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17 results for “leaf architecture”
Leaf growth response to mild drought: natural variation sheds light on trait architecture
<p>Plant growth and crop yield are negatively affected by a reduction in water availability. However, a clear understanding of how growth is regulated under non-lethal drought conditions is lacking. Recent advances in genomics, phenomics and transcriptomics allow in-depth analysis of natural variation. In this study, we conducted a detailed screening of leaf growth responses to mild drought in a worldwide collection of <em>Arabidopsis thaliana</em> accessions. </p> <p>The raw phenotyping can be found in:<br> - cellularData.txt -> mature (23 days after stratification; DAS) leaf epidermis (third leaf) analysed for cell area, cell number, pavement cell area, pavement cell number, stomatal index and leaf area of the analysed leaf.</p> <p>- leaf3AreaMaturity.txt -> area of the third leaf at maturity (23DAs) in mm<sup>2.</sup></p> <p>- leaf3AreaProliferation.txt -> area of the third leaf at proliferation (last day of full cell proliferation; 8-10 DAS) in mm<sup>2</sup>.</p> <p>- rosetteArea Maturity.txt -> projected rosette area at maturity (22DAS)</p> <p>The phenotyping results have been normalised for batch effects ('experiment' in raw data)</p> <p>- allPhenotypesNormalised.txt -> contains the normalised data for all the measured phenotypes</p> <p>All datafiles indicate the accession name ('Accession'), the unique identifier for each accessions ('Ecotype_ID') as used in the 1001genomes project (www.1001genomes.org) and the treatment ('C' indicate well-watered plants, 'S' the mild-drought treated plants).</p> <p>These results and methodological results are described in Clauw et al. (2016, The Plant Cell).</p> <p>Citation:</p> <p><strong>Clauw, Pieter, Frederik Coppens, Arthur Korte, Dorota Herman, Bram Slabbinck, Stijn Dhondt, Twiggy Van Daele, et al. 2016. “Leaf Growth Response to Mild Drought: Natural Variation in Arabidopsis Sheds Light on Trait Architecture.” The Plant Cell, October. doi:10.1105/tpc.16.00483.</strong></p> <p> </p> <p> </p> <p> </p> <p> </p> <p> </p>
Data for: Associations between leaf developmental stability, canalization and phenotypic plasticity in an architectural perspective
<p class="MsoNormal"><span>Associations between developmental stability, canalization and phenotypic plasticity have been predicted, but rarely supported by direct evidence. Architectural analysis may provide a more powerful approach to finding correlations among these mechanisms in plants. T</span><span>o investigate the relationships among the three mechanisms in architectural perspective, w</span><span>e </span><span>subjected plants of </span><em><span>Abutilon theophrasti</span></em><span> to three densities, measured and calculated </span><span>fluctuating asymmetry (FA), coefficients of variation (CV)</span><span> and </span><span>plasticity (PI) of three leaf traits, to analyze the </span><span>correlations among these variables.</span><span> As density increased, mean leaf size, petiole length and angle of most layers and mean leaf FA of some layers decreased (at both stages), CV of petiole angle increased (at day 50), and PI of petiole length and angle across all layers decreased (at day 70); leaf FA and CV of traits generally increased with higher layers at all densities. At both stages, there were more positive correlations between FA and CV at lower vs. high densities; at day 50, little correlation of plasticity with FA or CV was found; at day 70, more positive correlations between FA and PI occurred for response to high vs. low density than for response to medium vs. low density, and more positive correlations between CV and PI occurred at lower vs. high densities. Results suggested that developmental instability, decreased canalization and plasticity can be cooperative and the relationships between decreased canalization and plasticity are more likely to be positive if decreased canalization is due to vibrant growth rather than stressful effects. The relationships of plasticity with developmental instability differed from its relationship with decreased canalization in the way of variation. Decreased canalization should be more beneficial for possible plasticity in the future, while canalization may result from already-expressed plasticity.</span></p>
Data for: Associations between leaf developmental stability, canalization and phenotypic plasticity in an architectural perspective
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Genetic architecture of heritable leaf microbes
<p><em>Background</em></p> <p>Host-associated microbiomes are shaped by both their environment and host genetics, and often impact host performance. The scale of host genetic variation important to microbes is largely unknown, yet fundamental to the community assembly of host-associated microbiomes, and with implications for the eco-evolutionary dynamics of microbes and hosts. Using <em>Ipomoea hederacea</em>, Ivy-leaved morning glory, we generated matrilines differing in quantitative genetic variation and leaf shape, which is controlled by a single Mendelian locus. We then investigated the relative roles of Mendelian and quantitative genetic variation in structuring the leaf microbiome, and how these two sources of genetic variation contributed to microbe heritability.</p> <p><em>Results</em></p> <p>We found that despite large effects of the environment, both Mendelian and quantitative genetic host variation were important in contributing to microbe heritability, and that the cumulative small effect genomic differences due to matriline explained as much or more microbial variation than a single large effect locus. Furthermore, our results are the first to suggest that leaf shape itself contributes to variation in the abundances of some microbes in the leaf microbiome.</p> <p><em>Conclusions</em></p> <p>The genetic architecture of plant-associated microbiomes depends on both quantitative genetic variation and Mendelian traits, with similar contributions to microbe heritability. Our results demonstrate the roles of different scales of host genetic variation in the assembly of a natural microbiome. The genetic basis and heritability of a host's microbial phenotype is important for host evolution and ecology because microbes can affect host fitness, and because it can influence reciprocal selection between hosts and microbiomes. Additionally, when host-associated microbiomes have heritability, then this suggests they have the capacity to evolve as other host traits might, with potentially adaptive functions.</p>
Data for: Dissecting the genetic architecture of leaf morphology traits in mungbean (Vigna radiata (L.) Wizcek) using genome‐wide association study
<p><span>Mungbean (<em>Vigna radiata</em> (L) Wizcek) is an important pulse crop, increasingly used as a source of protein, fiber, low fat, carbohydrates, minerals, and bioactive compounds in human diets. Mungbean is a dicot plant with trifoliate leaves. Leaves are central to various plant processes like photosynthesis, light interception, and overall canopy structure. The objectives were to study leaf morphological traits, use image analysis to extract leaf traits from images from the Iowa Mungbean Diversity (IMD) panel, develop a regression model for the prediction of leaflet area, and conduct association mapping for leaf morphological traits. We collected more than 5000 leaf images of the IMD panel consisting of 484 accessions over two years (2020 and 2021) with two replications per experiment. Leaf traits were extracted using image analysis, analyzed, and used for association mapping. Morphological diversity included leaflet type (oval or lobed), leaflet size (small, medium, large), lobed angle (shallow, deep), and vein coloration (green, purple). A regression model was developed to predict each ovate leaflet's area (adjusted R<sup>2</sup> = 0.97; residual standard errors of <= 1.10). The candidate genes <em>Vradi01g07560</em>, <em>Vradi05g01240</em>, <em>Vradi02g05730</em>, and <em>Vradi03g00440</em>, are associated with multiple traits (length, width, perimeter, and area) across the leaflets (left, terminal, and right). These are suitable candidate genes for further investigation in their role in leaf development, growth, and function. Future studies will be needed to correlate the observed traits discussed here with yield or important agronomic traits for use as phenotypic or genotypic markers in marker-aided selection methods for mungbean crop improvement.</span></p>
Leaf architecture and functional traits for 122 species at the University of California at Berkeley botanical garden
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Genetic architecture of heritable leaf microbes
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Data for: Dissecting the genetic architecture of leaf morphology traits in mungbean (Vigna radiata (L.) Wizcek) using genome‐wide association study
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Data from: Plasticity in hydraulic architecture: Riparian trees respond to increased temperatures with genotype-specific adjustments to leaf traits
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RIP2 interacts with REL1 to control leaf architecture by modulating brassinosteroid signaling in rice
<p>FPKM (Fragments per kilobase of exon model per million mapped fragments) value of all detected genes in in WT, rel1, rip2, and rel1 rip2 mutants. ZH11_1, ZH11_2, ZH11_3 represent samples were collected from ZH11 with three independent biological replicates. rel1_1, rel1_2, rel1_3 represent samples were collected from <i>rel1 </i>mutants with three independent biological replicates. rip2_1, rip2_2, rip2_3 represent samples were collected from rip2 mutant with three independent biological replicates. rel1rip2_1, rel1rip2_2, rel1rip2_3<b> </b>represent samples were collected from rel1rip2 double mutant with three independent biological replicates.</p>
Data from: The genetic architecture of constitutive and induced trichome density in two new RIL populations of Arabidopsis thaliana: phenotypic plasticity, epistasis, and bidirectional leaf damage response
Background: Herbivory imposes an important selective pressure on plants. In Arabidopsis thaliana leaf trichomes provide a key defense against insect herbivory; however, trichome production incurs a fitness cost in the absence of herbivory. Previous work on A. thaliana has shown an increase in trichome density in response to leaf damage, suggesting a mechanism by which the cost associated with constitutively high trichome density might be mitigated; however, the genetic basis of trichome density induction has not been studied. Results: Here, we describe the mapping of quantitative trait loci (QTL) for constitutive and damage induced trichome density in two new recombinant inbred line populations of A. thaliana; mapping for constitutive and induced trichome density also allowed for the investigation of damage response (plasticity) QTL. Both novel and previously identified QTL for constitutive trichome density and the first QTL for induced trichome density and response are identified. Interestingly, two of the four parental accessions and multiple RILs in each population exhibited lower trichome density following leaf damage, a response not previously described in A. thaliana. Importantly, a single QTL was mapped for the response phenotype and allelic variation at this locus appears to determine response trajectory in RILs. The data also show that epistatic interactions are a significant component of the genetic architecture of trichome density. Conclusions: Together, our results provide further insights into the genetic architecture of constitutive trichome density and new insights into induced trichome density in A. thaliana specifically and to our understanding of the genetic underpinnings of natural variation generally.
Data from: The genetic architecture of constitutive and induced trichome density in two new RIL populations of Arabidopsis thaliana: phenotypic plasticity, epistasis, and bidirectional leaf damage response
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Data from: Leaf lifespan and the leaf economic spectrum in the context of whole plant architecture
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RIP2 interacts with REL1 to control leaf architecture by modulating brassinosteroid signaling in rice
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Decoding the regulatory architecture of the maize leaf
GEO Series GSE137972. Zea mays. 217 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Data from: Genetic architecture of quantitative flower and leaf traits in a pair of sympatric sister species of Primulina
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Modified Hi-C reveals distinct chromatin architecture in endosperm and leaf of Arabidopsis
GEO Series GSE145769. Arabidopsis thaliana. 4 samples. Type: Other.
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Allen Brain Atlas
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DANDI Archive for NWB datasets
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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.