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.
21
datasets available to search
ShareScore release 0.9.0
Dataset results
21 results for “Crop genetics”
Corpus and list of keywords from Improving sustainable crop protection using population genetics concepts
<p>Corpus extracted in April 2021 from the ISI Web of Science portal (https://www.webofscience.com) with the following request: ‘Plant AND Resistan* AND Durab*’. A first corpus of 2522 articles was built considering all publication years for this extraction. This collection was then refined by categories to remove articles outwith the scope of our search (e.g. related to durable resistant materials for constructions). We also kept only articles cited at least once. The final corpus was composed of 1783 articles from 1979 to 2021:</p> <ul> <li>CORPUS_plant_resistance_durability.zip</li> </ul> <p>List of keywords used for the network presented in the article:</p> <ul> <li>keywords_list.csv</li> </ul>
Supporting data and code for: Host plant and insecticides shape the evolution of genetic and clonal diversity in a major aphid crop pest
<p>This is the first release of the final data and code for the article accepted for publication in <em>Evolutionary Applications</em> journal. It contains the necessary scripts to produce most of the analyses and figures of the manuscript. All the necessary data can be found in the 'data' folder.</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: Maintenance and expansion of genetic and trait variation following domestication in a clonal crop: Enset tGBS individual genotype data
Open the record for dataset details and reuse information.
Data from: Weed evolution: genetic differentiation among wild, weedy, and crop radish
Open the record for dataset details and reuse information.
Data from: The genetic architecture of ecological adaptation: intraspecific variation in host plant use by the lepidopteran crop pest Chloridea virescens
Intraspecific variation in ecologically important traits is a cornerstone of Darwin's theory of evolution by natural selection. The evolution and maintenance of this variation depends on genetic architecture, which in turn determines responses to natural selection. Some models suggest that traits with complex architectures are less likely to respond to selection than those with simple architectures, yet rapid divergence has been observed in such traits. The simultaneous evolutionary lability and genetic complexity of host plant use in the Lepidopteran subfamily Heliothinae suggest that architecture may not constrain ecological adaptation in this group. Here we investigate the response of Chloridea virescens, a generalist that feeds on diverse plant species, to selection for performance on a novel host, Physalis angulata (Solanaceae). P. angulata is the preferred host of Chloridea subflexa, a narrow specialist on the genus Physalis. In previous experiments, we found that the performance of C. subflexa on P. angulata depends on many loci of small effect distributed throughout the genome, but whether the same architecture would be involved in the generalist's adoption of P. angulata was unknown. Here we report a rapid response to selection in C. virescens for performance on P. angulata, and establish that the genetic architecture of intraspecific variation is quite similar to that of the interspecific differences in terms of the number, distribution, and effect sizes of the QTL involved. We discuss the impact of genetic architecture on the ability of Heliothine moths to respond to varying ecological selection pressures.
Data from: Genetic diversity of oilseed rape fields and feral populations in the context of coexistence with GM crops
Despite growing concern about transgenes escaping from fields, few studies have analysed the genetic diversity of crops in an agroecosystem over several years. Accurate information about the dynamics and relationship of the genetic diversity of crops in an agroecosystem is essential for risk assessment and policies concerning the containment of genetically modified crops and their coexistence with crops grown by conventional practices. Here, we analysed the genetic diversity of oilseed rape plants from fields and feral populations over 4 years in an agricultural landscape of 41 km2. We used exact compatibility and maximum likelihood assignment methods to assign these plants to cultivars. Even pure lines and hybrid cultivar seed lots contained several genotypes. The cultivar diversity in fields reflected the conventional view of agroecosystems quite well: that is, there was a succession of cultivars, some grown for longer than others because of their good performance, some used for one year and then abandoned, and others gradually adopted. Three types of field emerged: fields sown with a single cultivar, fields sown with two cultivars, and unassigned fields (too many cultivars or unassigned plants to reliably assign the field). Field plant diversity was higher than expected, indicating the persistence of cultivars that were grown for only one year. The cultivar composition of feral populations was similar to that of field plants, with an increasing number of cultivars each year. By using genetic tools, we found a link between the cultivars of field plants in a particular year and the cultivars of feral population plants in the following year. Feral populations on road verges were more diverse than those on path verges. All of these findings are discussed in terms of their consequences in the context of coexistence with genetically modified crops.
Genetic composition and diversity of Arabica coffee in the crop's center of origin and its impact on four major fungal diseases
<p><span>Conventional wisdom states that </span><span>genetic variation reduces disease levels in plant populations. Nevertheless, crop species have been subject to a gradual loss of genetic variation through selection for specific traits during breeding, thereby increasing their vulnerability to biotic stresses such as pathogens. We explored how genetic variation in Arabica coffee sites in southwestern Ethiopia was related to the incidence of four major fungal diseases. Sixty sites were selected along a gradient of management intensity, ranging from nearly wild to intensively managed coffee stands. We used genotyping-by-sequencing of pooled leaf samples (pool-GBS) derived from 16 individual coffee shrubs in each of the sixty sites to assess the variation in genetic composition (multivariate: reference allele frequency) and genetic diversity (univariate: mean expected heterozygosity) between sites. </span><span>We found that genetic composition had a clear spatial pattern and that genetic diversity was higher in less managed sites</span><span>. The incidence of the four fungal diseases was related to the genetic composition of the coffee stands, but in a specific way for each disease. In contrast, genetic diversity was only related to the within-site variation of coffee berry disease, but not to the mean incidence of any of the four diseases across sites. Given that fungal diseases are major challenges of Arabica coffee in its native range, our findings that genetic composition of coffee sites impacted the major fungal diseases may serve as baseline information to study the molecular basis of disease resistance in coffee. </span><span>Overall, our study illustrates the need to consider both host genetic composition and genetic diversity when investigating the genetic basis for variation in disease levels</span><span>. </span></p>
Interspecific gene exchange introduces high genetic variability in crop pathogen - dataset and scripts
<p>The files found in this repository are the one used for generating the analyses presented in the Feurtey et al. manuscript submission accepted in GBE.</p>
Genetic composition and diversity of Arabica coffee in the crop’s center of origin and its impact on four major fungal diseases
Open the record for dataset details and reuse information.
Data from: Capturing genetic variation in crop wild relatives: an evolutionary approach
Open the record for dataset details and reuse information.
Data from:Insight into the durability of plant resistance to aphids from a demo-genetic study of Aphis gossypii in melon crops
Open the record for dataset details and reuse information.
Data from: Genetic diversity of oilseed rape fields and feral populations in the context of coexistence with GM crops
Open the record for dataset details and reuse information.
Data from: The genetic architecture of ecological adaptation: intraspecific variation in host plant use by the lepidopteran crop pest Chloridea virescens
Open the record for dataset details and reuse information.
Data from: Genetic diversity of Helosciadium repens (Jacq.) W.D.J. Koch (Apiaceae) in Germany, a Crop Wild Relative of celery
Open the record for dataset details and reuse information.
Data from: Monarch butterfly and milkweed declines substantially predate the use of genetically modified crops
Open the record for dataset details and reuse information.
Data from: Crop-to-wild gene flow and spatial genetic structure in the closest wild relatives of the cultivated apple
Crop-to-wild gene flow have important evolutionary and ecological consequences and require careful consideration in conservation programs for wild genetic resources of potential use in breeding programs and in assessments of the risk of transgene escape into natural ecosystems. Using 26 microsatellites and a set of 1181 trees, we investigated the extent of introgression from the cultivated apple, Malus domestica, to its three closest wild relatives, M. sylvestris in Europe, M. orientalis in the Caucasus and M. sieversii in Central Asia. We found footprints of introgression from M. domestica to M. orientalis (3.2% of hybrids), M. sieversii (14.8%) and M. sylvestris (36.7%). Malus sieversii and M. orientalis presented weak but significant genetic structures across their geographic range. Malus orientalis displayed genetic differentiation with three differentiated populations in Turkey, Armenia and Russia. Malus sieversii consisted of a main population spread over Central Asia and a smaller population in the Tian Shan Mountains. The low Sp values suggest high dispersal capacities for the wild apple relatives. High potential for crop-to-wild gene flow in apples needs to be considered in the implementation of in situ and ex situ actions for the conservation of wild apple genetic resources potentially useful to plant breeding.
Data from: Crop-to-wild gene flow and spatial genetic structure in the closest wild relatives of the cultivated apple
Open the record for dataset details and reuse information.
Genetic dependencies associated with transcription factor activities in human cancer cell lines [CROP-seq]
GEO Series GSE263747. Homo sapiens. 6 samples. Type: Expression profiling by high throughput sequencing; Other.
Epistatic transcriptional interations underlying oncogenic genetic interactions (GI) via combinatorial CROP-seq
GEO Series GSE164996. Homo sapiens. 20 samples. Type: Expression profiling by high throughput sequencing.
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.