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788 results for “genotypic data”
Data from: A RAD-sequencing approach to genome-wide marker discovery, genotyping, and phylogenetic inference in a diverse radiation of primates
Until recently, most phylogenetic and population genetics studies of nonhuman primates have relied on mitochondrial DNA and/or a small number of nuclear DNA markers, which can limit our understanding of primate evolutionary and population history. Here, we describe a cost-effective reduced representation method (ddRAD-seq) for identifying and genotyping large numbers of SNP loci for taxa from across the New World monkeys, a diverse radiation of primates that shared a common ancestor ~20-26 mya. We also estimate, for the first time, the phylogenetic relationships among 15 of the 22 currently-recognized genera of New World monkeys using ddRAD-seq SNP data using both maximum likelihood and quartet-based coalescent methods. Our phylogenetic analyses robustly reconstructed three monophyletic clades corresponding to the three families of extant platyrrhines (Atelidae, Pitheciidae and Cebidae), with Pitheciidae as basal within the radiation. At the genus level, our results conformed well with previous phylogenetic studies and provide additional information relevant to the problematic position of the owl monkey (Aotus) within the family Cebidae, suggesting a need for further exploration of incomplete lineage sorting and other explanations for phylogenetic discordance, including introgression. Our study additionally provides one of the first applications of next-generation sequencing methods to the inference of phylogenetic history across an old, diverse radiation of mammals and highlights the broad promise and utility of ddRAD-seq data for molecular primatology.
Data from: Genotypic traits and tradeoffs of fast growth in silver birch, a pioneer tree
<p>Fast-growing and slow-growing plant species are suggested to show integrated economics spectrums and the tradeoffs of fast growth are predicted to emerge as susceptibility to herbivory and resource competition. We tested if these predictions also hold for fast-growing and slow-growing genotypes within a silver birch, <i>Betula pendula</i> population. We exposed cloned saplings of 17 genotypes with slow, medium or fast height growth to reduced insect herbivory, using an insecticide, and to increasing resource competition, using naturally varying field plot grass cover. We measured shoot and root growth, ectomycorrhizal (EM) fungal production using ergosterol analysis and soil N transfer to leaves using <sup>15</sup>N-labelled pulse of NH<sub>4</sub><sup>+</sup>. We found that fast-growing genotypes grew on average 78% faster, produced 56% and 16% more leaf mass and ergosterol, and showed 78% higher leaf N uptake than slow-growing genotypes. The insecticide decreased leaf damage by 83% and increased shoot growth, leaf growth and leaf N uptake by 38%, 52% and 76%, without differences between the responses of fast-growing and slow-growing genotypes, whereas root mass decreased with increasing grass cover. Shoot and leaf growth of fast-growing genotypes decreased and EM fungal production of slow-growing genotypes increased with increasing grass cover. Our results suggest that fast growth is genotypically associated with higher allocation to EM fungi, better soil N capture and greater leaf production, and that the tradeoff of fast growth is sensitivity to competition, but not to insect herbivory. EM fungi may have a dual role: to support growth of fast-growing genotypes under low grass competition and to maintain growth of slow-growing genotypes under intensifying competition.</p>
Alfalfa genotyping-by-sequencing (GBS) data
<p>Alfalfa (<i>Medicago</i> <i>sativa</i> L.) quantitative trait loci (QTL) mapping population (184 F<sub>1</sub>) derived from cultivars 3010 (cold-tolerant) as female parent and CW 100 (cold-sensitive) as male parent were genotyped using genotyping-by-sequencing (GBS). Polymorphic SNPs unique to either 3010 (AB x AA) or CW 1010 (AA x AB) were identified as single dose allele (SDA) markers and used to generate the genetic linkage maps. Two sets of linkage maps, a set for each parent, were used to map the traits and the QTL were identified. With the genotyping and phenotyping informations we were able to map various alfalfa traits such as fall dormancy, winter-hardiness, freezing tolerance, flowering time, yield and leaf-rust resistance. The raw sequence data were deposited at NCBI SRA with the accession number SRP150116. This study identified several genomic regions and associated markers that can be further utilized in marker-assisted breeding to improve the alfalfa. </p>
Genotype data not consistent with clonal transmission of sea turtle fibropapillomatosis or goldfish schwannoma
<p>Recent<b> </b>discoveries of transmissible cancers in multiple bivalve species suggest that direct transmission of cancer cells within species may be more common than previously thought, particularly in aquatic environments. Fibropapillomatosis occurs with high prevalence in green sea turtles (Chelonia mydas) and the geographic range of disease has increased since fibropapillomatosis was first reported in this species. Widespread incidence of schwannomas, benign tumours of Schwann cell origin, reported in aquarium-bred goldfish (Carassius auratus), suggest an infectious aetiology. We investigated the hypothesis that cancers in these species arise by clonal transmission of cancer cells. Through analysis of polymorphic microsatellite alleles, we demonstrate concordance of host and tumour genotypes in diseased animals. These results imply that the tumours examined arose from independent oncogenic transformation of host tissue and were not clonally transmitted. Further, failure to experimentally transmit goldfish schwannoma via water exposure or inoculation suggest that this disease is unlikely to have an infectious aetiology.</p>
Fraxinus excelsior genotype data for "Genetic resources of common ash (Fraxinus excelsior L.) in Poland"
<p>The data set contains microsatellite genotypes (3 chloroplast + 10 nuclear loci) of Fraxinus excelsior trees, together with the information about sampling sites.<br> </p>
Data for: Trinity assembled transcriptome of a Eurasian (Myriophyllum spicatum) and a hybrid (M. spicatum × M. sibiricum) genotype of watermilfoil
<p>Aquatic plant managers frequently treat Eurasian watermilfoil (<em>Myriophyllum spicatum</em> L.; EWM) and hybrid watermilfoil (<em>Myriophyllum spicatum</em> L. × <em>Myriophyllum sibiricum</em> Komarov) with 2,4-dichlorophenoxyacetic acid (2,4-D) herbicide. However, watermilfoil genotypes can differ in their response to 2,4-D. In this study, we compared facultative and constitutive gene expression differences for two watermilfoil genotypes (one Eurasian and one hybrid) that differ in their sensitivity to 2,4-D. To do this, we compared between control and 0.5mg L-1 2,4-D treated plants at four time points after treatment. We also assembled the first de novo watermilfoil transcriptome. We found that while qualitatively similar, the facultative transcriptional response of the EWM genotype to 2,4-D treatment was much stronger than the hybrid genotype, indicated by a greater number and log-fold-change of differentially expressed genes at all time points after treatment. Further, we found that the EWM and hybrid genotype differed in their 9-cis-epoxycarotenoid dioxygenase (NCED) and abscisic acid (ABA) gene response, and that there was a greater amount of photosynthesis gene downregulation (both in number and log-fold-change) in the EWM than the hybrid genotype. At the constitutive level, overall, the hybrid expressed genes at a higher level than the EWM genotype, but not the genes of the 2,4-D response pathway. These differences in gene expression match with the degree of phenotypic difference in growth observed between these genotypes when exposed to 2,4-D. The hybrid genotype used here mitigates the effects of 2,4-D treatment better than the EWM genotype at both the molecular and phenotypic level. More study is needed to understand the mechanism(s) of mitigation and whether this is a cause of hybridity, or the specific genotypic backgrounds used here.</p>
Roe deer microsatellite genotype data
<p>In the early 1800s, the European roe deer (<em>Capreolus capreolus</em>) was probably extirpated from Switzerland, due to overhunting and deforestation. After a federal law was enacted in 1875 to protect lactating females and young, and limiting the hunting season, the roe deer successfully recovered and recolonised Switzerland. In this study, we use mitochondrial DNA and nuclear DNA markers to investigate the recolonisation and assess contemporary genetic structure in relation to broad topographic features, in order to understand underlying ecological processes, inform future roe deer management strategies and explore the opportunity for development of forensic traceability tools. The results concerning the recolonisation origin support natural, multidirectional immigration from neighbouring countries. We further demonstrate that there is evidence of weak genetic differentiation within Switzerland among topographic regions. Finally, we conclude that the genetic data support the recognition of a single roe deer management unit within Switzerland, within which there is a potential for broad scale geographic origin assignment using nuclear markers to support law enforcement.</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>
Genotype data for wild lupin populations from central Michigan
<p>Habitat degradation can have significant effects on native species inhabiting natural ecosystems. Within oak barrens and oak-pine barrens ecosystems, there is a complex interspecies interaction between the federally endangered Karner blue butterfly (<em>Lycaeides melissa samuelis</em>) and its obligate host plant, wild lupine (<em>Lupinus perennis</em> L.). Recruitment of wild lupine is critical for maintaining butterfly populations; however, this recruitment can be impeded by habitat fragmentation. Reduced recruitment can result in low genetic diversity in isolated populations, limiting its adaptive potential to respond to environmental change. This study was aimed at understanding the genetic diversity and population structure of wild lupine populations throughout central and west Michigan. We identified significant population structure across most of the populations sampled, with only two sites not significantly different from each other. No sites within our study area displayed statistically significant levels of inbreeding. There are also at least two genetic clusters of wild lupine present within our study region, although there is significant overlap among these groups, indicating that genetic differentiation among clusters may be limited.</p>
Data from: Maintenance and expansion of genetic and trait variation following domestication in a clonal crop: Enset tGBS individual genotype data
<p class="MsoNormal">Clonal propagation enables favourable crop genotypes to be rapidly selected and multiplied. However, the absence of sexual propagation can lead to low genetic diversity and accumulation of deleterious mutations, which may eventually render crops less resilient to pathogens or environmental change. To better understand this trade-off, we characterise the domestication and contemporary genetic diversity of Enset (<em>Ensete ventricosum</em>), an indigenous African relative of bananas (<em>Musa</em>) and principal starch staple for 20 million Ethiopians. Wild enset is strictly sexually outcrossing, but in cultivation is propagated clonally and associated with diversification and specialisation into hundreds of named landraces. We applied tGBS sequencing to generate genome-wide genotypes for 192 accessions from across enset's cultivated distribution, and surveyed 1340 farmers on enset agronomic traits. Overall, reduced heterozygosity in the domesticated lineage was consistent with a domestication bottleneck that retained 37% of wild diversity. However, an excess of putatively deleterious missense mutations at low frequency present as heterozygotes suggested accumulation of mutational load in clonal domesticated lineages. Our evidence indicates that the major domesticated lineages initially arose through historic sexual recombination associated with a domestication bottleneck, followed by amplification of favourable genotypes through an extended period of clonal propagation. Among domesticated lineages we found significant phylogenetic signal for multiple farmer-identified food, nutrition and disease resistance traits and little evidence of contemporary recombination. Development of future-climate adapted genotypes may require crop breeding, but outcrossing risks exposing deleterious alleles as homozygotes. This trade-off may partly explain the ubiquity and persistence of clonal propagation over recent centuries of comparative climate stability.</p>
Data from: A comparison of non-destructive visceral swab and tissue biopsy sampling methods for genotyping-by-sequencing in the freshwater mussel Fusconaia askewi
<p>Limiting harm to organisms via genetic sampling is an important consideration for rare species. Nondestructive sampling techniques have been developed to address this issue in freshwater mussels. Two methods, visceral swabbing and tissue biopsies, have proven to be effective for DNA sampling, though it is unclear as to which method is preferable for genotyping-by-sequencing (GBS). Tissue biopsies may cause undue stress and damage to organisms, while visceral swabbing potentially reduces the chance of such harm. Our study compared the efficacy of these two DNA sampling methods for generating GBS data for the Unionid freshwater mussel, Texas Pigtoe (<em>Fusconaia askewi</em>). Our results find both methods generate quality sequence data, though some considerations are in order. Tissue biopsies produced significantly higher DNA concentrations and larger numbers of reads when compared to swabs, though there was no significant association between starting DNA concentration and number of reads generated. Swabbing produced greater sequence depth (more reads per sequence) while tissue biopsies revealed greater coverage across the genome (at lower sequence depth). Patterns of genomic variation as characterized in principal component analyses were similar regardless of the sampling method, suggesting that the less invasive swabbing is a viable option for producing quality GBS data in these organisms.</p>
Data from: Reliable and fast genotyping protocol for galactosylceramidase (GALC) in the Twitcher (Twi) mouse
<p><span>The Twitcher (Twi) mouse is a neurological Krabbe disease (KD, or globoid cell leukodystrophy) spontaneous mutant line. The genome of the Twi mouse presents a single nucleotide polymorphism (SNP), leading to an enzymatically inactive galactosylceramidase (GALC) protein and causing KD. In this context, mouse Twi genotyping is an essential step in KD research. To date,</span><span> the genotyping method used is labor-intensive and often drives ambiguous results</span><span>.</span><span> </span><span>Here, we evaluate a novel protocol for the genotype determination of GALC mutation status in Twi mice based on the allele-discrimination real-time polymerase chain reaction (PCR).</span><br><br><span>DNA is extracted from Twi mice (n = 20, pilot study; n = 120, verification study) and control group (n = 10, pilot study; n = 30 verification study) and assessed by allele-discrimination real-time PCR to detect SNP c.355G>A.</span><br><br><span>Using the allele-discrimination PCR, all the samples are identified correctly with the genotype GG (wild-type, WT), GA (heterozygote, HET), or AA (homozygote, HOM) by the first analysis and no animals were not genotyped.</span><br><br><span>We demonstrated that this novel method can be used to distinguish timely, accurately and without </span><span>ambiguity among </span><span>HOM, WT, and HET animals. This protocol represents a great opportunity to increase accuracy and speed in KD research.</span></p>
Data for: Russian honey bee genotype identification through enhanced marker panel set
<p>Russian honey bees (RHB) are a breeding population developed by USDA-ARS as an effort to provide Varroa-resistant honey bees to beekeepers. The selection strategy for this breeding population was the first in honey bees to incorporate genetic stock identification (GSI). The original GSI approach has been in use for over a decade, and though effective, novel technologies and analytical approaches recently developed provide an opportunity for improvement. Here we outline a novel genotyping assay that capitalizes on the markers used in the GSI as well as novel loci recently identified in a whole genome pooled study of commercial honey bee stocks. Our approach utilizes a microfluidic platform and machine learning analyses to arrive at an accurate, high throughput assay. This novel approach provides an improved tool that can be readily incorporated into breeding decisions towards healthier more productive bees.</p>
Leukochimerism genotyping data
<p> </p> <p><span>Twinning in cattle is infrequent, and also undesired. It can result in increased occurrence of abortion and dystocia, reduced calf survival, and a high likelihood of freemartinism in mixed-sex twins. Twin gestations also commonly are associated with the formation of placental vascular anastomoses (PVA) between twins. Through this, they share blood, hormones (leading to freemartinism in mixed-sex twins) and hematopoietic stem cells, which are the progenitors of white blood cells. The sharing of stem cells between twins can result in leukochimeric twinsets; these are twins that have white blood cells derived from both self and co-twin owing to the fetal migration of hematopoietic stem cells from the extraembryonic mesoderm of the yolk sac to final sites like bone marrow and thymus. This study examined the degree to which this leukochimerism changes over time. DNA was extracted from hair bulbs to determine the individual's true genotype and blood samples obtained at six time points from 1 week to 8 months of age to assess leukochimerism. Samples were genotyped using a medium-density SNP chip, and quantitative estimates of allele frequency were determined using SNPs for which members of a twin set had alternative homozygous genotypes. Results indicated statistically significant changes in proportion self and co-twin with age and suggest that by four months of age, the genotypic mix in white blood cells represents the hematopoietic cell population resident in the individual. </span></p>
Red drum genotypes and raw fecundity data
<p>Understanding the processes that drive reproductive success in marine fish stocks is critical to effective fisheries management. These processes can be difficult to investigate, especially in age-structured populations, because they occur at transgenerational scales. Reproductive success is often attributed to a small portion of the adult population (< 0.01%) and thought to be driven primarily by random external factors, consistent with the concept of sweepstakes reproductive success (SRS). A competing concept, the reproductive resilience paradigm, posits that fish have evolved complex spawner-recruit systems to achieve lifetime reproductive success and maintain population stability within highly variable environments. Here, we examine these two concepts. First, we analyze the popular sport fish red drum (<em>Sciaenops</em> <em>ocellatus</em>), drawing on genetic and reproductive data to estimate a plausible range for the N<sub>e</sub>/N<sub>A</sub> ratio of effective population size (N<sub>e</sub>) to adult abundance (N<sub>A</sub>) and to infer variance in lifetime reproductive success (V*<sub>k</sub>). Then, we synthesize available data and infer for two other fishes that have ratios reportedly > 0.10, the southern bluefin tuna (<em>Thunnus</em> <em>maccoyii</em>, Scombridae) and the silver seabream (<em>Chrysophrys</em> <em>auratus</em>, Sparidae). Although commonly regarded as an SRS species, red drum did not meet the SRS criterion. Overdispersed values were inferred for all three species, with those for red drum and silver seabream being dependent upon population-closure assumptions. Results are presented within the conceptual framework of reproductive resilience, considering the roles of random extrinsic forces versus evolved traits to achieve lifetime reproductive success and population stability in high and variable mortality environments.</p>
Raw data containing microsatellite genotypes and otolith microchemistry data for Lutjanus argentiventris individuals from Galapagos (Ecuador) and the Gulf of California (Mexico)
<p>The dataset contains the raw microsatellite genotypes and otolith microchemistry data for yellow snapper (Lutjanus argentiventris) individuals from Galapagos (Ecuador) and the Gulf of California (Mexico), described in the journal publication:</p> <p>Cavole LM, Munguia-Vega A, Miller JA, Salinas-de-Leon P, Marin Jarrin JR, Johnson AF, Laplane ER, Giron-Nava A, Aburto-Oropeza O (2023) Combining otolith chemistry and genetics to infer the population structure of yellow snapper <em>Lutjanus argentiventris. </em>Ecosphere.</p> <p> </p> <p> </p>
Data for: A predominant role of genotypic variation in both expression of sperm competition genes and paternity success in Drosophila melanogaster
<p>The study focuses on investigating the impact of both environmental and genotypic variations on the expression of sperm competition genes and relative paternity success (i.e. second male paternity; P2) in Drosophila melanogaster. To address this, the research leverages the Drosophila Genetic Reference Panel (DGRP) inbred lines and introduces manipulation of developmental population density, specifically larval density. This experimental design allows for the examination of the effects of genotype, environment, and potential genotype-environment interactions (GEI) on the expression of seminal fluid genes, namely Sex Peptide, Acp36DE, and CG9997 and sperm competitiveness. In light of the observed genotypic influence on genes' expression, a genome-wide association study (GWAS) was also conducted for Sex Peptide and Acp36DE.</p>
Data for: The relative impact of parental and current environment on plant transcriptomes depends on type of stress and genotype
<p>Through developmental plasticity, an individual organism integrates influences from its immediate environment with those due to the environment of its parents. While both effects on phenotypes are well documented, their relative impact has been little studied in natural systems, especially at the level of gene expression. We examined this issue in four genotypes of the annual plant <em>Persicaria maculosa</em> by varying two key resources light and soil moisture in both generations. Transcriptomic analyses showed that the relative effects of parent and offspring environment on gene expression (i.e., the number of differentially expressed transcripts, DETs) varied both for the two types of resource stress and among genotypes. For light, immediate environment induced more DETs than parental environment for all genotypes (although the precise proportion of parental versus immediate DETs varied among genotypes). By contrast, the relative effect of soil moisture varied dramatically among genotypes, from 8-fold more DETs due to parental than immediate conditions to 10-fold fewer. These findings provide evidence at the transcriptome level that the relative impacts of parental and immediate environment on the developing organism may depend on the environmental factor and vary strongly among genotypes, providing potential for the interplay of these developmental influences to evolve.</p>
Data from: Evaluating predator control using two non-invasive population metrics: a camera trap activity index and density estimation from scat genotyping
<p>Includes datasets from the Wimmera and Mallee, Victoria, Australia:</p> <p>- Fox camera trap data used to model activity</p> <p>- Fox scat SECR capture and trap files used to model density</p>
Data From: Effects of measurement methods and growing conditions on phenotypic expression of photosynthesis in seven diverse rice genotypes
<p class="p1"><strong>Introduction: </strong>Light response curves are widely used to quantify phenotypic expression of photosynthesis by measuring a single sample and sequentially altering light intensity within a chamber (sequential method) or by measuring different samples that are each acclimated to a different light level (nonsequential method). Both methods are often conducted in controlled environments to achieve steady-state results, and neither method involves equilibrating the entire plant to the speci<span class="s1">fi</span>c light level.</p> <p class="p1"><strong>Methods: </strong>Here, we compare sequential and non-sequential methods in controlled (greenhouse), semi-controlled (plant grown in growth chamber and acclimated to <span class="s1">fi</span>eld conditions 2-3 days before measurements), and <span class="s1">fi</span>eld environments. We selected seven diverse rice genotypes (<span class="s1">fi</span>ve genotypes from the USDA rice minicore collection: 310588, 310723, 311644, 311677, 311795; and 2 additional genotypes: Nagina 22 and Zhe 733) to understand (1) the limitations of different methods, and (2) phenotypic plasticity of photosynthesis in rice grown under different environments.</p> <p class="p1"><strong>Results:</strong> Our results show that the non-sequential method was time-ef<span class="s1">fi</span>cient and captured more variability of <span class="s1">fi</span>eld conditions than the sequential method, but the model parameters were generally similar between the two methods except for the maximum photosynthesis rate (A<sub>max</sub>). A<span class="s2"><sub>max</sub> </span>was signi<span class="s1">fi</span>cantly lower across all genotypes under greenhouse conditions compared to the growth chamber and <span class="s1">fi</span>eld conditions consistent with prior work, but surprisingly the apparent quantum yield (α) and the mitochondrial respiration (R<sub><span class="s2">d</span></sub>) were generally not different among growing environments or measurement methods.</p> <p class="p1"><strong>Discussion: </strong>Our results suggest that <span class="s1">fi</span>eld conditions are best suited to quantify phenotypic differences across different genotypes, and the nonsequential method was better at capturing the variability in photosynthesis.</p>
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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.