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769 results for “CULTIVATE”
Networks of physiological adjustments and defenses, and their synergy with sodium (Na+) homeostasis explain the hidden variation for salinity tolerance across the cultivated Gossypium hirsutum germplasm
<p>The abilities to mobilize and/or sequester excess ions within and outside the plant cell are important components of salt-tolerance mechanisms. Mobilization and sequestration of Na<sup>+</sup> involves three transport systems facilitated by the plasma membrane H<sup>+</sup>/Na<sup>+</sup> antiporter (SOS1), vacuolar<i> </i>H<sup>+</sup>/Na<sup>+</sup> antiporter (NHX1), and Na<sup>+</sup>/K<sup>+</sup> transporter<i> </i>in vascular tissues (HKT1). Many of these mechanisms are conserved across the plant kingdom. While <i>Gossypium hirsutum</i> (upland cotton) is significantly more salt-tolerant relative to other crops, the critical factors contributing to the phenotypic variation hidden across the germplasm have not been fully unraveled. In this study, the spatio-temporal patterns of Na<sup>+</sup> accumulation along with other physiological and biochemical interactions were investigated at different severities of salinity across a meaningful genetic diversity panel across cultivated upland <i>Gossypium. </i>The aim was to define the importance of holistic or integrated effects relative to the direct effects of Na<sup>+</sup> homeostasis mechanisms mediated by <i>GhHKT1, GhSOS1,</i> and <i>GhNHX1. </i>Multi-dimensional physio-morphometric attributes were investigated in a systems-level context using univariate and multivariate statistics, <i>randomForest,</i> and path analysis. Results showed that mobilized or sequestered Na<sup>+</sup> contributes significantly to the baseline tolerance mechanisms. However, the observed variance in overall tolerance potential across a meaningful diversity panel were more significantly attributed to antioxidant capacity, maintenance of stomatal conductance, chlorophyll content, and divalent cation (Mg<sup>2+</sup>) contents other than Ca<sup>2+</sup> through a complex interaction with Na<sup>+</sup> homeostasis. The multi-tier macro-physiological, biochemical and molecular data generated in this study, and the networks of interactions uncovered strongly suggest that a complex physiological and biochemical synergy beyond the first-line-of defense (Na<sup>+</sup> sequestration and mobilization) accounts for the total phenotypic variance across the primary germplasm of <i>Gossypium hirsutum</i>. These findings are consistent with the recently proposed Omnigenic Theory for quantitative traits and should contribute to a modern look at phenotypic selection for salt tolerance in cotton breeding.</p>
PIBAC: Extensive cultivation of the pig gut microbiome identifies novel bacterial diversity and functions and enables tailored functional studies
<p>In-depth cultivation of the pig gut microbiome towards novel bacterial diversity and tailored functional studies:</p> <ul> <li>780 MAGs from all-in-one assembly of 295 pig gut metagenomic samples (Xiao, 2016)</li> <li>38 isolates representing novel species (single draft genomes)</li> <li>representing in total 617 species (hqMAGs-dereplicated_genomes, comp>90%, con<5%</li> </ul> <p>More information you can find here:</p> <p>https://github.com/tillrobin/PIBAC</p> <p>https://www.dsmz.de/pibac</p> <p> </p> <p>External study providing data:</p> <p>Xiao, Liang, et al. "A reference gene catalogue of the pig gut microbiome." Nature microbiology 1.12 (2016): 16161. <a href="https://doi.org/10.1038/nmicrobiol.2016.161">https://doi.org/10.1038/nmicrobiol.2016.161</a> </p>
Population structure of Rosa spinosissima L. on the Frisian Islands and introgression from cultivated material
<i>Rosa spinosissima</i> L. is part of the highly dynamic coastal habitat of the Wadden Sea, between the coast of northwestern continental Europe and the Frisian Islands. Plants of this species grow clonally via root suckers to form large patches, which stabilize dunes and help to protect the islands and used for this purpose locally on the island Sylt. <i>Rosa spinosissima</i> plants are affected by both water and wind in their harsh environment, and are threatened by human impact via habitat destruction and introduction of foreign species. In these northern parts of its range <i>R. spinosissima</i> is categorized as endangered. The population structure of <i>R. spinosissima</i> was investigated using ten microsatellite loci and 195 individuals of Frisian Island populations and European coastal continental samples. DAPC, Kmeans and Structure analyses were conducted to study the genetic composition and integrity of these natural populations relative to cultivated and nursery material mostly consisting of central continental genotypes. The DAPC and Structure analyses differentiated populations of the Frisian Islands between each other and separated them from nursery samples, but some natural populations showing an impact of nursery and cultivated genotypes. In addition, some clonal patches of <i>R. spinosissima</i> were detected. Our results show that the natural Frisian Island populations of <i>R. spinosissima</i> are threatened by the introduction of nonadaptive genotypes into the gene pool.
Data from: Pollinator-mediated interactions between cultivated papaya and co-flowering plant species
Many modern crop varieties rely on animal pollination to set fruit and seeds. Intensive crop plantations usually do not provide suitable habitats for pollinators so crop yield may depend on the surrounding vegetation to maintain pollination services. However, little is known about the effect of pollinator-mediated interactions among co-flowering plants on crop yield or the underlying mechanisms. Plant reproductive success is complex, involving several pre- and post-pollination events; however, the current literature has mainly focused on pre-pollination events in natural plant communities. We assessed pollinator sharing and the contribution to pollinator diet in a community of wild and cultivated plants that co-flower with a focal papaya plantation. In addition, we assessed heterospecific pollen transfer to the stigmatic loads of papaya and its effect on fruit and seed production. We found that papaya shared at least one pollinator species with the majority of the co-flowering plants. Despite this, heterospecific pollen transfer in cultivated papaya was low in open-pollinated flowers. Hand pollination experiments suggest that heterospecific pollen transfer has no negative effect on fruit production or weight, but does reduce seed production. These results suggest that co-flowering plants offer valuable floral resources to pollinators that are shared with cultivated papaya with little or no cost in terms of heterospecific pollen transfer. Although HP reduced seed production, a reduced number of seeds per se is not negative, given that from an agronomic perspective the number of seeds does not affect the monetary value of the papaya fruit.
Data from: Cultivation shapes genetic novelty in a globally important invader
Acacia saligna is a species complex that has become invasive in a number of countries worldwide where it has caused substantial environmental and economic impacts. Understanding genetic and other factors contributing to its success may allow managers to limit future invasions of closely related species. We used three molecular markers to compare the introduced range (South Africa) to the native range (Western Australia). Nuclear markers showed that invasive populations are divergent from native populations and most closely related to a cultivated population in Western Australia. We also found incongruence between nuclear and chloroplast data that, together with the long history of cultivation of the species, suggest that introgressive hybridization (coupled with chloroplast capture) may have occurred within A. saligna. While we could not definitively prove introgression, the genetic distance between cultivated and native A. saligna populations was comparable to known interspecific divergences among other Acacia species. Therefore, cultivation, multiple large-scale introductions and possibly introgressive hybridization have rapidly given rise to the divergent genetic entity present in South Africa. This may explain the known global variation in invasiveness and inaccuracy of native bioclimatic models in predicting potential distributions.
Data from: Genetic relationships, structure and parentage simulation among the olive tree (Olea europaea L. subsp. europaea) cultivated in Southern Italy revealed by SSR markers
In this work, we assess both the morphological and genetic diversity of 68 important olive cultivars from three Southern Italian regions: Calabria, Campania and Sicily. Twenty-five phenotypic traits were evaluated and 12 simple sequence repeat (SSR) markers were analysed. All SSR primers were polymorphic and reliable. The total number of alleles per locus varied from 5 to 19 with an average number of 13.1 and a mean polymorphic information content (PIC) of 0.81. These results suggested high genetic diversity within these three olive germplasm collections. Morphological traits also showed significant variability amongst cultivars. Two cases of identity were found and ten statistically significant cases of putative parent/sibling were discovered by performing a SSR-based parentage simulation analysis with CERVUS. The Mantel test indicated low but significant correlations between the morphological data and SSR allelic frequency, origin and SSR allelic frequency, and origin and morphology. Structure software allowed inference of relationships between the three olive germplasm collections and allowed us to obtain the most consistent grouping and to identify putative admixed or exchanged cultivars. Cluster and multivariate analysis, based on morphological traits, revealed geographic grouping in agreement with UPGMA dendrogram and structure analysis using SSRs. Sicilian cultivars showed a more homogenous genetic makeup, probably due to geographical isolation, whilst Calabrian and Campanian cultivars seemed to have a less distinct genetic structure, with a greater degree of intermixing. A correlation between the presence of certain SSR alleles and fruit size was also found.
Data from: A genetic discontinuity in root-nodulating bacteria of cultivated pea in the Indian trans-Himalayas
Evolutionary relationships of 120 root-nodulating bacteria isolated from the nodules of Pisum sativum cultivated at 22 different locations of the trans-Himalayan valleys of Lahaul and Spiti in the state of Himachal Pradesh of India were studied using 16S rRNA gene PCR-RFLP, ERIC-PCR, sequencing of 16S rRNA, atpD, recA, nodC and nifH genes, carbon-source utilization pattern (BIOLOG™), and whole-cell fatty acid profiling. The results demonstrated that all isolates belonged to Rhizobium leguminosarum symbiovar viciae (Rlv). Isolates from the two valleys were clearly separated on the basis of ERIC fingerprints, carbon-source utilization pattern, and whole-cell fatty acid methyl esters. Phylogenetic analysis of atpD, recA, nodC and nifH genes revealed a common Rlv sublineage in Spiti valley. Lahaul valley isolates were represented by 3 sequence types of atpD and recA genes, and four sequence types of nodC and nifH genes. Genotypes from the two valleys were completely distinct, except for two Lahaul isolates that shared nodC and nifH sequences with Spiti isolates but were otherwise more similar to other Lahaul isolates. Isolates from the two highest Spiti valley sites (above 4000m) had a distinctive whole-cell fatty acid profile. Spiti valley isolates are closely related to Rlv sublineages from Xinjiang and Shanxi provinces in China, while Lahaul valley isolates resemble cosmopolitan strains of the western world. The high mountain pass between these valleys represents a boundary between two distinct microbial populations.
Data from: Genetic diversity of wild grapevine populations in Spain and their genetic relationships with cultivated grapevines
The wild grapevine, Vitis vinifera L. ssp sylvestris (Gmelin) Hegi, considered as the ancestor of the cultivated grapevine, is native from Eurasia. In Spain natural populations of Vitis vinifera ssp sylvestris can still be found along river banks. In this work we have performed a wide search of wild grapevine populations in Spain and characterized the amount and distribution of their genetic diversity using 25 nuclear SSR loci. We have also analyzed the possible coexistence in the natural habitat of wild grapevines with naturalized grapevine cultivars and rootstocks. In this way, phenotypic and genetic analyses identified 19% of the collected samples as derived from cultivated genotypes, being either naturalized cultivars or hybrid genotypes derived from spontaneous crosses between wild and cultivated grapevines. The genetic diversity of wild grapevine populations was similar than that observed in the cultivated group. The molecular analysis showed that cultivated and wild germplasm are genetically divergent with low level of introgression. Using a model-based approach implemented in the software STRUCTURE we identified four genetic groups, with two of them fundamentally represented among cultivated genotypes and two among wild accessions. The analyses of genetic relationships among wild and cultivated grapevines could suggest a genetic contribution of wild accessions from Spain to current western cultivars.
Data from: Phenotypic landscapes: phenological patterns in wild and cultivated barley
Phenotypic variation in natural populations is the outcome of the joint effects of environmentally induced adaptations and neutral processes on the genetic architecture of quantitative traits. In this study we examined the role of adaptation in shaping wild barley phenotypic variation along different environmental gradients. Detailed phenotyping of 164 wild barley (Hordeum spontaneum) accessions from Israel (of the Barley1K collection), and 18 cultivated barley (H. vulgare) varieties, was conducted in common garden field trials. Cluster analysis based on phenotypic data indicated that wild barley in this region can be differentiated into three ecotypes in accordance with their ecogeographic distribution: north, coast, and desert. Population differentiation (Qst) for each trait was estimated using a hierarchical Bayesian model and compared to neutral differentiation (Fst) based on 42 microsatellite markers. This analysis indicated that the three clusters diverged in morphological but not in reproductive characteristics. To address the issue of phenotypic variation along environmental gradients, climatic and soil gradients were compared with each of the measured traits given the geographical distance between sampling sites using a partial Mantel test. Flowering time and plant growth were found to be differentially correlated with climatic and soil characteristic gradients, respectively. The H. vulgare varieties were superior to the H. spontaneum accessions in yield components yet resembled the Mediterranean types in vegetative characteristics and flowering time, which may indicate the geographic origin of domesticated barley.
Data from: Passive restoration of sub-tropical grassland after abandonment of cultivation
Passive restoration of grasslands after the abandonment of cultivation may be a viable restoration option where seed sources from remnant grasslands are available, and if the risk of deflected succession is low. Passive restoration of subtropical grassland in Queensland, Australia was evaluated along a chronosequence of abandoned cultivation (fallow) paddocks. Plant communities in fallow paddocks were compared with nearby remnant grassland. On average, species richness recovers after 60 years of abandonment and floristic composition shows affinities with nearby remnant grassland (Bray-Curtis ˜ 0·6). The risk of deflected succession, such as dominance by exotic grasses, has apparently been low in this ecosystem. Annual grasses and forbs are rapid colonizers of the abandoned fields, and richness of perennial forbs exhibits near-linear recovery. Perennial grasses are relatively slow to establish but all except two species have statistically insignificant differences in abundance between remnant grassland and fallow fields after 20 years. The perennial grasses that recover most rapidly in fallow paddocks have disseminules that are adorned with appendages for wind dispersal including the most important dominant grass, Dichanthium sericeum. The perennial grasses that are slowest to recover are probably less effective dispersers. Synthesis and applications. Passive restoration of grasslands after the abandonment of cultivation can be a viable contribution to grassland conservation where there is an adequate matrix of remnant grasslands in the vicinity of fallows, perennial exotic species do not monopolize fallows and the dominant native grasses are well dispersed.
Data from: Genome wide association mapping of floral traits in cultivated sunflower (Helianthus annuus)
Floral morphology and pigmentation are both charismatic and economically relevant traits associated with cultivated sunflower (Helianthus annuus L.). Recent work has linked floral morphology and pigmentation to pollinator efficiency and seed yield. Understanding the genetic architecture of such traits is essential for crop improvement, and gives insight into the role of genetic constraints in shaping floral diversity. A diversity panel of 288 sunflower genotypes was phenotyped for a variety of morphological, phenological, and color traits in both a greenhouse and a field setting. Association mapping was performed using 5788 SNP markers using a mixed linear model approach. Several dozen markers across ten linkage groups were significantly associated with variation in morphological and color trait variation. Substantial trait plasticity was observed between greenhouse and field phenotyping, and associations differed between environments. Color traits mapped more strongly than morphology in both settings, with markers together explaining 16% of petal carotenoid content in the greenhouse, and 17% and 24% of variation in disc anthocyanin presence in the field and greenhouse, respectively. Morphological traits like disc size mapped more strongly in the field, with markers together explaining up to 19% of disc size variation. Loci identified here through association mapping within cultivated germplasm differ from those identified through biparental crosses between modern cultivated sunflower and either its wild progenitor or domesticated landraces. Several loci lie within genomic regions involved in domestication. Differences between phenotype expression under greenhouse and field conditions highlight the importance of plasticity in determining floral morphology and pigmentation.
Data from: Metabolism and the rise of fungus cultivation by ants
Most ant colonies are comprised of workers that cooperate to harvest resources and feed developing larvae. Around 50 million years ago (MYA), ants of the attine lineage adopted an alternative strategy, harvesting resources used as compost to produce fungal gardens. While fungus cultivation is considered a major breakthrough in ant evolution, the associated ecological consequences remain poorly understood. Here, we compare the energetics of attine colony-farms and ancestral hunter-gatherer colonies using metabolic scaling principles within a phylogenetic context. We find two major energetic transitions. First, the earliest lower-attine farmers transitioned to lower mass-specific metabolic rates while shifting significant fractions of biomass from ant tissue to fungus gardens. Second, a transition 20 MYA to specialized cultivars in the higher-attine clade was associated with increased colony metabolism (without changes in garden fungal content) and with metabolic scaling nearly identical to hypometry observed in hunter-gatherer ants, although only the hunter-gatherer slope was distinguishable from isometry. Based on these evolutionary transitions, we propose that shifting living-tissue storage from ants to fungal mutualists provided energetic storage advantages contributing to attine diversification and outline critical assumptions that, when tested, will help link metabolism, farming efficiency, and colony fitness.
Data from: Ecological niche modeling for a cultivated plant species: a case study on taro (Colocasia esculenta) in Hawai'i
Under the threat of ongoing and projected climate change, communities in the Pacific Islands face challenges of adapting culture and lifestyle to accommodate a changing landscape. Few models can effectively predict how biocultural livelihoods might be impacted. Here, we examine how environmental and anthropogenic factors influence an ecological niche model (ENM) for the realized niche of cultivated taro (Colocasia esculenta) in Hawai'i. We created and tuned two sets of ENMs: one using only environmental variables, and one using both environmental and cultural characteristics of Hawa'i. These models were projected under two different Intergovernmental Panel on Climate Change (IPCC) Representative Concentration Pathways (RCPs) for 2070. Models were selected and evaluated using average omission rate and area under the receiver operating characteristic curve (AUC). We compared optimal model predictions by comparing the percentage of taro plots predicted present and measured ENM overlap using Schoener's D-statistic. The model including only environmental variables consisted of 19 Worldclim bioclimatic variables, in addition to slope, altitude, distance to perennial streams, soil evaporation, and soil moisture. The optimal model with environmental variables plus anthropogenic features also included a road density variable (which we assumed as a proxy for urbanization) and a variable indicating agricultural lands of importance to the State of Hawai'i. The model including anthropogenic features performed better than the environment-only model based on omission rate, AUC, and review of spatial projections. The two models also differed in spatial projections for taro under anticipated future climate change. Our results demonstrate how ENMs including anthropogenic features can predict which areas might be best suited to plant cultivated species in the future, and how these areas could change under various climate projections. These predictions might inform biocultural conservation priorities and initiatives. In addition, we discuss the incongruences that arise when traditional ENM theory is applied to species whose distribution has been significantly impacted by human intervention, particularly at a local scale relevant to biocultural conservation initiatives.
Cultivation of host-associated bacteria under sulfide-enriched microoxic and anoxic conditions
<p>Cultivation protocol</p>
FIGURE 4 in A new species of South American whitefly (Sternorrhyncha: Aleyrodidae) colonising cultivated bay laurel
FIGURE 4. Aleuroplatus biluminiporus sp. nov. Thirdinstar larva with expanded detail of (top to bottom) cephalic seta, mesothoracic seta, abdominal margin, geminate pore / porette and vasiform orifice / eighth abdominal seta.
FIGURES 23 in A new species of South American whitefly (Sternorrhyncha: Aleyrodidae) colonising cultivated bay laurel
FIGURES 23. Aleuroplatus biluminiporus sp. nov. (2) Outlines of two puparia, with cephalic "eyespots", moulting sutures, vasiform orifice and caudal setae marked; (3) Detail of puparial venter.
FIGURE 1 in A new species of South American whitefly (Sternorrhyncha: Aleyrodidae) colonising cultivated bay laurel
FIGURE 1. Aleuroplatus biluminiporus sp. nov. Puparium with expanded detail of (A) margin & submargin, (B) vasiform orifice region, (C) caudal margin and setae, (D) subdorsal thickrimmed "bright" pores, (E) submedian geminate pore / porettes.
FIGURES 23 in Crenidorsum aroidephagus Martin & Aguiar sp. nov. (Sternorrhyncha: Aleyrodidae), a New World whitefly species now colonising cultivated Araceae in Europe, Macaronesia and The Pacific Region
FIGURES 23. Crenidorsum aroidephagus Martin & Aguiar sp. nov. drawn from specimens ex Philodendron gloriosum, Berlin Botanic Garden. (2) Submedian detail of meso and metathorax, particularly showing setae, scalloped longitudinal folds and distribution of geminate pore / porettes and thickrimmed pores; (3) region of vasiform orifice, with lingula in resting, included, position.
FIGURE 1 in Crenidorsum aroidephagus Martin & Aguiar sp. nov. (Sternorrhyncha: Aleyrodidae), a New World whitefly species now colonising cultivated Araceae in Europe, Macaronesia and The Pacific Region
FIGURE 1. Computer-montage image of slidemounted puparium of Crenidorsum aroidephagus Martin & Aguiar sp. nov. ex-Philodendron gloriosum, Berlin Botanic Garden, with lingula unfolded and excluded from vasiform orifice.
FIGURE 5 in A new species of South American whitefly (Sternorrhyncha: Aleyrodidae) colonising cultivated bay laurel
FIGURE 5 (A-G). Aleuroplatus biluminiporus sp. nov. A. Habitus photograph of puparium. B. Scanning electron micrograph (SEM) of puparial vasiform orifice, with operculum raised. C. SEM of first-instar larva, habitus position. D. SEM of first-instar larva, thoracic marginal flanges. E. SEM of first-instar larva, abdominal marginal projections. F. SEM of first-instar larva, vasiform orifice. G. SEM of a group of eggs.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
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.