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1,019 results for “SNP”
Comparing mixed models and Random Forest association tests using naturalGWAS and a Striped Bass SNP dataset
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Obuasi case study data: Performance of neutral SNP barcodes to determine genetic diversity and structure of Plasmodium falciparum in Africa
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SNP genotypes of the international institute of tropical agriculture Cowpea Core
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Data from: Genome-wide SNP identification and association mapping for seed mineral concentration in Mung bean (Vigna radiata L.)
<p><span><span>Mung bean (<i>Vigna radiata</i> L.) quality is dependent on seed chemical composition, which in turn determines the benefits of mung bean consumption for human health. While rich in a range of nutritional components, such as protein, macro- and micro- nutrients, carbohydrates and vitamins, mung bean remains less well studied than other legume crops. Mung bean genomics and genetic resources are relatively sparse. To further improve nutritional levels of mung bean grain requires genome-wide marker system tools. The objectives of this research were to develop these tools and conduct nutrient analysis in order to 1) identify single nucleotide polymorphisms (SNPs) using genotyping by sequencing (GBS) and to 2) perform genome-wide association studies (GWAS) for levels of calcium, iron, potassium, manganese, phosphorous, sulfur, and zinc in mung bean grain produced over two years of field experiment. A total of 112 GWAS models were explored using 6,486 high quality SNPs discovered in 92 cultivated mung bean accessions chosen from USDA core collection that represented 13 countries. The data obtained allowed for the identification of 43 associated SNPs and 20 main genomic regions that explained on average 22 % of the overall variation in seed macro- and micro- nutrients concentration on the basis of a multiple-year analysis. Most of the regions discovered in this study provide valuable candidate gene to use in future breeding of new varieties of mung bean with novel nutritional properties. Identification of the <a>underlying genes</a> will help to reveal the genetic control of mung bean seed nutritional property. Other SNPs identified in this study will serve as important resources to enable marker-assisted selection (MAS) in the species <i>V</i>. <i>radiata</i>, including wide and narrow crosses with / between cultivated and wild mung bean.</span></span></p>
SNP array for parentage assignment of the Manila clam, Ruditapes philippinarum
<p>The Manila clam <i>Ruditapes philippinarum</i>, a major cultured shellfish species, is threatened by infection with the microparasite <i>Perkinsus olseni</i>, whose prevalence increases with high water temperatures. Under the current trend of climate change, the already severe effects of this parasitic infection might rapidly increase the frequency of mass mortality events. Treating infectious diseases in bivalves is notoriously problematic, therefore selective breeding for resistance represents a key strategy for mitigating the negative impact of pathogens. A crucial step in initiating selective breeding is the estimation of genetic parameters for traits of interest, which relies on the ability to record parentage and accurate phenotypes in a large number of individuals. Here, to estimate the heritability of resistance against <i>P. olseni</i>, a field experiment mirroring conditions in industrial clam production was set up, a genomic tool was developed for parentage assignment, and parasite load was determined through quantitative PCR.</p> <p>A mixed-family cohort of potentially 1479 clam families was produced in a hatchery by mass spawning of 53 dams and 57 sires. The progenies were seeded in a commercial clam production area in the Venice lagoon, Italy, where high prevalence of <i>P. olseni</i> had previously been reported. Growth and parasite load were monitored every month and, after one year, more than 1000 individuals were collected and DNA and phenotype records.</p> <p>A 245-SNP panel was developed using candidate markers obtained from a pooled sequencing approach on two DNA samples from all the potential parents and from a Venice lagoon clam population. For 246 individuals of the mixed-family F1, sire and dam representation were high (75 and 85%, respectively), indicating a very limited risk of inbreeding. Moderate heritability (0.20 – 0.30) was estimated for growth traits, while parasite load showed high heritability, estimated at 0.52. No significant genetic correlations were found between growth-associated traits and parasite load.</p> <p>Overall, the study shows high potential for selecting clams resistant to parasite<i> </i>load<i>.</i> Breeding for resistance may help limit the negative effects of climate change on clam production, as the prevalence of the parasite is predicted to increase under a future scenario of higher temperatures. Finally, the limited genetic correlation between resistance and growth suggests that breeding programs could incorporate dual selection without negative interactions.</p>
Filtered SNP tables - Rangewide, Hamilton, Tejon, and Madera transects
<p>Understanding how the environment shapes genetic variation provides critical insight about the evolution of local adaptation in natural populations. At multiple spatial scales and multiple geographic contexts within a single species, such information could address a number of fundamental questions about the scale of local adaptation and whether or not the same loci are involved at different spatial scales or geographic contexts. We used landscape genomic approaches from three local elevational transects and range-wide sampling to 1) identify genetic variation underlying local adaptation to environmental gradients in the California endemic oak, Quercus lobata, 2) examine whether putatively adaptive SNPs show signatures of selection at multiple spatial scales, and 3) map putatively adaptive variation to assess the scale and pattern of local adaptation. Of over 10k single-nucleotide polymorphisms (SNPs) generated with genotyping-by-sequencing, we found signatures of natural selection by climate or local environment at over 600 SNPs (536 loci), some at multiple spatial scales across multiple analyses. Candidate SNPs identified with gene–environment tests (LFMM) at the range-wide scale also showed elevated associations with climate variables compared to the background at both range-wide and elevational transect scales with gradient forest analysis. Some loci overlap with those detected in other oak species, raising the question of whether the same loci might be involved in local climate adaptation in different congeneric species that inhabit different geographic contexts. Mapping landscape patterns of adaptive versus background genetic variation identified regions of marked local adaptation and suggests nonlinear association of candidate SNPs and environmental variables. Taken together, our results offer robust evidence for novel candidate genes for local climate adaptation at multiple spatial scales.</p>
SNP discovery in Cryptomeria japonica var. sinensis using restriction-site associated DNA sequencing (RAD-seq)
<p>Our study is the first to explore the genetic composition of ancient <i>Cryptomeria</i> trees across distribution range in China. <i>Background and Objectives:</i> <i>Cryptomeria japonica </i>var. <i>sinensis</i> is a native forest species of China; it is widely planted in the south of the country to create forests and for wood production. Unlike <i>Cryptomeria</i> in Japan, genetic Chinese<i> Cryptomeria </i>has seldom been studied, although there is ample evidence of its great ecological and economic value. <i>Materials and Methods:</i> Because of overcutting, natural populations are rare in the wild. In this study, we investigated seven ancient tree populations to explore the genetic composition of Chinese <i>Cryptomeria</i> through ddRAD-seq technology. <i>Results:</i> The results reveal lower genetic variation but higher genetic differentiation (<i>Ho</i>=0.143, <i>F<sub>ST</sub></i>=0.1204) than Japanese <i>Cryptomeria </i>(<i>Ho</i>=0.245, <i>F<sub>ST</sub></i>=0.0455). The 86% within-population variation is based on analysis of molecular variance (AMOVA). Significant excess heterozygosity was detected in three populations and some outlier loci were found; these were considered to be the consequence of selection or chance. STRUCTURE analysis and dendrogram construction divided the seven ancient tree populations into four groups corresponding to the geographical provinces in which the populations are located, but there was no obvious correlation between genetic distance and geographic distance. Demographic history analysis conducted by a Stairway Plot showed that the effective population size of Chinese <i>Cryptomeria</i> had experienced a continuing decline from the mid-Pleistocene to the present. Our findings suggest that strong genetic drift caused by climate fluctuation and intense anthropogenic disturbance together contributed to the current low diversity and structure. Considering the species' unfavorable conservation status, strategies are urgently required to preserve the remaining genetic resources.</p>
Open Wild Wheat Consortium Variant (SNP) dataset
<p>Whole genome sequencing (7-30X) of Aegilops tauschii accessions (306) were aligned to reference genome AL8/78 using hisat2 (v2.1.0), variants were called using BCFtools (v1.9) and filtered and recalled using a custom awk script.</p>
Data from: Development of a Chinook salmon sex identification SNP assay based on the growth hormone pseudogene
Genotypic sex identification assays can provide valuable information about fish populations when phenotypic sex determination is difficult. Here we describe the development of a TaqMan® assay (Ots_SexID) designed to identify the genotypic sex of Winter-Run Chinook salmon collected from the Sacramento River and spawned at the Livingston Stone National Fish Hatchery. The TaqMan® assay targets a region previously examined in the growth hormone pseudogene. Accuracy of the marker was assessed by comparing genotypic sex assignments for Chinook salmon spawned at Livingston Stone National Fish hatchery in 2012 (n = 84) to phenotypic sex recorded during spawning. Genotypic sex was observed to be concordant with phenotypic sex identified using Ots_SexID in 83/84 individuals, suggesting that the assay could be used to predict phenotypic sex with ~99% accuracy. To evaluate the utility of the TaqMan® assay in other parts of the species' range, we examined collections from 29 other populations ranging from Alaska to California. Sex assignments based on the assay were generally concordant with observed phenotypes, but there were some strong exceptions. These results suggest that the new assay will be very useful in Sacramento River Winter-Run Chinook salmon, but also highlight the importance of thoroughly testing any sex identification assay prior to application in a population of interest.
Data from: A study of applicability of SNP chips developed for bovine and ovine species to whole-genome analysis of reindeer Rangifer tarandus
Two sets of commercially available single nucleotide polymorphisms (SNPs) developed for cattle (BovineSNP50 BeadChip) and sheep (OvineSNP50 BeadChip) have been trialed for whole-genome analysis of 4 female samples of Rangifer tarandus inhabiting Russia. We found out that 43.0% of bovine and 47.0% of Ovine SNPs could be genotyped, while only 5.3% and 2.03% of them were respectively polymorphic. The scored and the polymorphic SNPs were identified on each bovine and each ovine chromosome, but their distribution was not unique. The maximal value of runs of homozygosity (ROH) was 30.93Mb (for SNPs corresponding to bovine chromosome 8) and 80.32Mb (for SNPs corresponding to ovine chromosome 7). Thus, the SNP chips developed for bovine and ovine species can be used as a powerful tool for genome analysis in reindeer R. tarandus.
Data from: RAD sequencing yields a high success rate for westslope cutthroat and rainbow trout species-diagnostic SNP assays
Hybridization with introduced rainbow trout threatens most native westslope cutthroat trout populations. Understanding the genetic effects of hybridization and introgression requires a large set of high-throughput, diagnostic genetic markers to inform conservation and management. Recently, we identified several thousand candidate single nucleotide polymorphism (SNP) markers based on RAD sequencing of 11 westslope cutthroat trout and 13 rainbow trout individuals. Here we used flanking sequence for 56 of these candidate SNP markers to design high-throughput genotyping assays. We validated the assays on a total of 92 individuals from 22 populations and seven hatchery strains. Forty-six assays (82%) amplified consistently and allowed easy identification of westslope cutthroat and rainbow trout alleles as well as heterozygote controls. The 46 SNPs will provide high power for early detection of population admixture and improved identification of hybrid and non-hybridized individuals. This technique shows promise as a very low-cost, reliable, and relatively rapid method for developing and testing SNP markers for non-model organisms with limited genomic resources.
Data from: Insights into the genetic history of French cattle from dense SNP data on 47 worldwide breeds
BACKGROUND: Modern cattle originate from populations of the wild extinct aurochs through a few domestication events which occurred about 8,000 years ago. Newly domesticated populations subsequently spread worldwide following breeder migration routes. The resulting complex historical origins associated with both natural and artificial selection have led to the differentiation of numerous different cattle breeds displaying a broad phenotypic variety over a short period of time. METHODOLOGY/PRINCIPAL FINDINGS: This study gives a detailed assessment of cattle genetic diversity based on 1,121 individuals sampled in 47 populations from different parts of the world (with a special focus on French cattle) genotyped for 44,706 autosomal SNPs. The analyzed data set consisted of new genotypes for 296 individuals representing 14 French cattle breeds which were combined to those available from three previously published studies. After characterizing SNP polymorphism in the different populations, we performed a detailed analysis of genetic structure at both the individual and population levels. We further searched for spatial patterns of genetic diversity among 23 European populations, most of them being of French origin, under the recently developed spatial Principal Component analysis framework. CONCLUSIONS/SIGNIFICANCE: Overall, such high throughput genotyping data confirmed a clear partitioning of the cattle genetic diversity into distinct breeds. In addition, patterns of differentiation among the three main groups of populations—the African taurine, the European taurine and zebus—may provide some additional support for three distinct domestication centres. Finally, among the European cattle breeds investigated, spatial patterns of genetic diversity were found in good agreement with the two main migration routes towards France, initially postulated based on archeological evidence.
Data from: Genome-wide SNP data reveal cryptic phylogeographic structure and microallopatric divergence in a rapids-adapted clade of cichlids from the Congo River
The lower Congo River (LCR) is a freshwater biodiversity hotspot in Africa characterized by some of the world's largest rapids. However, little is known about the evolutionary forces shaping this diversity, which include numerous endemic fishes. We investigated phylogeographic relationships in Teleogramma, a small clade of rheophilic cichlids, in the context of regional geography and hydrology. Previous studies have been unable to resolve phylogenetic relationships within Teleogramma due to lack of variation in nuclear genes and discrete morphological characters among putative species. To sample more broadly across the genome we analyzed double-digest restriction-associated sequencing (ddRAD) data from 53 individuals across all described species in the genus. We also assessed body shape and mitochondrial variation within and between taxa. Phylogenetic analyses reveal previously unrecognized lineages and instances of microallopatric divergence across as little as ~1.5 km. Species ranges appear to correspond to geographic regions broadly separated by major hydrological and topographic barriers, indicating these features are likely important drivers of diversification. Mitonuclear discordance indicates one or more introgressive hybridization events, but no clear evidence of admixture is present in nuclear genomes, suggesting these events were likely ancient. A survey of female fin patterns hints that previously undetected lineage-specific patterning may be acting to reinforce species cohesion. These analyses highlight the importance of hydrological complexity in generating diversity in certain freshwater systems, as well as the utility of ddRAD-Seq data in understanding diversification processes operating both below and above the species level.
Data from: "Polar bear (Ursus maritimus) transcriptome assembly and SNP discovery" in Genomic Resources Notes accepted 1 August 2013-30 September 2013
Polar bears (Ursus maritimus) in the Western Hudson Bay subpopulation have been declining in size and body condition for decades, as climate change causes earlier sea ice breakup, reduced hunting time on the ice, and an increasingly long fasting season. As Western Hudson Bay females have decreased in size, rates of litter production and average litter size have also decreased, while cub mortality and average time to independence have increased. Although these changes have potential evolutionary consequences, little is yet known about the adaptive genetic variation in body size or fat accumulation that would have to underlie any such change. In this study, we used high-throughput Illumina sequencing to develop SNPs from pooled blood and fat transcriptomes, using samples from five adult female polar bears and five (unrelated) dependent cubs. In total, we generated 371,258 transcripts of which 36,755 were deemed to be "full length" (i.e., covered more than 90% of their best BLAST hit), and we identified 63,020 SNPs. Since this study was conducted, we have used a subset of these SNPs to develop an Illumina BeadArray for quantitative genetics research in Western Hudson Bay.
Data from: Identifying litchi (Litchi chinensis Sonn.) cultivars and their genetic relationships using single nucleotide polymorphism (SNP) markers
Litchi is an important fruit tree in tropical and subtropical areas of the world. However, there is widespread confusion regarding litchi cultivar nomenclature and detailed information of genetic relationships among litchi germplasm is unclear. In the present study, the potential of single nucleotide polymorphism (SNP) for the identification of 96 representative litchi accessions and their genetic relationships in China was evaluated using 155 SNPs that were evenly spaced across litchi genome. Ninety SNPs with minor allele frequencies above 0.05 and a good genotyping success rate were used for further analysis. A relatively high level of genetic variation was observed among litchi accessions, as quantified by the expected heterozygosity (He = 0.305). The SNP based multilocus matching identified two synonymous groups, 'Heiye' and 'Wuye', and 'Chengtuo' and 'Baitangli 1'. A subset of 14 SNPs was sufficient to distinguish all the non-redundant litchi genotypes, and these SNPs were proven to be highly stable by repeated analyses of a selected group of cultivars. Unweighted pair-group method of arithmetic averages (UPGMA) cluster analysis divided the litchi accessions analyzed into four main groups, which corresponded to the traits of extremely early-maturing, early-maturing, middle-maturing, and late-maturing, indicating that the fruit maturation period should be considered as the primary criterion for litchi taxonomy. Two subpopulations were detected among litchi accessions by STRUCTURE analysis, and accessions with extremely early- and late-maturing traits showed membership coefficients above 0.99 for Cluster 1 and Cluster 2, respectively. Accessions with early- and middle-maturing traits were identified as admixture forms with varying levels of membership shared between the two clusters, indicating their hybrid origin during litchi domestication. The results of this study will benefit litchi germplasm conservation programs and facilitate maximum genetic gains in litchi breeding programs.
Data from: Finding the right coverage: The impact of coverage and sequence quality on SNP genotyping error rates
Restriction-enzyme-based sequencing methods enable the genotyping of thousands of single nucleotide polymorphism (SNP) loci in non-model organisms. However, in contrast to traditional genetic markers, genotyping error rates in SNPs derived from restriction-enzyme-based methods remain largely unknown. Here, we estimated genotyping error rates in SNPs genotyped with double digest RAD sequencing from Mendelian incompatibilities in known mother-offspring dyads of Hoffman's two-toed sloth (Choloepus hoffmanni) across a range of coverage and sequence quality criteria, for both reference-aligned and de novo-assembled datasets. Genotyping error rates were more sensitive to coverage than sequence quality and low coverage yielded high error rates, particularly in de novo-assembled datasets. For example, coverage ≥5 yielded median genotyping error rates of ≥0.03 and ≥0.11 in reference-aligned- and de novo-assembled datasets, respectively. Genotyping error rates declined to ≤0.01 in reference-aligned datasets with a coverage >30, but remained >0.04 in the de novo-assembled datasets. We observed approximately 10- and 13-fold declines in the number of loci sampled in the reference-aligned and de novo-assembled datasets when coverage was increased from >5 to >30 at quality score ≥30, respectively. Finally, we assessed the effects of genotyping coverage on a common population genetic application, parentage assignments, and showed that the proportion of incorrectly assigned maternities was relatively high at low coverage. Overall, our results suggest that the tradeoff between sample size and genotyping error rates be considered prior to building sequencing libraries, reporting genotyping error rates become standard practice, and that effects of genotyping errors on inference be evaluated in restriction-enzyme-based SNP studies.
Data from: "White-tailed deer (Odocoileus virginianus) transcriptome assembly and SNP discovery" in Genomic Resources Notes accepted 1 June 2013-31 July 2013
White-tailed deer (Odocoileus virginianus) are among the most abundant and widespread large mammals in the Americas, comprising up to 38 subspecies ranging from Northern Canada to Peru. Although believed to have high genetic diversity, surprisingly few genomic resources are currently available, despite the species' ecological and economic importance. White-tailed deer and other cervids throughout central North America are currently being afflicted by chronic wasting disease (CWD), one of the degenerative prion diseases collectively known as transmissible spongiform encephalopathies. Although CWD is of major importance to white-tailed deer management, little is currently known about innate resistance or susceptibility to CWD outside of polymorphisms in the prion protein gene, Prnp, though a recent study using microsatellites suggests that the disease may have additional underlying genetic components. Further association analysis is hindered by low marker density. In this study, we used high-throughput SOLiD sequencing to create novel sequence data for white-tailed deer and identify single-nucleotide polymorphisms, using the pooled blood transcriptomes of six individuals. In total, we generated 14,010 contigs of length ≥ 200 nt, representing 4,104,760 nt of unique sequence data, and we identified 66,596 SNPs. This data represents one of the largest genetic resources currently available for any cervid. We hope it will facilitate future research for population genomics and assist with the identification of genetic factors that underlie disease resistance and other traits relevant for conservation and management.
Data from: Transatlantic secondary contact in Atlantic salmon, comparing microsatellites, a SNP array, and Restriction Associated DNA sequencing for the resolution of complex spatial structure
Identification of discrete and unique assemblages of individuals or populations is central to the management of exploited species. Advances in population genomics provide new opportunities for re-evaluating existing conservation units but comparisons among approaches remain rare. We compare the utility of RAD-seq, a single nucleotide polymorphism (SNP) array and a microsatellite panel to resolve spatial structuring under a scenario of possible trans-Atlantic secondary contact in a threatened Atlantic Salmon, Salmo salar, population in southern Newfoundland. Bayesian clustering indentified two large groups subdividing the existing conservation unit and multivariate analyses indicated significant similarity in spatial structuring among the three data sets. mtDNA alleles diagnostic for European ancestry displayed increased frequency in southeastern Newfoundland and were correlated with spatial structure in all marker types. Evidence consistent with introgression among these two groups was present in both SNP data sets but not the microsatellite data. Asymmetry in the degree of introgression was also apparent in SNP data sets with evidence of gene flow towards the east or European type. This work highlights the utility of RAD-seq based approaches for the resolution of complex spatial patterns, resolves a region of trans-Atlantic secondary contact in Atlantic Salmon in Newfoundland and demonstrates the utility of multiple marker comparisons in identifying dynamics of introgression.
Data from: Microevolution in time and space: SNP analysis of historical DNA reveals dynamic signatures of selection in Atlantic cod
Little is known about how quickly natural populations adapt to changes in their environment and how temporal and spatial variation in selection pressures interact to shape patterns of genetic diversity. We here address these issues with a series of genome scans in four overfished populations of Atlantic cod (Gadus morhua) studied over an 80-year period. Screening of >1000 gene-associated single-nucleotide polymorphisms (SNPs) identified 77 loci that showed highly elevated levels of differentiation, likely as an effect of directional selection, in either time, space or both. Exploratory analysis suggested that temporal allele frequency shifts at certain loci may correlate with local temperature variation and with life history changes suggested to be fisheries induced. Interestingly, however, largely nonoverlapping sets of loci were temporal outliers in the different populations and outliers from the 1928 to 1960 period showed almost complete stability during later decades. The contrasting microevolutionary trajectories among populations resulted in sequential shifts in spatial outliers, with no locus maintaining elevated spatial differentiation throughout the study period. Simulations of migration coupled with observations of temporally stable spatial structure at neutral loci suggest that population replacement or gene flow alone could not explain all the observed allele frequency variation. Thus, the genetic changes are likely to at least partly be driven by highly dynamic temporally and spatially varying selection. These findings have important implications for our understanding of local adaptation and evolutionary potential in high gene flow organisms and underscore the need to carefully consider all dimensions of biocomplexity for evolutionarily sustainable management.
Data from: SNP-array reveals genome wide patterns of geographical and potential adaptive divergence across the natural range of Atlantic salmon (Salmo salar)
Atlantic salmon (Salmo salar) is one of the most extensively studied fish species in the world due to its significance in aquaculture, fisheries and ongoing conservation efforts to protect declining populations. Yet, limited genomic resources have hampered our understanding of genetic architecture in the species and the genetic basis of adaptation to the wide range of natural and artificial environments it occupies. In this paper, we describe the development of a medium density Atlantic salmon SNP-array based on Expressed Sequence Tags (ESTs) and genomic sequencing. The array was used in the most extensive assessment of population genetic structure performed to date in this species. A total of 6176 informative SNPs were successfully genotyped in 38 anadromous and freshwater wild populations distributed across the species natural range. Principal component analysis clearly differentiated European and North American populations, and within Europe, three major regional genetic groups were identified for the first time in a single analysis. We assessed the potential for the array to disentangle neutral and putative adaptive divergence of SNP allele frequencies across populations and among regional groups. In Europe, secondary contact zones were identified between major clusters where endogenous and exogenous barriers could be associated, rendering the interpretation of environmental influence on potentially adaptive divergence equivocal. A small number of markers highly divergent in allele frequencies (outliers) were observed between (multiple) freshwater and anadromous populations, between northern and southern latitudes, and when comparing Baltic populations to all others. We also discuss the potential future applications of the SNP-array for conservation, management and aquaculture.
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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.
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DANDI Archive for NWB datasets
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