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505 results for “apples”
Data from: Resource allocation trade-offs and the loss of chemical defences during apple domestication
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Genetic mechanisms associated with floral initiation and the repressive effect of fruit on flowering in apple (Malus x domestica Borkh)
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Data from: Rapid and Repeatable Host Plant Shifts Drive Reproductive Isolation Following a Recent Human-Mediated Introduction of the Apple Maggot Fly, Rhagoletis pomonella
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Data from: Decrease in diversity and changes in community composition of arbuscular mycorrhizal fungi in roots of apple trees with increasing orchard management intensity across a regional scale
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Enhancing ecosystem services in apple orchards: Nest boxes increase pest control by insectivorous birds
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Proximity to natural habitat and flower plantings increases insect populations and pollination services in South African apple orchards
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Data from: Population structure of Venturia inaequalis, a causal agent of apple scab, in response to heterogeneous apple tree cultivation
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Data from: Biodiversity in agricultural landscapes: the effect of apple cultivar on epiphyte diversity
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Data from: Postglacial recolonization history of the European crabapple (Malus sylvestris Mill.), a wild contributor to the domesticated apple
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Morphological and olfactory tree traits influence the susceptibility and suitability of the apple species Malus domestica and M. sylvestris to Anthonomus pomorum
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DS1_LH_Tullii et al._ACS Appl. Mater. Interfaces_2019_EIS data
<p>electrochemical impedance spectroscopy measurements dataset</p>
Montana surveys of codling moth damage to apple fruit 2019-2020
<p>Codling moth (<em>Cydia pomonella</em>) is the major insect pest of pome fruit (apples and pears) in Montana. This dataset reports codling moth damage to apple fruit ("strikes") in Montana orchards where site managers were not applying pesticides to control codling moth. Data was collected in August or September of 2019 and 2020. Certain sites east of the continental divide have nominally lower incidence of codling moth damage to fruit than sites west of the divide. Due differences in weather year-to-year, we recommend continued monitoring. </p>
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Data from: AmpuBase: a transcriptome database for eight species of apple snails (Gastropoda: Ampullariidae)
Background: Gastropoda, with approximately 80,000 living species, is the largest class of Mollusca. Among gastropods, apple snails (family Ampullariidae) have members that are widely distributed in tropical and subtropical freshwater ecosystems and are ecologically and economically important. They exhibit various morphological and physiological adaptations to their respective habitats, which make them ideal candidates for studying adaptation, population divergence, speciation, and larger-scale patterns of diversity, including biogeography of native and invasive populations. The limited availability of genomic data, however, hinders in-depth ecological and evolutionary studies of these non-model organisms. Results: Using Illumina Hiseq platforms, we sequenced 1,220 million reads for seven species of apple snails. Together with the RNA-Seq data of two apple snails, we conducted de novo transcriptome assembly of eight species covering five genera of Ampullariidae, including representatives of the Old World and New World lineages. There were 20,730 to 35,828 unigenes with predicted open read frames for the eight species, with N50 (shortest sequence length at 50% of the unigenes) ranging from 1,320 to 1,803 bp. 69.7 % to 80.2 % of these unigenes were functionally annotated by searching against databases of NCBI's non-redundant, Gene Ontology and Kyoto Encyclopaedia of Genes and Genomes. With these data we developed AmpuBase, a relational database that features online BLAST for DNA/protein sequences, keyword search for unigenes/functional terms, and download functions for sequences and whole transcriptomes. Conclusions: In summary, we have generated comprehensive transcriptome data for multiple ampullariid genera and species, and created a publicly accessible database with a user-friendly interface to facilitate future basic and applied studies on ampullariids, and comparative molecular studies with other invertebrates.
Data from: Sylleptic branching in winter-headed apple (Malus × domestica) trees: accession-dependent responses and their relationships with other tree architectural characteristics
Well-feathered apple trees are essential for commercial orchards to optimize yields. However, most cultivars do not form these sylleptic branches readily in commercial nurseries due to high apical dominance. Several treatments exist to promote their formation in the nurseries, one of which is heading. However, not all cultivars are expected to react similarly to these treatments. We studied the branching response of 155 genotypes following heading and its relation to other architectural traits as a function of the cultivar's genetic background. Trees were grown for two consecutive years after grafting in a nursery, and the main axes were headed in the winter following growth in year 1. After heading, a single shoot was retained when growth resumed in the second year. Plant architectural traits such as growth of the main shoot, internode length, sylleptic branching, etc. were measured before and after heading and were statistically compared using a mixed model. This model showed the effect of heading for all architectural traits studied. In addition significant genotype and genotype × treatment interactions were found. In general, genotypes that showed a more vigorous growth during the first year also reacted more vigorously to heading. Accounting for the genetic substructure of this collection, no clear distinction in tree response could be found except in a small group of individuals that belonged to an F1 mapping population. This study shows that heading is not favorable for all genotypes to promote sufficient sylleptic branching and that other methods are needed to promote branching in these accessions.
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: Signatures of divergence, invasiveness and terrestralization revealed by four apple snail genomes
The family Ampullariidae includes both aquatic and amphibious apple snails. They are an emerging model for evolutionary studies due to the high diversity, ancient history and wide geographical distribution. Insight into drivers of ampullariid evolution is hampered, however, by the lack of genomic resources. Here we report the genomes of four ampullariids spanning the Old World (Lanistes nyassanus) and New World (Pomacea canaliculata, Pomacea maculata and Marisa cornuarietis) clades. The ampullariid genomes have conserved ancient bilaterial karyotype features and a novel Hox gene cluster rearrangement, making them valuable in comparative genomic studies. They have expanded gene families related to environmental sensing and cellulose digestion, which may have facilitated some ampullarids to become notorious invasive pests. In the amphibious Pomacea, novel acquision of an egg neurotoxin and a protein for making the calcareous eggshell may have been key adaptations enabling their transition from underwater to terrestrial egg deposition.
Data from: Genome-wide association studies in apple reveal loci of large effect controlling apple polyphenols
Apples are a nutritious food source with significant amounts of polyphenols that contribute to human health and wellbeing, primarily as dietary antioxidants. Although numerous pre- and post-harvest factors can affect the composition of polyphenols in apples, genetics is presumed to play a major role because polyphenol concentration varies dramatically among apple cultivars. Here we investigated the genetic architecture of apple polyphenols by combining high performance liquid chromatography (HPLC) data with ~100,000 single nucleotide polymorphisms (SNPs) from two diverse apple populations. We found that polyphenols can vary in concentration by up to two orders of magnitude across cultivars, and that this dramatic variation was often predictable using genetic markers and frequently controlled by a small number of large effect genetic loci. Using GWAS, we identified candidate genes for the production of quercitrin, epicatechin, catechin, chlorogenic acid, 4-O-caffeoylquinic acid and procyanidins B1, B2, and C1. Our observation that a relatively simple genetic architecture underlies the dramatic variation of key polyphenols in apples suggests that breeders may be able to improve the nutritional value of apples through marker-assisted breeding or gene editing.
Data from: Evolution of pathogenicity traits in the apple scab fungal pathogen in response to the domestication of its host
Understanding how pathogens emerge is essential to bring disease-causing agents under durable human control. Here, we used cross-pathogenicity tests to investigate changes in life history traits of the fungal pathogen Venturia inaequalis associated with host-tracking during the domestication of apple and subsequent host range expansion on the wild European crabapple (Malus sylvestris). Pathogenicity of 40 isolates collected in wild and domesticated ecosystems were assessed on the domesticated apple, its central Asian main progenitor (M. sieversii) and M. sylvestris. Isolates from wild habitats in the centre of origin of the crop were not pathogenic on the domesticated apple and less aggressive than other isolates on their host of origin. Isolates from the agro-ecosystem in central Asia infected a higher proportion of plants with higher aggressiveness, on both the domesticated host and its progenitor. Isolates from the European crabapple were still able to cause disease on other species but were less aggressive and less frequently virulent on these hosts than their endemic populations. Our results suggest that the domestication of apple was associated with the acquisition of virulences in the pathogen following host-tracking. The spread of the disease in the agro-ecosystem would also have been accompanied by an increase in overall pathogenicity.
Genetic variation of morpho-physiological traits in an apple core collection
<p>Dataset used for the preparation of the manuscript “Genetic variation of morphological traits and transpiration in an apple core collection under well-watered conditions: towards the identification of morphotypes with high water use efficiency”</p> <p>The dataset presented includes information for morphological and physiological traits for 183 genotypes of an INRA apple core collection. This collection was grown under well-watered condition in the Phenoarch phenotyping platform in Montpellier (France). Trees were evaluated during the first year of growth after grafting them on M9 rootstock. A first file includes individual information for four plants for each genotype. A second file includes the Best Linear Unbiased Predictors (BLUP’s) of genetic values for each morpho-physiological trait and genotype. Mixed effect models taking into account the spatial heterogeneity within the phenotyping platform were used to estimate BLUPs values.</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.