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1,155 results for “loci”
FIGURE 1 in Population genetics of the endangered catfish Pseudoplatystoma magdaleniatum (Siluriformes: Pimelodidae) based on species-specific microsatellite loci
FIGURE 1 | Sampling sites of Pseudoplatystoma magdaleniatum in the Magdalena-Cauca basin.
Conserved loci and tandem arrays of P450s facilitate evolution of insecticide resistance in noctuid moths
<p><span>Noctuid moths are major agricultural pests causing extensive crop damage worldwide. Their enhanced insecticide resistance is largely attributed to expansions and variations of cytochrome P450 genes, which play a pivotal role in adapting to environmental pressures. In this study, we analyzed genomic data from eight noctuid species and four representative Lepidopteran species to explore the evolutionary patterns and functional diversification of P450s. Our results reveal substantial expansions in the CYP3 and CYP4 subfamilies in noctuids, primarily driven by gene duplications forming extensive tandem arrays. Synteny analysis identified two conserved P450 loci across all examined Lepidopteran species; notably, noctuid species exhibit significant expansions at these loci—including a 20-gene cluster in <em>Spodoptera frugiperda </em>and an 18-gene cluster in <em>S. littoralis</em>. Phylogenetic analyses indicate that these expansions are lineage-specific to noctuids. Furthermore, molecular docking of P450s from these loci with nine pesticides suggests that these gene expansions may confer resistance to pyrethroids. Our findings provide crucial insights into the molecular mechanisms underlying noctuid adaptation and resistance, with important implications for developing more sustainable pest management strategies.</span></p>
Data from: Genome-wide search for quantitative trait loci controlling important plant and flower traits in petunia using an interspecific recombinant inbred population of Petunia axillaris and Petunia exserta
A major bottleneck in plant breeding has been the much limited genetic base and much reduced genetic diversity in domesticated, cultivated germplasm. Identification and utilization of favorable gene loci or alleles from wild or progenitor species can serve as an effective approach to increasing genetic diversity and breaking this bottleneck in plant breeding. This study was conducted to identify quantitative trait loci (QTL) in wild or progenitor petunia species that can be used to improve important horticultural traits in garden petunia. An F7 recombinant inbred population derived between Petunia axillaris and P. exserta was phenotyped for plant height, plant spread, plant size, flower counts, flower diameter, flower length, and days to anthesis, in Florida in two consecutive years. Transgressive segregation was observed for all seven traits in both years. The broad-sense heritability estimates for the traits ranged from 0.20 (days to anthesis) to 0.62 (flower length). A genome-wide genetic linkage map consisting 368 single nucleotide polymorphism bins and extending over 277 cM was searched to identify QTL for these traits. Nineteen QTL were identified and localized to five linkage groups. Eleven of the loci were identified consistently in both years; several loci explained up to 34.0% and 24.1% of the phenotypic variance for flower length and flower diameter, respectively. Multiple loci controlling different traits are co-localized in four intervals in four linkage groups. These intervals contain desirable alleles that can be introgressed into commercial petunia germplasm to expand the genetic base and improve plant performance and flower characteristics in petunia.
Genome-wide association study identifies 18 novel loci associated with left atrial volume and function
<p><strong>README</strong></p> <p>Publication: Genome-wide association study identifies 18 novel loci associated with left atrial volume and function</p> <p>Ahlberg and Andreasen et al.</p> <p>Published: 29 July 2021, doi: <a href="https://doi.org/10.1093/eurheartj/ehab466">https://doi.org/10.1093/eurheartj/ehab466</a></p> <p>summary statistics for LAmax: rntrn_ilamax.bgen.stats.betastd.tsv.gz <br> summary statistics for LAmin: rntrn_ilamin.bgen.stats.betastd.tsv.gz <br> summary statistics for LAAEF: rntrn_laaef.bgen.stats.betastd.tsv.gz <br> summary statistics for LAPEF: rntrn_lapef.bgen.stats.betastd.tsv.gz <br> summary statistics for LATEF: rntrn_latef.bgen.stats.betastd.tsv.gz </p> <p> </p> <p>Description:</p> <p>SNP: rs number or ID string<br> CHR: chromosome<br> BP: physical (base pair) position<br> GENPOS: genetic position either from bim file or interpolated from genetic map<br> ALLELE1: first allele in bim file (usually the minor allele), used as the effect allele<br> ALLELE0: second allele in bim file, used as the reference allele<br> A1FREQ: frequency of first allele<br> F_MISS: fraction of individuals with missing genotype at this SNP<br> BETA: effect size from BOLT-LMM approximation to infinitesimal mixed model<br> SE: standard error of effect size<br> P_BOLT_LMM_INF: infinitesimal mixed model association test p-value<br> P_BOLT_LMM: non-infinitesimal mixed model association test p-value<br> N: sample size <br> bstd: standardized effect size from BOLT-LMM <br> sestd: standardized standard error of effect size</p>
Supplementary tables and figures - Excluding loci with substitution saturation improves inferences from phylogenomic data
<p>Supplementary tables and figures - Excluding loci with substitution saturation improves inferences from phylogenomic data</p>
Clustering of loci controlling species differences in male chemical bouquets of sympatric Heliconius butterflies
<p>The degree to which loci promoting reproductive isolation cluster in the genome – <i>i.e. </i>the genetic architecture of reproductive isolation - can influence the tempo and mode of speciation. Tight linkage between these loci can facilitate speciation in the face of gene flow. Pheromones play a role in reproductive isolation in many Lepidoptera species, and the role of endogenously-produced compounds as secondary metabolites decreases the likelihood of pleiotropy associated with many barrier loci. <i>Heliconius </i>butterflies use male sex pheromones to both court females (aphrodisiac wing pheromones) and ward off male courtship (male-transferred anti-aphrodisiac genital pheromones), and it is likely that these compounds play a role in reproductive isolation between <i>Heliconius </i>species. Using a set of backcross hybrids between <i>H. melpomene </i>and <i>H. cydno</i>, we investigated the genetic architecture of putative male pheromone compound production. We found a set of 40 significant quantitative trait loci (QTL) representing 33 potential pheromone compounds. QTL clustered significantly on two chromosomes, chromosome 8 for genital compounds and chromosome 20 for wing compounds, and chromosome 20 was enriched for potential pheromone biosynthesis genes. There was minimal overlap between pheromone QTL and known QTL for mate choice and color pattern. Nonetheless, we did detect linkage between a QTL for wing androconial area and <i>optix</i>, a color pattern locus known to play a role in reproductive isolation in these species. This tight clustering of putative pheromone loci might contribute to coincident reproductive isolating barriers, facilitating speciation despite ongoing gene flow.</p>
S and Z loci nucleotide sequences of Lolium multiflorum cultivar Rabiosa
<p>Nucleotide sequences of two scaffolds spanning the <em>S</em>-locus and two scaffolds the <em>Z</em>-locus in <em>Lolium multiflorum</em> cultivar Rabiosa</p>
Migration direction in a songbird explained by two loci
<p><span>Migratory routes and remote wintering quarters in birds are often species and even population specific. It has been known for decades that songbirds mainly migrate solitarily and that the migration direction is genetically controlled. Yet, the underlying genetic mechanisms remain unknown. To investigate the genetic basis of migration direction, we track genotyped willow warblers <em>Phylloscopus</em> <em>trochilus</em> from a migratory divide in Sweden, where South-West migrating and South-East migrating subspecies form a hybrid swarm. We find that migration direction follows a dominant inheritance pattern with epistatic interaction between the two loci explaining 74% of variation. Consequently, most hybrids migrate similarly to one of the parental subspecies and therefore do not suffer from the cost of following an inferior, intermediate route. This has significant implications for understanding the selection processes that maintain narrow migratory divides.</span></p>
Data from: Genomic loci involved in sensing environmental cues and metabolism affect seasonal coat shedding in Bos taurus and Bos indicus cattle
<p class="MsoNormal"><span>Seasonal shedding of winter hair at the start of summer is well-studied in wild and domesticated populations. However, the genetic influences on this trait and their interactions are poorly understood. We use data from 13,364 cattle with 36,899 repeated phenotypes to investigate the relationship between hair shedding and environmental variables, single nucleotide polymorphisms, and their interactions to understand quantitative differences in seasonal shedding. Using de-regressed estimated breeding values from a repeated records model in a genome-wide association analysis (GWAA) and meta-analysis of year-specific GWAA gave remarkably similar results. These GWAA identified hundreds of variants associated with seasonal hair shedding. There were especially strong associations on chromosomes 5 and 23. Genotype-by-environment interaction GWAA identified 1,040 day-length-by-genotype interaction associations and 17 apparent temperature-by-genotype interaction associations with hair shedding, highlighting the importance of day length on hair shedding. Accurate genomic predictions of hair shedding were created for the entire dataset, Angus, Hereford, Brangus, and multi-breed datasets. Loci related to metabolism and light-sensing have a large influence on seasonal hair shedding. This is one of the largest genetic analyses of a phenological trait and provides insight for both agriculture production and basic science.</span></p>
Meiosis at three loci in autotetraploids: Probabilities of gamete modes and genotypes without and with preferential cross-over formation
<div class="abstract">A long-standing goal in the field of polyploid biology has been the derivation of mathematical models of gamete mode formation. These models form the basis of statistical inference and evolutionary theory. Here, we present 3-locus models of gamete mode formation in autotetraploids without and with preferential cross-over formation. The three loci are assumed to occur on one arm of the same chromosome. For preferential cross-over formation, one of the three loci affects the tendency for sets of sister chromatids to pair and therefore affects rates of recombination. The models are derived such that the process of double reduction is a function of rates of synaptic partner switches and recombination, as opposed to being independent of these processes. We assume potentially one synaptic partner switch per meiosis. We also assume the coefficient of coincidence is one, such that cross-over events are independent, given a set of cross-over rates. Illustrative cases are examined demonstrating differences in the gamete mode probabilities without and with preferential cross-over formation. Lastly, we explore the accuracy of maximum likelihood estimates of the probability of synaptic partner switches and preferential cross-over formation when the locus controlling preferences is at a proximal, middle or distal location on the chromosome arm. All Supplementary Information is available at https://github.com/ckgriswold/3-locus-autotetraploid-meiosis.</div>
Stochastic motion and transcriptional dynamics of pairs of distal DNA loci on a compacted chromosome
<p>This repository contains the trajectory data from "Stochastic motion and transcriptional dynamics of pairs of distal DNA loci on a compacted chromosome".</p> <p><strong>Data sets</strong></p> <p>We provide data sets for the following constructs and imaging conditions, where we give the name of the construct and the MS2-parS genomic separation in kb:</p> <ul> <li>data_line0.csv: parS-homie-evePr-PP7, 58 kb</li> <li>data_line1.csv: parS-homie-evePr-PP7, 82 kb</li> <li>data_line2.csv: parS-homie-evePr-PP7, 88 kb</li> <li>data_line3.csv: parS-homie-evePr-PP7, 149 kb</li> <li>data_line4.csv: parS-homie-evePr-PP7, 190 kb</li> <li>data_line5.csv: parS-homie-evePr-PP7, 595 kb</li> <li>data_line6.csv: parS-homie-evePr-PP7, 3.3 Mb</li> <li>data_line3_5s.csv: parS-homie-evePr-PP7, 149 kb, 5 second time interval</li> <li>data_line0_nohomie.csv: parS-lambda-evePr-PP7, 58 kb</li> <li>data_line3_nohomie.csv: parS-lambda-evePr-PP7, 149 kb</li> </ul> <p><strong>Structure of Data</strong></p> <p>The trajectory data are provided as csv files consisting of 13 columns. The column headers are:</p> <ul> <li>cell_id: a unique cell index</li> <li>time_point: the time frame</li> <li>x_blue: x-coordinate of the locus in the blue channel (units in nm)</li> <li>y_blue: y-coordinate of the locus in the blue channel (units in nm)</li> <li>z_blue: z-coordinate of the locus in the blue channel (units in nm)</li> <li>x_green: x-coordinate of the locus in the green channel (units in nm) </li> <li>y_green: y-coordinate of the locus in the green channel (units in nm)</li> <li>z_green: z-coordinate of the locus in the green channel (units in nm) </li> <li>x_Rij: x-component of the aberration corrected 3D distance vector connecting the blue and green loci (units in nm)</li> <li>y_Rij: y-component of the aberration corrected 3D distance vector connecting the blue and green loci (units in nm)</li> <li>z_Rij: z-component of the aberration corrected 3D distance vector connecting the blue and green loci (units in nm)</li> <li>red: intensity in the red channel (a.u.)</li> <li>state: inferred state using a 3-state HMM, with entries 0 (O_off), 1 (P_off), 2 (P_on)</li> </ul>
Sol Genome Annotations and Quantitative Traits Loci
<p>RDF data graphs</p>
Integrative multi-ancestry genetic analysis of gene regulation in coronary arteries prioritizes disease risk loci
<p>All full-sample files contain results generated in coronary artery tissue from 138 American adults. Subset analyses utilized 80 individuals selected from the original 138. Scripts accompanying some of these data in downstream analyses can be viewed on our Github, which also contains a link to the current version of our accompanying manuscript: https://github.com/MillerLab-CPHG/CAD_QTL</p> <p>Full summary statistics for eQTL associations using mixQTL (https://github.com/hakyimlab/mixqtl/wiki) by chromosome are located in UVA_coronary_mixQTL_sumstats_by_chromosome.zip</p> <p>Full summary statistics for eQTL associations using mixQTL in the subset of 100% European-ancestry study sample members by chromosome are located in Hodonsky_mixQTL_Euro_sumstats.zip</p> <p>Full summary statistics for eQTL associations using mixQTL in the genetically diverse downsampled subset by chromosome are located in Hodonsky_mixQTL_downsample_sumstats.zip</p> <p>Full summary statistics for nominal pass for all genes identified as significant in the permutation pass using QTLtools (https://qtltools.github.io/qtltools/) adjusting for local ancestry by gene by chromosome are located in Local_ancestry_UVA_coronary_QTLtools_nominal_sumstats.zip</p> <p>Full summary statistics for sQTL associations with splice junctions using QTLtools by gene are located in sQTL_results_UVA_coronary_full_sumstats.zip</p>
Genotypes for yardstick population from the Nakai Plateau, Lao PDR at 25 loci
<p>Conservation biologists often deal with species that have small, fragmented populations throughout their range, making it necessary to prioritize populations for management. Genetics provides tools to assist with prioritization according to the levels and distribution of genetic diversity and evolutionary distinctiveness. Many studies have used nuclear microsatellite loci to measure genetic diversity in disparate populations and mitochondrial DNA to assess genetic distinctiveness. However, comparing metrics based on microsatellite genotypes ascertained in different laboratories is complicated by the selection of different loci with distinct nucleotide repeat motifs. This issue may be resolved by comparing metrics to a well-characterized reference population with shared microsatellite markers. The Asian elephant, <em>Elephas</em> <em>maximus</em>, is an endangered species with 50–60% of populations in India and Sri Lanka, and small, fragmented populations throughout southeast and insular Asia. We assessed range-wide genetic diversity of the Asian elephant by directly comparing allelic diversity and heterozygosity estimates from 35 populations, overcoming marker selection bias by calibrating metrics to a large population on the Nakai Plateau, Lao PDR, genotyped at 25 loci. We coupled these results with mtDNA analysis to evaluate genetic distinctiveness and identify potential conservation management units. We found the greatest diversity in the populations of southeast Asia and the greatest genetic distinctiveness among the subspecies designations, particularly Borneo and Sumatra, and other southeast Asian populations. The populations of southeast Asia, albeit small, fragmented, and at high risk of extirpation, contain valuable diversity and distinctiveness and are thus of high priority for the preservation of the Asian elephant.</p>
Identification of quantitative trait loci and associated candidate genes for pregnancy success in Angus – Brahman crossbred heifers
<p>Development of genomic tools to identify females with high genetic merit for reproductive function could increase the profitability and sustainability of beef production. Here, genome-wide association studies (GWAS) were performed on pregnancy outcome traits from a population of Angus – Brahman crossbred heifers. Furthermore, a validation GWAS was performed using data from another location. Heifers were genotyped with the Bovine GGP F250 array that contains ~250,000 SNPs. In the discovery population, heifers were bred in winter breeding seasons involving a single round of timed artificial insemination (AI) followed by natural mating for three months. Three phenotypes were analyzed: pregnancy outcome to first-service AI (PAI; n = 1481), pregnancy status at the end of the breeding season (PEBS; n = 1725), and pregnancy score (Pregscore where 1 = pregnant to first-service AI, 2 = pregnant to bull, 3 = not pregnant; n =1481). The heritability for PAI was estimated as 0.149. One large quantitative trait locus (QTL) that explained ~3% of the genetic variation for PAI was found on BTA7, in a region containing a cluster of γ-protocadherin genes and SLC25A2. Other QTLs explaining between 0.5-1% of the genetic variation were found on BTA12 and 25. The heritability of PEBS was estimated at 0.122. A large QTL on BTA7 was synonymous with the QTL for PAI, with minor QTL located on BTA5, 9, 10, 11, 19, and 20. Estimated heritability for Pregscore was 0.189. There was a large QTL on BTA7 synonymous with the other two traits as well as smaller QTLs on BTA1, 10, 15, 18, 19, and 20. The validation population for pregnancy status at the end of the breeding season were Angus-Brahman crossbred heifers bred by natural mating. In concordance with the discovery population, the large QTL on BTA7 and QTL on BTA10, 12 and 18 were identified. In summary, QTL and candidate SNPs associated with pregnancy outcomes in beef heifers were identified, including a large QTL associated with a group of protocadherin genes. Confirmation of these associations with larger populations could lead to the development of genomic estimates of reproductive function in beef cattle.</p>
Computationally defined and in vitro validated putative genomic safe harbour loci for transgene expression in human cells
<p>Selection of the target site is an inherent question for any project aiming for directed transgene integration. Genomic safe harbour (GSH) loci have been proposed as safe sites in the human genome for transgene integration. Although several sites have been characterised for transgene integration in the literature, most of these do not meet criteria set out for a GSH, and the limited set that do have not been characterised extensively. Here, we conducted a computational analysis using publicly available data to identify 25 unique putative GSH loci that reside in active chromosomal compartments. We validated stable transgene expression and minimal disruption of the native transcriptome in three GSH sites <em>in vitro</em> using human embryonic stem cells (hESCs) and their differentiated progeny. Furthermore, for easily targeted transgene expression, we have engineered constitutive landing pad expression constructs into the three validated GSH in hESCs.</p>
Meiosis at three loci in autotetraploids: Probabilities of gamete modes and genotypes without and with preferential cross-over formation
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Genetic and functional analysis of Raynaud’s syndrome implicates loci in vasculature and immunity
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Data from: Molecular mapping and identification of quantitative trait loci for domestication traits in field cress (Lepidium campestre L.) genome
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Population genetic structure of Nephrops norvegicus from the Adriatic Sea inferred using microsatellite loci
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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.