Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
187
datasets available to search
ShareScore release 0.9.0
Dataset results
187 results for “phenotypic traits”
Trait-fitness associations do not predict within-species phenotypic evolution over 2 million years
Long-term patterns of phenotypic change are the cumulative results of tens of thousands to millions of years of evolution. Yet, empirical and theoretical studies of phenotypic selection are largely based on contemporary populations. The challenges in studying phenotypic evolution, in particular trait-fitness associations in the deep past, are barriers to linking micro- and macroevolution. Here, we capitalize on the unique opportunity offered by a marine colonial organism commonly preserved in the fossil record to investigate trait-fitness associations over 2 million years. We use the density of female polymorphs in colonies of <em>Antartothoa tongima</em> as a proxy for fecundity, a fitness component, and investigate multivariate signals of trait-fitness associations in six time intervals on the backdrop of Pleistocene climatic shifts. We detect negative trait-fitness associations for feeding polymorph (autozooid) sizes, positive associations for autozooid shape but no particular relationship between fitness and brood chamber size. In addition, we demonstrate that long-term trait patterns are explained by palaeoclimate and to a lesser extent by ecological interactions. Our analyses show that macroevolutionary outcomes of trait evolution are not a simple scaling-up from the trait-fitness associations.
A codon model for associating phenotypic traits with altered selective patterns of sequence evolution
<p>Detecting the signature of selection in coding sequences and associating it with shifts in phenotypic states can unveil genes underlying complex traits. Of the various signatures of selection exhibited at the molecular level, changes in the pattern of selection at protein coding genes have been of main interest. To this end, phylogenetic branch-site codon models are routinely applied to detect changes in selective patterns along specific branches of the phylogeny. Many of these methods rely on a pre-specified partition of the phylogeny to branch categories, thus treating the course of trait evolution as fully resolved and assuming that phenotypic transitions have occurred only at speciation events. Here we present TraitRELAX, a new phylogenetic model that alleviates these strong assumptions by explicitly accounting for the uncertainty in the evolution of both trait and coding sequences. This joint statistical framework enables the detection of changes in selection intensity upon repeated trait transitions. We evaluated the performance of TraitRELAX using simulations and then applied it to two case studies. Using TraitRELAX, we found an intensification of selection in the primate SEMG2 gene in polygynandrous species compared to species of other mating forms, as well as changes in the intensity of purifying selection operating on sixteen bacterial genes upon transitioning from a free-living to an endosymbiotic lifestyle.</p>
Weak genetic signal for phenotypic integration implicates developmental processes as major regulators of trait covariation
<p>Phenotypic integration is an important metric that describes the degree of covariation among traits in a population, and is hypothesized to arise due to selection for shared functional processes. Our ability to identify the genetic and/or developmental underpinnings of integration is marred by temporally overlapping cell-, tissue-, and structure-level processes that serve to continually 'overwrite' the structure of covariation among traits through ontogeny. Here we examine whether traits that are integrated at the phenotypic level, also exhibit a shared genetic basis (e.g., pleiotropy). We micro-CT scanned two hard tissue traits, and two soft tissue traits (mandible, pectoral girdle, atrium, and ventricle respectively) from an F<sub>5</sub> hybrid population of Lake Malawi cichlids, and used geometric morphometrics to extract 3D shape information from each trait. Given the large degree of asymmetric variation that may reflect developmental instability, we separated symmetric- from asymmetric-components of shape variation. We then performed quantitative trait loci (QTL) analysis to determine the degree of genetic overlap between shapes. While we found ubiquitous associations among traits at the phenotypic level, except for a handful of notable exceptions, our QTL analysis revealed few overlapping genetic regions. Taken together, this indicates developmental interactions can play a large role in determining the degree of phenotypic integration among traits, and likely obfuscate the genotype to phenotype map, limiting our ability to gain a comprehensive picture of the genetic contributors responsible for phenotypic divergence.</p>
Data for 'Phenotypic plasticity and genetic variation in leaf traits of Yushania niitakayamensis (Bambusoideae; Poaceae) in contrasting light environments'
<p>This is the Data for the article entitled 'Phenotypic plasticity and genetic variation in leaf traits of Yushania niitakayamensis (Bambusoideae; Poaceae) in contrasting light environments' submitted to 'Journal of Plant Research'</p> <p><a href="https://doi.org/10.1007/s10265-021-01327-y">https://doi.org/10.1007/s10265-021-01327-y</a></p> <p>Traits' names are listed below:</p> <p>Leaf length (LL), Leaf width (LW), Specific leaf area (SLA), Stomatal density (SD), Leaf thickness (LT), Relative frequency of cavities formed by the collapsed fusoid cells (CFC), Leaf chlorophyll content per unit area ([Chl]area), Ratio of chlorophyll a to chlorophyll b (Chl a/b), Leaf nitrogen content per unit area ([N]area), Leaf stable carbon isotope ratio (δ13C), Photosynthetic photon flux density (PPFD), Actual quantum yield of PSII electron transport (ΦPSII), Electron transport rate (ETR), Light-saturated photosynthetic rate (Asat), Stomatal conductance (gs), Dark respiration rate (Rd), Apparent quantum yield (AQY), The ratio of intercellular to ambient CO2 concentration (Ci/Ca), Photosynthetic water use efficiency (WUE)</p>
Data from: Phenotypic selection on floral traits in an urban landscape
Native species are increasingly living in urban landscapes associated with abiotic and biotic changes that may influence patterns of phenotypic selection. However, measures of selection in urban and non-urban environments, and exploration of the mechanisms associated with such changes, are uncommon. Plant-animal interactions have played a central role in the evolution of flowering plants and are sensitive to changes in the urban landscape, and thus provide opportunities to explore how urban environments modify selection. We evaluated patterns of phenotypic selection on floral and resistance traits of Gelsemium sempervirens in urban and non-urban sites. The urban landscape had increased florivory and decreased pollen receipt, but showed only modest differences in patterns of selection. Directional selection for one trait, larger floral display size, was stronger in urban compared to non-urban sites. Neither quadratic nor correlational selection significantly differed between urban and non-urban sites. Pollination was associated with selection for larger floral display size in urban compared to non-urban sites, due to differences in the translation of pollination into seeds rather than pollinator selectivity. Thus, our data suggest that urban landscapes may not result in sweeping differences in phenotypic selection but rather modest differences for some traits, potentially mediated by species interactions.
Data from: Phenotypic integration in an extended phenotype: among‐individual variation in nest‐building traits of the alfalfa leafcutting bee (Megachile rotundata)
Structures such as nests and burrows are an essential component of many organisms' life-cycle and requires a complex sequence of behaviors. Because behaviors can vary consistently among individuals and be correlated with one another, we hypothesized that these structures would 1) show evidence of among-individual variation, 2) be organized into distinct functional modules, and 3) show evidence of trade-offs among functional modules due to limits on energy budgets. We tested these hypotheses using the alfalfa leafcutting bee, Megachile rotundata, a solitary bee and important crop pollinator. M. rotundata constructs complex nests by gathering leaf materials to form a linear series of cells in pre-existing cavities. In this study, we examined variation in the following nest construction traits: reproduction (number of cells per nest and nest length), nest protection (cap length and number of leaves per cap), cell construction (cell size and number of leaves per cell), and cell provisioning (cell mass) from 60 nests. We found a general decline in investment in cell construction and provisioning with each new cell built. In addition, we found evidence for both repeatability and plasticity in cell provisioning with little evidence for trade-offs among traits. Instead, most traits were positively, albeit weakly, correlated (r ~ 0.15), and traits were loosely organized into covarying modules. Our results show that individual differences in nest construction are detectable at a level similar to that of other behavioral traits and that these traits are only weakly integrated. This suggests that nest components are capable of independent evolutionary trajectories.
Supporting data: Prevalence of sexual dimorphism in mammalian phenotypic traits
<p>Supporting material for the manuscript <strong>“</strong><strong>Prevalence of sexual dimorphism in mammalian phenotypic traits”</strong> . This manuscript was published in Nature Communication 26th January 2017</p>
Supplementary data for Inter-provenance variability and phenotypic plasticity of wood and leaf traits related to hydraulic safety and efficiency in seven European beech (Fagus sylvatica L.) provenances differing in yield
<p>Dataset and supplementary file for <strong>Inter-provenance variability and phenotypic plasticity of wood and leaf traits related to hydraulic safety and efficiency in seven European beech (<em>Fagus sylvatica</em> L.) provenances differing in yield </strong>paper.</p> <p>The ANFS_data file includes individual level measurements of xylem safety and efficiency traits, leaf traits and growth among 7 provenances planted at two common garden sites in Germany and Slovakia. More details related to the methodology might be found in the published paper by Kurjak et al. 2024.</p> <p>The ANFS_supplementary file includes the test for differences in distance to tip between sites and provenances, based on the branch diameter-branch length scaling.</p>
Phenotypic traits of 17 populations of Spartina alterniflora in China
<p>Understanding the ecological and evolutionary processes that underlie phenotypic and genetic variation among invasive plant populations and the capacity of such populations to colonize a broad range of environments is a major goal in ecology. Rapid adaptation to local environmental conditions often leads to latitudinal clines in both phenotypes and genotypes of invasive plant species. Previous studies suggest that natural selection influenced a latitudinal cline in phenotypic traits of the invasive plant <em>Spartina alterniflora</em> in China. However, little is understood of the relationship between genetic and phenotypic differentiation and environmental factors among <em>S. alterniflora</em> populations. Here, we studied whether <em>S. alterniflora</em> exhibits a latitudinal cline in genetic diversity across the east coast of China and whether genetic and phenotypic differentiation among populations were correlated with environmental factors. The Restriction-site Associated DNA (RAD-seq) sequencing was used to obtained genomic information of 17 populations of <em>S. alterniflora</em> in China. A redundancy analysis (RDA) was performed to assess whether environmental variables were corelated with genetic and phenotypic differentiation among the populations. A univariate environmental association analysis (implemented through Latent Factor Mixed Model; LFMM) and a principal component analysis (PCAdapt) were used to test for signature of local adaptation. A total of 3, 310 SNPs showed a clear genetic structure among populations in three climatic regions (northern, mid-latitude and southern). Positive correlations between genetic differentiation and variation in reproductive characteristics of <em>S. alterniflora</em> were revealed, suggesting that sexual reproduction traits might be stable and genetically heritable. Outlier loci that were identified by both PCAdapt and LFMM methods were significantly correlated to soil phosphorus content, soil salinity, and precipitation. These results provide evidence of molecular signatures of local adaptation of <em>S. alterniflora</em> and suggest that rapid adaptive evolution may facilitate invasiveness of <em>S. alterniflora</em> in China.</p>
Phenotypic and Genetic data for "Evolution of fruit and seed traits during almond naturalization"
<p>1- Cultivated plant species often naturalize and enter wild communities in a process known as feralization. To successfully feralize, crops must overcome ecological barriers and may undergo selection on certain traits, diverging phenotypically and genetically from their crop ancestors. In spite of the agronomic and ecological relevance of crop feralization, the eco-evolutionary dynamics driving it remain understudied.</p> <p>2- In this paper, we evaluated phenotypic and genotypic differentiation in fruit and seed traits during the naturalization of the almond tree (Prunus dulcis (Mill.) D.A. Webb) in SE Iberia and evaluated the potential role of natural selection in this process. To do so, we investigated patterns of genetic divergence between cultivated and feral populations using functional (the cyanogenesis Sk gene) and neutral (17 SSR loci) markers and analyzed morphological and biochemical traits in kernels of 342 individuals from 15 cultivated and 24 feral populations.</p> <p>3- We detected very little genetic differentiation in neutral markers between cultivated and feral populations. The majority of the observed genetic variation was due to differences within each type. Conversely, the recessive allele sk responsible for seed toxicity was significantly more frequent in feral populations. Phenotypic differentiation between cultivated and naturalized almond populations was also significant. Feral almond kernels were smaller and lighter, had denser and more resistant shells (endocarps) and more toxic seeds. Selection analyses indicated that these genetic and phenotypic patterns might be driven by directional selection on fruit and seed traits, potentially linked to defense against predation.</p> <p>4- Synthesis. Our findings indicate that almond naturalization is consistent with strong directional selection on fruits and seeds, leading to smaller and more toxic seeds encased in harder endocarps. Accordingly, we propose that feralization of this crop is, at least to some degree, driven by adaptive evolution of dispersal and recruitment traits.</p>
Datasets and scripts from: Sensory-based quantification of male colour patterns in Trinidadian guppies reveals no support for parallel phenotypic evolution in multivariate trait space
<p>Parallel evolution, in which independent populations evolve along similar phenotypic trajectories, offers insights into the repeatability of adaptive evolution. Here, we revisit a classic example of parallelism, that of repeated evolution of brighter males in the Trinidadian guppy (<em>Poecilia reticulata</em>). In guppies, colonisation of low predation habitats is associated with emergence of 'more colourful' phenotypes since predator-induced viability selection for crypsis weakens while sexual selection by female preference for conspicuousness remains strong. Our study differs from previous investigations in three respects. First, we adopt a multivariate phenotyping approach to characterise parallelism in multi-trait space. Second, we use ecologically-relevant colour traits defined by the visual systems of the two selective agents (i.e. guppy, predatory cichlid). Third, we estimate population genetic structure to test for adaptive (parallel) evolution against a model of neutral phenotypic divergence. We find strong phenotypic differentiation that is inconsistent with a neutral model but very limited support for the predicted pattern of greater conspicuousness at low predation. Effects of predation regime on each trait were in the expected direction, but weak, largely non-significant, and explained little among-population variation. In multi-trait space, phenotypic trajectories of lineages colonising low from high predation regimes were not parallel. Our results are consistent with reduced predation risk facilitating adaptive differentiation, potentially by female choice, but suggest that this proceeds in independent directions of multi-trait space across lineages. Pool-sequencing data also revealed SNPs showing greater differentiation than expected under neutrality, among which some are found in genes contributing to colour pattern variation, presenting opportunities for future genetic study.</p>
A high-throughput assay for quantifying phenotypic traits of microalgae
<p>High-throughput methods for phenotyping microalgae are in demand across a variety of research and commercial purposes. Many microalgae can be readily cultivated in multi-well plates for experimental studies which can reduce overall costs, while measuring traits from low volume samples can reduce handling. Here we develop a high-throughput quantitative phenotypic assay (QPA) that can be used to phenotype microalgae grown in multi-well plates. The QPA integrates 10 low-volume, relatively high-throughput trait measurements (growth rate, cell size, granularity, chlorophyll a, neutral lipid content, silicification, reactive oxygen species accumulation, and photophysiology parameters: ETRmax, Ik, and alpha) into one workflow. We demonstrate the utility of the QPA on Thalassiosira spp., a cosmopolitan marine diatom, phenotyping six strains in a standard nutrient rich environment (f/2 media) using the full 10-trait assay. The multivariate phenotypes of strains can be simplified into two dimensions using principal component analysis, generating a trait-scape. We determine that traits show a consistent pattern when grown in small volume compared to more typical large volumes. The QPA can thus be used for quantifying traits across different growth environments without requiring exhaustive large-scale culturing experiments, which facilitates experiments on trait plasticity. We confirm that this assay can be used to phenotype newly isolated diatom strains within 4 weeks of isolation. The QPA described here is highly amenable to customisation for other traits or unicellular taxa and provides a framework for designing high-throughput experiments. This method will have applications in experimental evolution, modelling, and for commercial applications where screening of phytoplankton traits is of high importance.</p>
Natural distribution and phenotypic traits of Prosopis flexuosa var. depressa in Argentina
<p>Table S1: Registered information of collection site, and environment (soil and climate).</p> <p>Table S2: Spinescence of adult plant in Prosopis flexuosa DC. var. depressa F.A. Roig populations.</p> <p>Table S3: Soil seed bank persistence of Prosopis flexuosa DC. var. depressa F.A. Roig populations.</p> <p>Table S4: Seeds sown and seedlings established to the phenotypic traits evaluation in Prosopis flexuosa DC. var. depressa F.A. Roig populations.</p> <p>Table S5: Seedling traits of Prosopis flexuosa DC. var. depressa F.A. Roig populations.</p> <p>Table S6: Pearson's correlation of seedling traits in Prosopis flexuosa DC. var. depressa F.A. Roig populations.</p>
Ecological determinants of variation in phenotypic selection on quantitative immune defence traits
Immune defence is an important determinant of organismal fitness. While theoretical models based on trade-offs in resource allocation predict quantitative immune traits to be subject to stabilizing selection due to associated energetic costs and self-harm, empirical studies report mainly positive directional selection. This discrepancy may arise from multiple ecological factors that vary in nature and could influence selection. We examined if selection on immune activity varies depending on immune challenge/infection risk, between immune traits, and among populations in the freshwater snail Lymnaea stagnalis. We assessed selection on the phenoloxidase-like and antibacterial activity of snail haemolymph while manipulating the level of immune challenge imposed by environmental microbes. We did this using snails from multiple populations and also quantified within-population family-level variation (i.e., evolutionary potential) in the snails' immune activity. We found that the strength of immune challenge and the examined immune trait determined selection on the snails' immune function. Thus, variation in infection risk can be an important factor in maintaining genetic variation in defence traits. Additionally, immune traits showed low among-population differentiation but high within-population genetic variation. This pattern could arise if natural snail populations are exposed to higher temporal than spatial variation in infection risk.
Data from: Phenotypic selection on an ornamental trait is not modulated by breeding density in a pied flycatcher population
<p>Most studies of phenotypic selection in the wild have focused on morphological and life-history traits and looked at abiotic (climatic) variation as the main driver of selection. Consequently, our knowledge of the effects of biotic environmental variation on phenotypic selection on sexual traits is scarce. Population density can be considered a proxy for the intensity of intra- and inter-sexual competition and could therefore be a key factor influencing the covariation between individual fitness and the expression of sexual traits. Here, we used an individual-based data set from a population of pied flycatchers (<em>Ficedula hypoleuca</em>) monitored over 24 years to analyse the effect of breeding density on phenotypic selection on dorsal plumage colouration, a heritable and sexually selected ornament in males of this species. Using the number of recruits as a fitness proxy, our results show overall stabilizing selection on male dorsal colouration, with intermediate phenotypes being favoured over extremely dark and dull individuals. However, our results did not support the hypothesis that breeding density mediates phenotypic selection on this sexual trait. We discuss the possible role of other biotic factors influencing selection on ornamental plumage.</p>
Predicting Phenotypic Traits Using Conglomerate RNA-seq Datasets -- Datasets
<p>Phenotype Annotations and Corresponding Gene Expression Matrices created for the paper Hadish et al. [REF]. Raw Phenotypic Annotations were downloaded and processed from NCBI BioProject and raw RNA-seq data was downloaded from NCBI SRA. All annotations are contained within a single file for either Tissue or Age. Gene expression matrices are for each of the 12 species used in this project in their unproccessed form. </p> <p>Scripts used in this project are located here: </p> <p>GitLab Repository: </p> <p>https://gitlab.com/ficklin-lab/predicting-phenotypic-traits-using-conglomerate-rna-seq-datasets</p> <p>Paper Citation: </p> <p>[REF]</p>
Exploring phenotypic diversity of pigmented traits and iris features in Pakistani population
<p><span>Phenotypic variations of eye color, skin color, and iris surface features have been well-explored in certain populations. However, there has been comparatively little research on variations in these features in Pakistani population. The aim of this study is to</span> discover phenotypic diversity and correlations of pigmented traits and iris surface features in Punjab and Khyber-Pakhtunkhwa (KPK)<b> </b>province of Pakistan<b>.</b> Digital images of eyes and skin were examined by investigators to determine color using Fitzpatrick Phototype Scale. Similarly, iris patterns were characterized by Edward iris feature software and association studies were conducted through SPSS program. Intermediate eye color was frequent in KPK (44%) while brown was higher in Punjab (47%). <span>Contrarily</span>, light to medium brown skin color was recurring (55%) in Punjab whereas lighter skin color prevailed in KPK (69%). Furthermore, Fuchs' crypts were significantly correlated with contraction furrows in both populations. Likewise, crypts were significantly associated with Wolfflin nodules and furrows were significantly related to conjunctival melanosis and pigment spots in KPK sample set. Based on unique iris patterns, these phenotypic traits would be helpful for individuals' discrimination in the population<b>. </b>In future, there is need to explore genetic associations and functional differences of these traits.</p>
Data for: Strong phenotypic trait correlations between mating partners do not result from assortative mating in wild great tits (Parus major)
<p>There is considerable debate about the occurrence of assortative mating between phenotypic traits measured within natural populations. Meta-analyses have implied that assortative mating occurs generally in natural populations but recent work indicates these conclusions largely result from biased data. Specifically, estimates of phenotypic correlations between mating partners do not solely result from non-random associations between individual-level traits of partners but also from other biological processes (joint phenotypic plasticity, indirect genetic effects), methodological practices (observer bias), and other unexplained residual correlations (e.g. correlated measurement error). This paper puts this critique to test. First, we estimated the overall phenotypic correlation between phenotypic traits of mating partners for a wild population of great tits. Second, we estimated various key variance components to reveal the extent to which phenotypic correlations between partners resulted from assortative mating, reversible plasticity, social partner effects, and methodological practices. We performed our analyses for a range of phenotypic traits (body mass, breathing rate, exploration behaviour, wing and tarsus length) to derive general conclusions not hinging on the specifics of the traits involved. Our analyses support the conclusion that patterns of assortative mating exist at first glance but occur because of the biasing effects of correlated residuals likely caused by a combination of phenotypic responses to unknown environmental factors or measurement error – not because of intrinsic patterns of assortative mating.</p>
Phenotypic traits evolution and morphological traits associated with echolocation calls in cryptic horseshoe bats (Rhinolophidae)
<p><span>Bats provide an excellent case study for studying evolution due to their remarkable flight and echolocation capabilities. In this study, we sought to understand the phenotypic evolution of key traits in Rhinolophidae (horseshoe bats) using phylogenetic comparative methods. We aim to test the phylogenetic signals of traits and evaluated the best-fit evolutionary models given the data for each trait considering different traits may evolve under different models (i.e., Brownian Motion (BM), Ornstein-Uhlenbeck (OU) and Early Burst (EB)) and reconstruct ancestral character states. We examined how phenotypic characters are associated with echolocation calls and minimum detectable prey size. We measured 34 traits of 10 Asian rhinolophids species (187 individuals). We found that the majority of traits showed a high phylogenetic signal based on Blomberg's K and Pagel's λ, but each trait may evolve under different evolutionary models. Sella traits were shown to evolve under stabilizing selection based on OU models, indicating sella traits have the tendency to move forward along the branches toward some medial value in equilibrium. Our findings highlight the importance of sella characters in association with echolocation call emissions in Rhinolophidae, as calls are important for spatial cognition and also influence dietary preferences. Minimum detectable prey size in Rhinolophidae was associated with call frequency, bandwidth, call duration, wingspan and wing surface area. Ultimately, understanding trait evolution requires sensitivity due to the differential selective pressures which may apply to different characteristics.</span></p>
Alamo x Kanlow genotypic and phenotypic data for biomass yield and yield-related traits in lowland switchgrass (Panicum virgatum L.) crosses
<p>Switchgrass (<em>Panicum virgatum</em> L.) is a model herbaceous bioenergy crop in the USA. It is a native, perennial, warm-season grass, and has broad adaptability. Many breeding programs focus on the genetic improvement of switchgrass for increasing biomass yield. Significant genetic variation for biomass yield observed in lowland switchgrass hybrids. Due to the quantitative inheritance of biomass yield, varietal improvement for the trait through conventional breeding is slow. Therefore, quantitative trait loci (QTL) mapping is used to discover marker-trait associations and accelerate the breeding process through marker-assisted selection. To identify significant QTL, this study mapped seven biparental crosses and one combined cross of two biparental crosses (30 to 96 F1s) between lowland Alamo and Kanlow genotypes. The crosses were evaluated for biomass yield, plant height, and clonal mass scores in a simulated-sward plot with two replications at two locations in Tennessee from 2019 to 2021. The crosses were genotyped using 17,251 single nucleotide polymorphisms generated through genotyping-by-sequencing. QTL mapping was performed using a single-QTL model in R-QTL. The study identified major QTL for biomass yield, plant height, and clonal mass scores resided on chromosomes 7K, 4K, and 3K and had 0.47, 0.63, and 0.62 heritability, respectively.</p> <p>The dataset contains five files describing the phenotype and genotype of each individual used in the quantitative trait loci (QTL) analysis.</p> <ul> <li>'File 1' contains biomass yield, plant height, and clonal mass data for each genotype and parents evaluated at two locations in Tennessee; the Plateau Research and Education Center (PREC), Crossville and East Tennessee Research and Education Center (ETREC), Knoxville from 2019 to 2021. Plant height and biomass yield were measured at maturity, and clonal mass scores were evaluated after harvesting biomass.</li> <li>'File 2' has the genotype name, library, index, total reads, bases, and the Phred quality score (Q30). Young leaf tissue was collected from each F1 progeny and parent, and DNA was extracted using the cetyltrimethylammonium bromide (CTAB) procedure. The extracted DNA was genotyped at the USDA-ARS Western Regional Research Center laboratory in Albany, CA. Genotyping by sequencing (GBS) was performed on 951 lines (F1s and their parents) using the PstI-MspI GBS protocol. The quality of these sequences showed that 94.4% of the bases were at or above Q30. Reads were mapped to version 5.0 of the switchgrass reference genome. Single nucleotide polymorphism (SNP) calling was performed, and redundant markers were filtered out for linkage map construction. 'File 3' has SNP ID numbers, SNP locations on chromosomes, map positions, and SNP scores. The cross was used as a four-way cross for QTL analysis, where the male parent Kanlow (K) was assigned as '1', and the female parent Alamo (A) was assigned as '2'.</li> <li>The phased output data from the four-way cross, i.e., 11, 12, 21, and 22, were represented by AC, BC, AD, and BD, respectively ('File 3').</li> <li>The progeny file ('File 4') contains the name of the parents used for making crosses and their progenies.</li> <li>A consensus linkage map ('File 5') was produced with Lep-Map3 software. The linkage map contains 18 linkage groups associated with 18 switchgrass chromosomes, marker size (bp), map position (cM) based on male and female maps, and map order.</li> </ul>
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.