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Dataset results
15 results for “haplotype analysis”
Fig 4. Median-joining haplotype network for M in Evolutionary relationships of Macaca fascicularis fascicularis (Raffles 1821) (Primates: Cercopithecidae) from Singapore revealed by Bayesian analysis of mitochondrial DNA sequences
Fig 4. Median-joining haplotype network for M. fascicularis. The size of the circular nodes representing haplotypes is proportional to the number of sequences comprising the haplotype. Shading of circular nodes corresponds to general geographic groupings including Sundaic islands (white), mainland Indochina (gray), Malay Peninsula and northern Sumatra (dark gray), and Singapore (black). Haplotype identifications are presented in Table 1.
Haplotype analysis of GWAS candidates identified for root:shoot ratio changes under salt stress in Arabidopsis
<p>The haplotype analysis was performed on 7 loci identified through GWAS by Magdalena Julkowska, while she was a PostDoc at KAUST, Saudi Arabia, workin in the lab of Dr. Mark Tester.</p>
Population genomics and haplotype analysis in spelt and bread wheat identifies a gene regulating glume color
<p>The cloning of agriculturally important genes is often complicated by haplotype variation across crop cultivars. Access to pan-genome information greatly facilitates the assessment of structural variations and rapid candidate gene identification. Here, we identified the <i>red glume 1</i> (<i>Rg-B1</i>) gene using association genetics and haplotype analyses in ten reference-grade wheat genomes. Glume color is an important trait to characterize wheat cultivars. Red glumes are frequent among Central European spelt, a dominant wheat subspecies in Europe before the 20<sup>th</sup> century. We used genotyping-by-sequencing to characterize a global diversity panel of 267 spelt accessions, which provided evidence for two independent introductions of spelt into Europe. A single region at the <i>Rg-B1</i> locus on chromosome 1BS was associated with glume color in the diversity panel. Haplotype comparisons across ten high-quality wheat genomes revealed a <i>MYB</i> transcription factor as candidate gene. We found extensive haplotype variation across the ten cultivars, with a particular group of <i>MYB</i> alleles that was conserved in red glume wheat cultivars. Genetic mapping and transient infiltration experiments allowed us to validate this particular <i>MYB</i> transcription factor variants. Our study demonstrates the value of multiple high-quality genomes to rapidly resolve copy number and haplotype variations in regions controlling agriculturally important traits.</p>
Haplotype analysis of the mitochondrial DNA d-loop region reveals the maternal origin and historical dynamics among the indigenous goat populations in east and west of the Democratic Republic of Congo (DRC)
<p><span>This study aimed at assessing haplotype diversity and population dynamics of three Congolese indigenous goat populations that included Kasai goat (KG), small goat (SG), and dwarf goat (DG) of the Democratic Republic of Congo (DRC). The 1,169 bp <em>d-loop</em> region of mitochondrial DNA (mtDNA) was sequenced for 339 Congolese indigenous goats. The total length of sequences was used to generate the haplotypes and evaluate their diversities, whereas the hypervariable region (HVI, 453 bp) was analyzed to define the maternal variation and the demographic dynamic. A total of 568 segregating sites that generated 192 haplotypes were observed from the entire <em>d-loop</em> region (1,169 bp <em>d-loop</em>). Phylogenetic analyses using reference haplotypes from the six globally defined goat mtDNA haplogroups showed that all the three Congolese indigenous goat populations studied clustered into the dominant haplogroup A, as revealed by the Neighbor-joining (NJ) tree and median-joining (MJ) network. Nine haplotypes were shared between the studied goats and goat populations from Pakistan (1 haplotype), Kenya, Ethiopia and Algeria (1 haplotype), Zimbabwe (1 haplotype), Cameroon (3 haplotypes), and Mozambique (3 haplotypes). The population pairwise analysis (<em>F<sub>ST</sub></em>) indicated a weak differentiation between the Congolese indigenous goat populations. Negative and significant (<em>p</em>-value < 0.05) values for <em>F</em>u's <em>F</em>s (-20.418) and Tajima's (-2.189) tests showed the expansion in the history of the three Congolese indigenous goat populations. These results suggest a weak differentiation and a single maternal origin for the studied goats. This information will contribute to the improvement of the management strategies and long-term conservation of indigenous goats in DRC</span><span>.</span></p>
Population genomics and haplotype analysis in spelt and bread wheat identifies a gene regulating glume color
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Data from: Rapid identification of chloroplast haplotypes using High-Resolution Melting analysis
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Haplotype analysis of the mitochondrial DNA d-loop region reveals the maternal origin and historical dynamics among the indigenous goat populations in east and west of the Democratic Republic of Congo (DRC)
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FIGURE 5. Haplotype analysis for C in The Oracle of Delphi-a molecular phylogenetic approach to Greek Cordulegaster Leach in Brewster, 1815 (Odonata: Anisoptera: Cordulegastridae)
FIGURE 5. Haplotype analysis for C. heros (TCS-network made in PopART 1.7).
FIGURE 6. Haplotype analysis for the Clade II in The Oracle of Delphi-a molecular phylogenetic approach to Greek Cordulegaster Leach in Brewster, 1815 (Odonata: Anisoptera: Cordulegastridae)
FIGURE 6. Haplotype analysis for the Clade II (TCS-network made in PopART 1.7).
CGH: Rag2_and_Rsv1-h_recombinant_haplotype_analysis
GEO Series GSE285240. Glycine max. 7 samples. Type: Genome variation profiling by genome tiling array.
Integrative analysis of haplotype-resolved epigenomes across human tissues
GEO Series GSE58752. Homo sapiens. 4 samples. Type: Other.
Microarray expression analysis of PRF1 (perforin 1) haplotypes in patients with primary progressive multiple sclerosis
GEO Series GSE23205. Homo sapiens. 10 samples. Type: Expression profiling by array.
Dissecting Agronomically Favorable Genotypes in Temperate Japonica Rice via Haplotype Analysis of a Japan-MAGIC Population
GEO Series GSE315158. Oryza sativa. 200 samples. Type: Expression profiling by high throughput sequencing.
Haplotype-Resolved Analysis of the Filaggrin Gene Elucidates its Complex Role in Human Adaptation and Disease
GEO Series GSE316840. Homo sapiens. 6 samples. Type: Expression profiling by high throughput sequencing.
Non-invasive prenatal paternity testing by analysis of Y-chromosome mini-STR haplotype using next-generation sequencing
GEO Series GSE186434. Homo sapiens. 14 samples. Type: Other.
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Allen Brain Atlas
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DANDI Archive for NWB datasets
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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
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