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opencc-by-4.0Oct 2023View details →

Integrative genome-wide analyses identify novel loci associated with kidney stones and provide insights into its genetic architecture

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opencc-by-4.0Mar 2022View details →

Genetic mutations and decreased protein expression of ABCG2 urate transporters are associated with susceptibility to gout, disease severity and renal-overload hyperuricemia

We are releasing the data and code of our study of clinically defined gouty patients.

opencc-zeroJul 2022View details →

Data from: Genetic dissection of grain iron and zinc, and thousand kernel weight in wheat (Triticum aestivum L.) using genome-wide association study

The study material in GWAS panel with 280 common bread wheat genotypes was selected from All India Coordinated Research Project on Wheat and Barley to map the genomic regions responsible for enhanced Grain Zinc Content (GZnC), Grain Iron Content (GZnC) and Thousand Kernel weight (TKW). Phenotypic data: The GWAS panel was evaluated at five different environments: E1-University of Agricultural Sciences, research farm, Dharwad (15°29'20.71"N, 74°59'3.35"E, 750m AMSL), E2-ICAR- Indian Agricultural Research Institute, New Delhi (28°38′30.5″N, 77°09′58.2″E, 228 m AMSL), E3-Indian Agricultural Research Institute, Jharkhand (24°16'58.4"N, 85°21'16.1"E, 651m AMSL), E4-ICAR-Indian Institute of Wheat and Barley, Karnal (29°41'8.2644''N, 76°59'25.9692''E, 250m AMSL), and E5-Punjab Agricultural University, Ludhiana (30o54' N, 75o48'E, 247m AMSL). Around 20 g of grain sample from each genotype were used for phenotyping GFeC and GZnC through high-throughput Energy Dispersive X-ray Fluorescence (ED-XRF) machine (model X-Supreme 8000; Oxford Instruments plc, Abingdon, United Kingdom) calibrated with glass beads-based values. To record TKW, the Numigral grain counter was used to count the grain number, the reading was set at 1000 grains and the weight of the grains was recorded in grams with an electronic balance. The GFeC, GZnC were expressed as milligram per kilogram (mg/kg), GPC in percentage (%), TKW in grams (gms). Genotypic data: Genomic DNA of the GWAS panel was extracted from the leaves of 21 days-old 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 14,790 high-quality SNPs was used in GWAS analysis. The detailed information of the methods and software used, data analysis and GWAS is available at DOI: 10.1038/s41598-022-15992-z.

opencc-by-4.0May 2024View details →

Molecular screening and genetic diversity of tick-borne pathogens associated with dogs and livestock ticks in Egypt

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opencc-by-4.0May 2024View details →

Supplemental files associated with the the manuscript "Genetic screening and metabolomics identify glial adenosine metabolism as a therapeutic target in Parkinson's disease"

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opencc-by-4.0Jul 2024View details →

Genetic alterations and expression programs of oral squamous cell carcinoma associated with betel quid chewing

Betel quid (BQ) chewing is a profound risk for oral squamous cell carcinoma (OSCC) in Southeast Asia. To decipher contributory genomic abnormalities and transcriptional reprogramming in these malignancies, we conducted a multi-omics survey, including exome sequencing of tumor-normal pairs from 261 male patients with OSCC (129 habitual BQ chewers and 132 non-BQ users), alone with integrated single-cell and spatial transcriptomics of a set of tumors. Comparative analyses of the mutational catalog identified enrichment of significantly altered genes (e.g mutations of TP53 and CHUK, copy gains of MAP3K13 and FADD, copy losses of CDKN2A) and mutational signatures associated with BQ chewing. Assessment of oncogenic and co-occurring actionable alterations demonstrated frequently altered oncogenic pathways (Hippo and p53 signaling) and potential combination therapy opportunities linked to BQ use. In addition, evaluation of epithelial, immune, stromal expression programs in the corresponding tissue compartments revealed a shift of tumor microenvironment in BQ-related OSCC, characterized by induced hypoxia of tumor epithelium, altered immunosuppression of dendritic cells, and raised sprouting angiogenesis of tumor endothelium. Quantitative predictions of intercellular communications inferred a more heterogeneous cell-cell crosstalk among BQ-related OSCC, highlighted by extensive interactions of fibroblasts and dendritic cells with other non-epithelial cell types via mostly extracellular matrix-receptor signaling pathways. Collectively, these differences in genomic landscape and tumor niche suggest that OSCC caused by BQ chewing could be an etiological subtype different from their BQ-negative counterparts.

opencc-by-4.0Sep 2024View details →

Identification of genetic loci and functional analysis of candidate gene, OsCycB1;5 associated with seed callus induction in rice (Oryza sativa L.)

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opencc-by-4.0Oct 2024View details →

Supplementary Figure S3 The leave-one-out analysis of the association between insomnia and MetS components genetically in the reverse MR analysis.

This figure described the leave-one-out analysis of the association between insomnia and MetS components  genetically in the reverse MR analysis.

opencc-by-4.0Oct 2024View details →

Supplementary Figure S2.The funnel plots of the association between insomnia and MetS components genetically in the reverse MR analysis.

This figure described the funnel plots of the association between insomnia and MetS components genetically in the reverse MR analysis.

opencc-zeroDec 2012View details →

Data from: Northern range expansion of European populations of the wasp spider Argiope bruennichi is associated with global warming correlated genetic admixture and specific temperature adaptations

Poleward range expansions are observed for an increasing number of species, which may be an effect of global warming during the past decades. However, it is still not clear in how far these expansions reflect simple geographical shifts of species ranges, or whether new genetic adaptations play a role as well. Here, we analyse the expansion of the wasp spider Argiope bruennichi into Northern Europe during the last century. We have used a range-wide sampling of contemporary populations and historical specimens from museums to trace the phylogeography and genetic changes associated with the range shift. Based on the analysis of mitochondrial, microsatellite and SNP markers, we observe a higher level of genetic diversity in the expanding populations, apparently due to admixture of formerly isolated lineages. Using reciprocal transplant experiments for testing overwintering tolerance, as well as temperature preference and tolerance tests in the laboratory, we find that the invading spiders have possibly shifted their temperature niche. This may be a key adaptation for survival in Northern latitudes. The museum samples allow a reconstruction of the invasion's genetic history. A first, small-scale range shift started around 1930, in parallel with the onset of global warming. A more massive invasion of Northern Europe associated with genetic admixture and morphological changes occurred in later decades. We suggest that the latter range expansion into far Northern latitudes may be a consequence of the admixture that provided the genetic material for adaptations to new environmental regimes. Hence, global warming could have facilitated the initial admixture of populations and this resulted in genetic lineages with new habitat preferences.

opencc-zeroDec 2017View details →

Data from: Standing genetic diversity and selection at functional gene loci are associated with differential invasion success in two non-native fish species

Invasive species are expected to experience a unique combination of high genetic drift due to demographic factors while also experiencing strong selective pressures. The paradigm that reduced genetic diversity should limit the evolutionary potential of invasive species and thus their potential for range expansion has received little empirical support, possibly due to the choice of genetic markers. Our goal was to test for effects of genetic drift and selection at functional genetic markers as they relate to the invasion success of two paired invasive goby species, one widespread (successful) and one with limited range expansion (less successful). We genotyped fish using two marker types: single nucleotide polymorphisms (SNPs) in known-function, protein-coding genes and microsatellites to contrast the effects of neutral genetic processes. We identified reduced allelic variation in the invaded range for the less-successful tubenose goby. SNPs putatively under selection were responsible for the observed differences in population structure between marker types for round goby (successful) but not tubenose goby (less successful). A higher proportion of functional loci experienced divergent selection for round goby, suggesting increased evolutionary potential in invaded ranges may be associated with round goby's greater invasion success. Genes involved in thermal tolerance were divergent for round goby populations but not tubenose goby, consistent with the hypothesis that invasion success for fish in temperate regions is influenced by capacity for thermal tolerance. Our results highlight the need to incorporate functional genetic markers in studies to better assess evolutionary potential for the improved conservation and management of species.

opencc-zeroDec 2015View details →

Data from: Genetic basis of adult migration timing in anadromous steelhead discovered through multivariate association testing

Migration traits are presumed to be complex and to involve interaction among multiple genes, thus we employed both univariate analyses and multivariate Random Forest (RF) machine learning algorithm to conduct association mapping of 15,239 single nucleotide polymorphisms (SNPs) for adult migration-timing phenotype in steelhead (Oncorhynchus mykiss). Our study focused on a model natural population of steelhead that exhibits two distinct migration-timing life histories with high levels of admixture in nature. Neutral divergence was limited between fish exhibiting summer- and winter-run migration owing to high levels of interbreeding, but a univariate mixed linear model found three SNPs from a major effect gene to be significantly associated with migration-timing (p < 0.000005) that explained 46% of trait variation. Alignment to the annotated S. salar genome provided evidence that all three SNPs localize within a 46 kb region overlapping GREB1-like (an estrogen target gene) on chromosome Ssa03. Additionally, multivariate analyses with RF identified that these 3 SNPs plus 15 additional SNPs explained up to 60% of trait variation. These candidate SNPs may provide the ability to predict adult migration-timing of steelhead to facilitate conservation management of this species and this study demonstrates the benefit of multivariate analyses for association studies.

opencc-zeroJul 2021View details →

Data from: Harvest is associated with the disruption of social and fine-scale genetic structure among matrilines of a solitary large carnivore

Harvest can disrupt wildlife populations by removing adults with naturally high survival. This can reshape sociospatial structure, genetic composition, fitness, and potentially affect evolution. Genetic tools can detect changes in local, fine-scale genetic structure (FGS) and assess the interplay between harvest-caused social and FGS in populations. We used data on 1,614 brown bears, Ursus arctos, genotyped with 16 microsatellites, to investigate whether harvest intensity (mean low: 0.13 from 1990-2005, mean high: 0.28 from 2006-2011) caused changes in FGS among matrilines (8 matrilines; 109 females ≥ 4 years of age), sex-specific survival and putative dispersal distances, female spatial genetic autocorrelation, matriline persistence, and male mating patterns. Increased harvest decreased FGS of matrilines. Female dispersal distances decreased and male reproductive success was redistributed more evenly. Adult males had lower survival during high harvest, suggesting that higher male turnover caused this redistribution and helped explain decreased structure among matrilines, despite shorter female dispersal distances. Adult female survival and survival probability of both mother and daughter were lower during high harvest, indicating that matriline persistence was also lower. Our findings indicate a crucial role of regulated harvest in shaping populations, decreasing differences among 'groups', even for solitary-living species, and potentially altering the evolutionary trajectory of wild populations.

opencc-by-4.0Dec 2018View details →

Supporting Data: S3 Data for the Genetic Epidemiology paper: "Spinning convincing stories for both true and false association signals"

The 'S3 Data' set, part of the Supporting Information for the Genetic Epidemiology paper: "Spinning convincing stories for both true and false association signals" by Richard J. Biedrzycki, Ashley E. Sier, Dongjing Liu, Erika N. Dreikorn, and Daniel E. Weeks. S3 Data. A zip file containing the set of information given to the annotators for the schizophrenia scan, the annotation summary sheets completed by each annotator, a csv file containing the scored data that were derived from the annotation sheets, and an R Markdown document containing the R commands used to carry out the analyses.

opencc-zeroNov 2022View details →

Genetic loci associated with winter survivorship in diverse lowland switchgrass populations: SNP read count data

High winter mortality is the most important factor limiting biomass yield of lowland switchgrass planted in the northern latitudes of North America. Due to the perennial growth habit and strong dependence on weather conditions to generate sufficient selection pressure to identify winter-hardy individuals, breeding of cold tolerant switchgrass cultivars requires many years. Identification of causal genetic variants for winter survivorship would accelerate the improvement of switchgrass biomass production. The objective of this study was to identify allelic variation associated with winter survivorship in lowland switchgrass populations using bulk segregant analysis (BSA). Twenty-nine lowland switchgrass populations were evaluated for winter survival at two locations in southern Wisconsin and 21 population with differential winter survivorship was used for BSA. A maximum of 10% of the individuals per population (8-20) was bulked to create survivor and non-survivor DNA pools. The DNA pools were evaluated using exome capture sequencing and allele frequencies were used to conduct statistical tests. The BSA tests revealed nine QTL from tetraploid populations and seven QTL from octoploid populations. Some markers were identified in multiple populations that originated across a broad geographic landscape, while other markers were site-specific. QTL at positions 88 Mb on chromosome 2N, 115 Mb on chromosome 5K, and 1 and 100 Mb on chromosome 9N were potentially the most useful QTL. Markers associated with winter survivorship in this study can be used to accelerate breeding cycles of lowland switchgrass populations and should lead to improvements in adaptation within USDA hardiness zones 4 and 5.

openNov 2022View details →

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

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).

Fig. 6 in Prey-associated genetic differentiation in two species of silver fly (Diptera: Chamaemyiidae), Leucotaraxis argenticollis and L. piniperda

Fig. 6. Haplotype network of Leucotaraxis piniperda DNA barcode sequences.The area of each pie chart is proportional to the number of samples sharing that haplotype. Small black dots represent unsampled haplotypes. Pie charts indicate the proportions of flies sampled from different host plant genera of adelgid prey.

Fig. 3. STRUCTURE plot for Leucotaraxis argenticollis genotyped with 15 in Prey-associated genetic differentiation in two species of silver fly (Diptera: Chamaemyiidae), Leucotaraxis argenticollis and L. piniperda

Fig. 3. STRUCTURE plot for Leucotaraxis argenticollis genotyped with 15 microsatellite loci.The height of each bar represents the proportion of an individual′s genotype assigned to each of K = 4 clusters.The names of the clusters correspond to those in Fig. 1C. Vertical black lines separate groups of individuals collected in different states or provinces and on different adelgid host plant genera.

Fig. 4. STRUCTURE plot for Leucotaraxis piniperda genotyped with 16 in Prey-associated genetic differentiation in two species of silver fly (Diptera: Chamaemyiidae), Leucotaraxis argenticollis and L. piniperda

Fig. 4. STRUCTURE plot for Leucotaraxis piniperda genotyped with 16 microsatellite loci. The height of each bar represents the proportion of an individual′s genotype assigned to: A) each of K = 2 clusters for analysis of all individuals, and B) each of K = 2 clusters for analysis of only western individuals.The names of the clusters correspond to those in Fig. 1D. Vertical black lines separate groups of individuals collected in different states or provinces and on different adelgid host plant genera.

Fig. 2 in Prey-associated genetic differentiation in two species of silver fly (Diptera: Chamaemyiidae), Leucotaraxis argenticollis and L. piniperda

Fig. 2. Individual-based isolation by distance for eastern and western groups of both Leucotaraxis species. Pairwise genetic distance was calculated as linear genotypic distance and Euclidean geographic distance was calculated from collection site coordinates. Points are differentially shaded for distances between two individuals collected from the same adelgid prey host plant genus (e.g., Tsuga—Tsuga), or for two individuals collected from different adelgid prey host plant genera (e.g., Tsuga—Pinus).