cross population with two parents were sampled to construct the linkage map using genotyping by sequencing (GBS). A total of 664,630,534 clean reads and 56,686 SNPs were generated. In sum, 3,345 segregating SNPs were used to construct a consensus linkage map. The map spanned 1,747.023 cM with 18 linkage groups and an average interval of 0.55 cM. QTL analysis revealed two significant QTL in LG10 on the consensus linkage map in each growth-related trait. Both the QTLs are located in the telomere region of the chromosome. Moreover, four potential candidate genes for growth-related traits were identified in the QTL region. Expression analysis revealed that identified genes are involved in growth regulation of abalone. The newly constructed genetic linkage map, growth-related QTLs and potential candidate genes identified in the present study can be used as valuable genetic resources and will be useful for marker-assisted selection (MAS) of Pacific abalone in molecular breeding program.</span></a></p>
Data from: Mass production of SNP markers in a nonmodel passerine bird through RAD sequencing and contig mapping to the zebra finch genome
Here, we present an adaptation of restriction-site-associated DNA sequencing (RAD-seq) to the Illumina HiSeq2000 technology that we used to produce SNP markers in very large quantities at low cost per unit in the Réunion grey white-eye (Zosterops borbonicus), a nonmodel passerine bird species with no reference genome. We sequenced a set of six pools of 18–25 individuals using a single sequencing lane. This allowed us to build around 600 000 contigs, among which at least 386 000 could be mapped to the zebra finch (Taeniopygia guttata) genome. This yielded more than 80 000 SNPs that could be mapped unambiguously and are evenly distributed across the genome. Thus, our approach provides a good illustration of the high potential of paired-end RAD sequencing of pooled DNA samples combined with comparative assembly to the zebra finch genome to build large contigs and characterize vast numbers of informative SNPs in nonmodel passerine bird species in a very efficient and cost-effective way.
Fig. 1. Map showing the collection sites for 5 in Efficiency of RAPD, ISSR, iPBS, SCoT and phytochemical markers in the genetic relationship study of five native and economical important bamboos of North-East India
Fig. 1. Map showing the collection sites for 5 different native bamboos of North-East India. Number indicates the collection sites for the study, 1-Manipur hill; 2- Manipur Valley; 3-Mizoram; 4-Assam and 5-Sikkim. (Mapsource: https://eros.usgs.gov/).
MAP-IDM: Identification of Molecular Markers of Sudden Death at the Acute Phase of Myocardial Infarction
ClinicalTrials.gov study NCT00859300. IPD Sharing: Not stated. Countries: 1. Publications: 2.
Data from: Mass production of SNP markers in a nonmodel passerine bird through RAD sequencing and contig mapping to the zebra finch genome
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Construction of genetic linkage map based on SNP markers, QTL mapping and detection of candidate genes of growth-related traits in Pacific abalone using genotyping-by-sequencing
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Genetic maps and marker effects of four maize biparental crosses
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Data from: Mapping phenotypic, expression and transmission ratio distortion QTL using RAD markers in the Lake Whitefish (Coregonus clupeaformis)
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QTL mapping and marker development for tolerance to sulfur phytotoxicity in melon (Cucumis Melo)
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Data from: Mapping migration in a songbird using high-resolution genetic markers
Neotropical migratory birds are declining across the Western Hemisphere, but conservation efforts have been hampered by the inability to assess where migrants are most limited – the breeding grounds, migratory stopover sites, or wintering areas. A major challenge has been the lack of an efficient, reliable, and broadly applicable method for measuring the strength of migratory connections between populations across the annual cycle. Here we show how high-resolution genetic markers can be used to identify genetically distinct groups of a migratory bird, the Wilson's warbler (Cardellina pusilla), at fine enough spatial scales to facilitate assessing regional drivers of demographic trends. By screening 1626 samples using 96 highly divergent single nucleotide polymorphisms (SNPs) selected from a large pool of candidates (~450,000), we identify novel region-specific migratory routes and timetables of migration along the Pacific Flyway. Our results illustrate that high-resolution genetic markers are more reliable, precise, and amenable to high throughput screening than previously described intrinsic marking techniques, making them broadly applicable to large-scale monitoring and conservation of migratory organisms.
Data from: QTL linkage mapping of wing length in zebra finch using genome-wide single nucleotide polymorphisms markers
Avian wing length is an important trait that covaries with the ecology and migratory behaviour of a species and tends to change rapidly when the conditions are altered. Long-distance migrants typically have longer wings than short-distance migrants and sedentary species, and long-winged species also tend to be more dispersive. Although the substantial heritability of avian wing length is well established, the identification of causal genes has remained elusive. Based on large-scale genotyping of 1404 informative single nucleotide polymorphisms (SNP) in a captive population of 1067 zebra finches, we here show that the within-population variation of relative wing length (h2 = 0.74 ± 0.05) is associated with standing genetic variation in at least six genomic regions (one genome-wide significant and five suggestive). The variance explained by these six quantitative trait loci (QTL) sums to 36.8% of the phenotypic variance (half of the additive genetic variance), although this likely is an overestimate attributable to the Beavis effect. As avian wing length is primarily determined by the length of the primary feathers, we then searched for candidate genes that are related to feather growth. Interestingly, all of the QTL signals co-locate with Wnt growth factors and closely interacting genes (Wnt3a, Wnt5a, Wnt6, Wnt7a, Wnt9a, RhoU and RhoV). Our findings therefore suggest that standing genetic variation in the Wnt genes might be linked to avian wing morphology, although there are many other genes that also fall within the confidence regions.
Data from: QTL linkage mapping of wing length in zebra finch using genome-wide single nucleotide polymorphisms markers
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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)
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.