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1,155 results for “loci”
miRNA-independent function of long noncoding pri-miRNA loci
GEO Series GSE137048. Homo sapiens. 39 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing.
Pleiotropic loci associated with foot disorders and common periparturient diseases in Holstein cattle
GEO Series GSE186266. Bos taurus. 417 samples. Type: Genome variation profiling by SNP array.
Mapping quantitative trait loci and developing their KASP markers for Pre-harvest Sprouting resistance of Henan wheat varieties in China
GEO Series GSE222342. Triticum aestivum. 27 samples. Type: Expression profiling by high throughput sequencing.
Determinants of gastric cancer immune escape identified from non-coding immune-landscape quantitative trait loci
GEO Series GSE261709. Homo sapiens. 7 samples. Type: Other.
Data from: Annotation of pseudogenic gene segments by massively parallel sequencing of rearranged lymphocyte receptor loci
Background: The adaptive immune system generates a remarkable range of antigen-specific T-cell receptors (TCRs), allowing the recognition of a diverse set of antigens. Most of this diversity is encoded in the complementarity determining region 3 (CDR3) of the β chain of the αβ TCR, which is generated by somatic recombination of noncontiguous variable (V), diversity (D), and joining (J) gene segments. Deletion and non-templated insertion of nucleotides at the D-J and V-DJ junctions further increases diversity. Many of these gene segments are annotated as non-functional owing to defects in their primary sequence, the absence of motifs necessary for rearrangement, or chromosomal locations outside the TCR locus. Methods: We sought to utilize a novel method, based on high-throughput sequencing of rearranged TCR genes in a large cohort of individuals, to evaluate the use of functional and non-functional alleles. We amplified and sequenced genomic DNA from the peripheral blood of 587 healthy volunteers using a multiplexed polymerase chain reaction assay that targets the variable region of the rearranged TCRβ locus, and we determined the presence and the proportion of productive rearrangements for each TCRβ V gene segment in each individual. We then used this information to annotate the functional status of TCRβ V gene segments in this cohort. Results: For most TCRβ V gene segments, our method agrees with previously reported functional annotations. However, we identified novel non-functional alleles for several gene segments, some of which were used exclusively in our cohort to the detriment of reported functional alleles. We also saw that some gene segments reported to have both functional and non-functional alleles consistently behaved in our cohort as either functional or non-functional, suggesting that some reported alleles were not present in the population studied. Conclusions: In this proof-of-principle study, we used high-throughput sequencing of the TCRβ locus of a large cohort of healthy volunteers to evaluate the use of functional and non-functional alleles of individual TCRβ V gene segments. With some modifications, our method has the potential to be extended to gene segments in the α, γ, and δ TCR loci, as well as the genes encoding for B-cell receptor chains.
Data from: The identification of loci for immune traitsin chickens using a genome-wide association study
The genetic improvement of disease resistance in poultry continues to be a challenge. To identify candidate genes and loci responsible for these traits, genome-wide association studies using the chicken 60k high density single nucleotide polymorphism (SNP) array for six immune traits, total serum immunoglobulin Y (IgY) level, numbers of, and the ratio of heterophils and lymphocytes, and antibody responses against Avian Influenza Virus (AIV) and Sheep Red Blood Cell (SRBC), were performed. RT-qPCR was used to quantify the relative expression of the identified candidate genes. Nine significantly associated SNPs (P < 2.81E-06) and 30 SNPs reaching the suggestively significant level (P < 5.62E-05) were identified. Five of the 10 SNPs that were suggestively associated with the antibody response to SRBC were located within or close to previously reported QTL regions. Fifteen SNPs reached a suggestive significance level for AIV antibody titer and seven were found on the sex chromosome Z. Seven suggestive markers involving five different SNPs were identified for the numbers of heterophils and lymphocytes, and the heterophil/lymphocyte ratio. Nine significant SNPs, all on chromosome 16, were significantly associated with serum total IgY concentration, and the five most significant were located within a narrow region spanning 6.4kb to 253.4kb (P = 1.20E-14 to 5.33E-08). After testing expression of five candidate genes (IL4I1, CD1b, GNB2L1, TRIM27 and ZNF692) located in this region, changes in IL4I1, CD1b transcripts were consistent with the concentrations of IgY, while abundances of TRIM27 and ZNF692 showed reciprocal changes to those of IgY concentrations. This study has revealed 39 SNPs associated with six immune traits (total serum IgY level, numbers of, and the ratio of heterophils and lymphocytes, and antibody responses against AIV and SRBC) in Beijing-You chickens. The narrow region spanning 247kb on chromosome 16 is an important QTL for serum total IgY concentration. Five candidate genes related to IgY level validated here are novel and may play critical roles in the modulation of immune responses. Potentially useful candidate SNPs for marker-assisted selection for disease resistance are identified. It is highly likely that these candidate genes play roles in various aspects of the immune response in chickens.
Data from: Contrasting evolutionary histories of MHC class I and class II loci in grouse - effects of selection and gene conversion
Genes of the major histocompatibility complex (MHC) encode receptor molecules that are responsible for recognition of intra- and extra-cellular pathogens (class I and class II genes, respectively) in vertebrates. Given the different roles of class I and II MHC genes, one might expect the strength of selection to differ between these two classes. Different selective pressures may also promote different rates of gene conversion at each class. Despite these predictions, surprisingly few studies have looked at differences between class I and II genes in terms of both selection and gene conversion. Here, we investigated the molecular evolution of MHC class I and II genes in five closely related species of prairie grouse (Centrocercus and Tympanuchus) that possess one class I and two class II loci. We found striking differences in the strength of balancing selection acting on MHC class I versus class II genes. More than half of the putative antigen-binding sites (ABS) of class II were under positive or episodic diversifying selection, compared with only 10% at class I. We also found that gene conversion played a stronger role in shaping the evolution of MHC class II than class I. Overall, the combination of strong positive (balancing) selection and frequent gene conversion has maintained higher diversity of MHC class II than class I in prairie grouse. This is one of the first studies clearly demonstrating that macroevolutionary mechanisms can act differently on genes involved in the immune response against intra- and extra-cellular pathogens.
Data from: Genetic identification of Iberian rodent species using both mitochondrial and nuclear loci: application to non-invasive sampling
Species identification through non-invasive sampling is increasingly used in animal conservation genetics, given that it obviates the need to handle free-living individuals. Non-invasive sampling is particularly valuable for elusive and small species such as rodents. Although rodents are not usually assumed to be the most obvious target for conservation, of the 21 species or near-species present in Iberia, three are considered endangered and declining while several others are poorly studied. Here we develop a genetic tool for identifying all rodent species in Iberia by non-invasive genetic sampling. To achieve this purpose we selected one mitochondrial gene (cytochrome b – cyt-b) and one nuclear gene (interphotoreceptor retinoid-binding protein – IRBP), which we first sequenced using tissue samples. Both genes allow for the phylogenetic distinction of all species except the sibling species Microtus lusitanicus and M. duodecimcostatus. Overall, cyt-b showed higher resolution than IRBP, revealing a clear barcoding gap. To allow these markers to be applied to non-invasive samples, we selected a short highly-diagnostic fragment from each gene, which we used to obtain sequences from faeces and bones from owl pellets. Amplification success for the cyt-b and IRBP fragment was 85% and 43% in faecal and 88% and 64% in owl-pellet DNA extractions, respectively. The method allows the unambiguous identification of the great majority of Iberian rodent species from non-invasive samples, with application in studies of distribution, spatial ecology and population dynamics, and for conservation.
Data from: Lineage-specific mapping of quantitative trait loci
We present an approach for quantitative trait locus (QTL) mapping, termed "lineage-specific QTL mapping", for inferring allelic changes of QTL evolution along branches in a phylogeny. We describe and analyze the simplest case: by adding a third taxon into the normal procedure of QTL mapping between pairs of taxa, such inferences can be made along lineages to a presumed common ancestor. While comparisons of QTL maps among species can identify homology of QTLs by apparent co-location, lineage specific mapping of QTL can classify homology into (1) orthology (shared origin of QTL) versus (2) paralogy (independent origin of QTL within resolution of map distance). In this light, we present a graphical method that identifies six modes of QTL evolution in a three taxon comparison. We then apply our model to map lineage-specific QTLs for inbreeding among three taxa of yellow monkeyflower: Mimulus guttatus and two inbreeders M. platycalyx and M. micranthus, but critically assuming outcrossing was the ancestral state. The two most common modes of homology across traits were orthologous (shared ancestry of mutation for QTL alleles). The outbreeder M. guttatus had the fewest lineage- specific QTL, in accordance with the presumed ancestry of outbreeding. Extensions of lineage-specific QTL mapping to other types of data and crosses, and to inference of ancestral QTL state, are discussed.
Data from: Severity of mitral valve degeneration is associated with chromosome 15 loci in Whippet dogs
Mitral valve degeneration (MVD) is the most common form of heart disease in dogs, frequently leading to left-sided congestive heart failure and cardiac mortality. Although breed-specific disease characteristics and overrepresentation point towards a genetic origin for MVD, a causative mutation and complete molecular pathogenesis are unknown. Whippet dogs are overrepresented in incidence of MVD, suggesting an inherited component in this breed. Expressivity of this condition is variable with some dogs showing evidence of more severe disease at earlier ages than other dogs. This phenomenon makes a traditional case versus control genetic study prone to phenotyping error. This study sought to avoid these common pitfalls by identifying genetic loci associated with severity of MVD in Whippets through a genome-wide association study (GWAS). 138 Whippet dogs were characterized for MVD by echocardiographic examination and a novel disease severity score was developed and adjusted for age in each subject. Single nucleotide polymorphism (SNP) genotype data (170k Illumina CanineHD SnpChip) was obtained for DNA isolated from blood of each study subject. Continuous variable genome wide association was performed after correction for population stratification by efficient mixed model association expedited (EMMAX) in 130 dogs. A genome wide significant association was identified on chromosome 15 (peak locus 57,770,326; Padj = 0.049) and secondary loci of suggestive association were identified on chromosome 2 (peak locus 37,628,875; Padj = 0.079). Positional candidate genes were identified within the primary and secondary loci including follistatin-related protein 5 precursor (FSTL5) and Rho GTPase-activating protein 26 (ARHGAP26). These results support the hypothesis that severity of MVD in whippets has a genetic basis and warrants further study by either candidate gene sequencing or next-generation techniques.
Data from: Effects of interference between selected loci on the mutation load, inbreeding depression and heterosis
A classical prediction from single-locus models is that inbreeding increases the efficiency of selection against partially recessive deleterious alleles (purging), thereby decreasing the mutation load and level of inbreeding depression. However, previous multilocus simulation studies found that increasing the rate of self-fertilization of individuals may not lead to purging and argued that selective interference among loci causes this effect. In this article, I derive simple analytical approximations for the mutation load and inbreeding depression, taking into account the effects of interference between pairs of loci. I consider two classical scenarios of nonrandomly mating populations: a single population undergoing partial selfing and a subdivided population with limited dispersal. In the first case, correlations in homozygosity between loci tend to reduce mean fitness and increase inbreeding depression. These effects are stronger when deleterious alleles are more recessive, but only weakly depend on the strength of selection against deleterious alleles and on recombination rates. In subdivided populations, interference increases inbreeding depression within demes, but decreases heterosis between demes. Comparisons with multilocus, individual-based simulations show that these analytical approximations are accurate as long as the effects of interference stay moderate, but fail for high deleterious mutation rates and low dominance coefficients of deleterious alleles.
Data from: Genetic mapping of three quantitative trait loci for soybean aphid resistance in PI 567324
Host-plant resistance is an effective method for controlling soybean aphid (Aphis glycines Matsumura), the most damaging insect pest of soybean (Glycine max (L.) Merr.) in North America. Recently, resistant soybean lines have been discovered and at least four aphid resistance genes (Rag1, Rag2, Rag3 and rag4) have been mapped on different soybean chromosomes. However, the evolution of new soybean aphid biotypes capable of defeating host-plant resistance conferred by most single genes demonstrates the need for finding germplasm with multigenic resistance to the aphid. This study was conducted to map quantitative trait loci (QTL) for aphid resistance in PI 567324. We identified two major QTL (QTL_13_1 and QTL_13_2) for aphid resistance on soybean chromosome 13 using 184 recombinant inbred lines from a 'Wyandot' × PI 567324 cross. QTL_13_1 was located close to the previously reported Rag2 gene locus, and QTL_13_2 was close to the rag4 locus. A minor QTL (QTL_6_1) was also detected on chromosome 6, where no gene for soybean aphid resistance has been reported so far. These results indicate that PI 567324 possesses oligogenic resistance to the soybean aphid. The molecular markers closely linked to the QTL reported here will be useful for development of cultivars with oligogenic resistance that are expected to provide broader and more durable resistance against soybean aphids compared with cultivars with monogenic resistance.
Database of MSTN gene multi-loci genotypes of samples of the 1st trial (A22) of sheep breeds of Latvia within the framework of the project of the Latvian Council of Science LZP-2021/1-0489 project
<p><span>Project of The Latvian Council of Science (LCS) - LZP-2021/1-0489 project: “<strong>Development of an innovative approach to identify biological determinants involved in the between-animal variation in feed efficiency in sheep farming</strong>”.</span></p> <p><span>The <strong>aim of the project</strong> is</span><span> to determine whether the feed efficiency status of <span>Latvian meat sheep breeds</span> could be predicted using a panel of genetic and molecular markers previously found to be associated with divergent FE status in a training population of lambs when fed the same diet.</span></p> <p><strong><span>Novelty</span></strong><span>: to determine the parameters predicting the most productive result of lamb rearing, we set out to develop the cheapest and most effective method for determining markers of feed efficiency - based on molecular and genetic markers obtained from the blood of live lambs. </span></p> <p><strong><span>About the project:</span></strong></p> <p><span>The costs associated with lambing (buying or keeping sheep) and preparing or purchasing feed are the two most significant components of variable costs in sheep raising. Feed costs are high due to poor grain growing conditions in major producing countries, the use of feed grains in ethanol production, and increased competition for land in crop production compared to urban development<span>.</span> <span>Feed efficiency </span>in growing lambs (i.e., the animal’s ability to reach a market or adult body weight (BW) with the least feed intake) is a critical factor in the sheep industry. <span>Improving FE reduces production costs. Improving FE by 5% can bring economic benefits up to four times higher than a 5% increase in average daily gain (ADG).</span></span></p> <p><span>Traditionally, meat breeding programs have focused on outputs due mainly to the routine availability of phenotypic data on outputs or correlated traits. Currently, no marker has successfully explained enough of the variability in <span>feed efficiency </span>that they were used as part of a routine improvement program. According to our data, no genetic parameters for performance and feed efficiency traits are available for sheep. <span>The physiological determinants of feed efficiency or putative biomarkers used to analyse animal-to-animal variation in live lambs could be a cost-effective and rapid tool for genetic selection or management decisions.</span></span></p> <p><span>Myostatin (MSTN), a highly conserved member of the transforming growth factor-beta (TGF-b) superfamily, also known as growth/differentiation factor 8 (GDF8), the major regulator of myogenesis, functions as a negative regulator of muscle growth and development in mammals. Myostatin is a transforming growth factor (TGF)-β superfamily member and cannot be classified into the existing TGF-β subfamilies, such as inhibins or bone morphogenic proteins.<span> Mutations <em><span>MSTN</span></em> produce a “double-muscle” phenotype, making it commercially invaluable for improving livestock meat production and providing high-quality human protein. However, mutations at different loci of the <em><span>MSTN</span></em> often produce a variety of different phenotypes.</span></span></p> <p><strong><span>About the data of the project:</span></strong></p> <p><span>LZP-2021/1-0489 project data on lamb samples of the year 2022, or the A22 group, which consists of 76 intensively fattened lambs from six breeds.</span></p> <p><span><span>The whole MSTN gene was sequenced using Illumina NGS technology (AmpliSeq).</span></span><span><span> </span></span><span><span>The MSTN gene has been fully sequenced in lambs of Latvia (in sheep research in Latvia) for the first time. Information about 23 loci (</span></span><span><a href="https://doi.org/10.5281/zenodo.8146724"><span>https://doi.org/10.5281/zenodo.8146724</span></a></span><u><span>)</span></u><span><span> <span>compared with the last </span></span></span><span>reference sequences <span>ARS_UI_Ramb_v2.0.</span></span></p> <p><span>All variable SNPs in the MSTN gene were constructed by combining 24 distinct multi-loci genotypes. Reducing the number of loci to 16 by excluding those variables in only one sample or complete linkage disequilibrium did not decrease the number of genotypes. Among these 16 loci, 12 multi-locus genotypes were found in only one sample. To streamline the association analysis, the MSTN gene was divided into four regions: the promoter and exon 1, intron 1, intron 2, and the 3′UTR. This division helped reduce the number of multilocus genotypes.</span></p> <p><span>The database contains information on multiloci genotypes for four regions of the MSTN gene. </span><span>The multi-locus genotypes are presented using standard IUB/IUPAC nucleic acid codes, representing the genotype of two alleles at a single locus with a single letter.</span></p> <p> </p> <p><span><span>The data is the<strong><span> joint property</span></strong> of the participants of the LCS project: the University of Latvia and the Latvian University of Life Sciences and Technologies</span></span></p>
supplemental data for QTL MAPPING TO IDENTIFY LOCI AND CANDIDATE GENES ASSOCIATED WITH FREEZING TOLERANCE TRAIT IN CAMELINA SATIVA
Open the record for dataset details and reuse information.
Figure 1 from: Li Y, Lin L-S, Gao T-X (2018) Genetic signatures of polymorphic microsatellite loci in the Ambiguous silver pomfret, Pampus argenteus (Teleostei, Stromateidae). ZooKeys 810: 139-151. https://doi.org/10.3897/zookeys.805.25602
Figure 1 Locations (black circle) for sample collection of P.argenteus.
Microsatellite data of 21 EST-SSR loci from all 469 Emmenopterys henryi samples
<p>Several hypotheses are available to predict change in genetic diversity at expanding range margins. However, empirical evidence to test predictions of the central-marginal hypothesis (CMH) at contracting range limits is scarce. To address this issue, we assessed spatial patterns of genetic variation, effective population size, and contemporary and historical gene flow in a widespread, Tertiary relict tree species from subtropical China, <i>Emmenopterys henryi</i>.</p>
Polymorphisms at Distinct Genetic Loci Affect Response to Anti-CD20 Monoclonal Antibody Therapies
ClinicalTrials.gov study NCT02694913. IPD Sharing: NO. Countries: 1. Publications: 0.
Identification of Genomic Loci Determining Susceptibility to the Development of High Myopia
ClinicalTrials.gov study NCT02583620. IPD Sharing: Not stated. Countries: 1. Publications: 0.
GWAS Identified Susceptibility Loci for Glucocorticoid-induced FHN in the Chinese Population
ClinicalTrials.gov study NCT02365077. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Biological constraints on GWAS SNPs at suggestive significance thresholds reveal true BMI loci [hMSC_adipocytes_captureC]
GEO Series GSE164911. Homo sapiens. 3 samples. Type: Other.
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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.
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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.