1,721,030 research outputs found
Springer Lab UAV Maize Phenotyping Project at UMN StPaul: 2018 and 2019
No full textFiles include digital elevation models for all flights of our maize field in the summer of 2018 and 2019, the plot boundary shapefiles, information on each plot including planting date and density and stand counts, yield data for all plots, and weather station data for both summers. More detailed info can be found in the readme file.This dataset provides a valuable resource for evaluating the utility of unmanned aerial vehicles to collect phenotypic data in agricultural fields. Many flights throughout the growing season of a maize experiment were conducted and this dataset includes digital elevation models generated from images within these flights, the plot boundary shapefiles for plot identification, plant height values extracted following Tirado et al., 2019 procedure, hand measurement height values conducted following flights, and yield data for each plot. This maize experiment consisted of twelve hybrids planted at three different planting densities (low, medium and high) and two planting dates (early and late) across two years and therefore provides a valuable resource for evaluating how temporal data collected from UAVs can aid in assessing plant productivity. It can also be utilized to develop and test different protocols for plant height extraction from DEMs at different growth stages as the hand measurements can be used to test the accuracy.NATirado, Sara B; Hirsch, Candice N; Springer, Nathan M. (2020). Springer Lab UAV Maize Phenotyping Project at UMN StPaul: 2018 and 2019. Retrieved from the University Digital Conservancy, https://doi.org/10.13020/j01t-wq81
Temporally resolved growth patterns in diverse maize panel
No full textPlant height is used in many breeding programs for assessing plant health across environments and predicting yield, which can be used in identifying superior hybrids or evaluating abiotic stress factors. This has often been measured at a single time point when plants have reached their terminal height for the season. Collection of plant height using unoccupied aerial vehicles (UAVs) is faster, allowing for measurements throughout the growing season which could facilitate a better understanding of plant-environment interaction and responses. To assess variation in plant height and growth rate throughout development, plant height data was collected weekly for a panel of ~500 diverse inbred lines over four growing seasons. The variation in plant height throughout the season was found to be significantly explained by genotype, year, and genotype-by-year interactions throughout vegetative growth. However, the relative contributions of these different sources of variation fluctuated throughout development. This variation was further captured by Fréchet distance values which identified genotypes with consistently high or low distances in each of the four years - high distance genotypes being more dissimilar between replications and therefore capturing more environmental variation. Genome-wide association studies revealed many significant SNPs associated with plant height and growth rate at different parts of the growing season that would not be identified by terminal height alone. When comparing growth rates estimated from plant height to growth rates estimated from another morphological characteristic, canopy cover, we found greater stability in growth curves estimated by plant height. This potentially makes canopy cover more useful for understanding environmental modulation of overall plant growth and plant height better for understanding genotypic modulation of overall plant growth. Overall, this suggests evaluations of plant growth throughout the season provide more information than terminal plant height alone.Minnesota Corn Growers AssociationNational Science FoundationBayer Crop ScienceUMII-MnDRIVE PhD Graduate AssistantshipSweet, Dorothy D; Tirado, Sara B; Cooper, Julian S; Springer, Nathan M; Hirsch, Cory D; Hirsch, Candice N. (2023). Temporally resolved growth patterns in diverse maize panel. Retrieved from the University Digital Conservancy, https://doi.org/10.13020/SKJN-QX31
Data for: Meta gene regulatory networks in maize highlight functionally relevant regulatory interactions
No full textThese are the processed datasets used to create networks (raw and filtered expression tables) and predicted interactionsRegulation of gene expression is central to many biological processes. Gene regulatory networks (GRNs) link transcription factors (TFs) to their target genes and represent a map of potential transcriptional regulation. A consistent analysis of a large number of public maize transcriptome datasets including >6000 RNA-Seq samples was used to generate 45 co- expression based GRNs that represent potential regulatory relationships between TFs and other genes in different populations of samples (cross-tissue, cross-genotype, tissue-and-genotype, etc). While these networks are all enriched for biologically relevant interactions, different networks capture distinct TF-target associations and biological processes.This study was funded by grants from the National Science Foundation (IOS-1546899 and IOS- 1733633). This work is supported in part by Michigan State University and the National Science Foundation Research Traineeship Program (DGE-1828149) to FGC. No conflict of interest declared.Zhou, Peng; Springer, Nathan M.. (2020). Data for: Meta gene regulatory networks in maize highlight functionally relevant regulatory interactions. Retrieved from the University Digital Conservancy, https://doi.org/10.13020/p3g0-3170
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Gene regulatory effects of a large chromosomal inversion in highland maize.
Full text linkChromosomal inversions play an important role in local adaptation. Inversions can capture multiple locally adaptive functional variants in a linked block by repressing recombination. However, this recombination suppression makes it difficult to identify the genetic mechanisms underlying an inversion's role in adaptation. In this study, we used large-scale transcriptomic data to dissect the functional importance of a 13 Mb inversion locus (Inv4m) found almost exclusively in highland populations of maize (Zea mays ssp. mays). Inv4m was introgressed into highland maize from the wild relative Zea mays ssp. mexicana, also present in the highlands of Mexico, and is thought to be important for the adaptation of these populations to cultivation in highland environments. However, the specific genetic variants and traits that underlie this adaptation are not known. We created two families segregating for the standard and inverted haplotypes of Inv4m in a common genetic background and measured gene expression effects associated with the inversion across 9 tissues in two experimental conditions. With these data, we quantified both the global transcriptomic effects of the highland Inv4m haplotype, and the local cis-regulatory variation present within the locus. We found diverse physiological effects of Inv4m across the 9 tissues, including a strong effect on the expression of genes involved in photosynthesis and chloroplast physiology. Although we could not confidently identify the causal alleles within Inv4m, this research accelerates progress towards understanding this inversion and will guide future research on these important genomic features
The alternative reality of plant mitochondrial DNA: One ring does not rule them all
Full text linkPlant mitochondrial genomes are usually assembled and displayed as circular maps based on the widely-held view across the broad community of life scientists that circular genome-sized molecules are the primary form of plant mitochondrial DNA, despite the understanding by plant mitochondrial researchers that this is an inaccurate and outdated concept. Many plant mitochondrial genomes have one or more pairs of large repeats that can act as sites for inter- or intramolecular recombination, leading to multiple alternative arrangements (isoforms). Most mitochondrial genomes have been assembled using methods unable to capture the complete spectrum of isoforms within a species, leading to an incomplete inference of their structure and recombinational activity. To document and investigate underlying reasons for structural diversity in plant mitochondrial DNA, we used long-read (PacBio) and short-read (Illumina) sequencing data to assemble and compare mitochondrial genomes of domesticated (Lactuca sativa) and wild (L. saligna and L. serriola) lettuce species. We characterized a comprehensive, complex set of isoforms within each species and compared genome structures between species. Physical analysis of L. sativa mtDNA molecules by fluorescence microscopy revealed a variety of linear, branched, and circular structures. The mitochondrial genomes for L. sativa and L. serriola were identical in sequence and arrangement and differed substantially from L. saligna, indicating that the mitochondrial genome structure did not change during domestication. From the isoforms in our data, we infer that recombination occurs at repeats of all sizes at variable frequencies. The differences in genome structure between L. saligna and the two other Lactuca species can be largely explained by rare recombination events that rearranged the structure. Our data demonstrate that representations of plant mitochondrial genomes as simple, circular molecules are not accurate descriptions of their true nature and that in reality plant mitochondrial DNA is a complex, dynamic mixture of forms
Shade avoidance components and pathways in adult plants revealed by phenotypic profiling.
Full text linkShade from neighboring plants limits light for photosynthesis; as a consequence, plants have a variety of strategies to avoid canopy shade and compete with their neighbors for light. Collectively the response to foliar shade is called the shade avoidance syndrome (SAS). The SAS includes elongation of a variety of organs, acceleration of flowering time, and additional physiological responses, which are seen throughout the plant life cycle. However, current mechanistic knowledge is mainly limited to shade-induced elongation of seedlings. Here we use phenotypic profiling of seedling, leaf, and flowering time traits to untangle complex SAS networks. We used over-representation analysis (ORA) of shade-responsive genes, combined with previous annotation, to logically select 59 known and candidate novel mutants for phenotyping. Our analysis reveals shared and separate pathways for each shade avoidance response. In particular, auxin pathway components were required for shade avoidance responses in hypocotyl, petiole, and flowering time, whereas jasmonic acid pathway components were only required for petiole and flowering time responses. Our phenotypic profiling allowed discovery of seventeen novel shade avoidance mutants. Our results demonstrate that logical selection of mutants increased success of phenotypic profiling to dissect complex traits and discover novel components
Appropriate Similarity Measures for Author Cocitation Analysis
Full text linkWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
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