Data Analysis

Wickham, Hadley

doi:10.1007/978-3-319-24277-4_9

Cited by 9,448 publications

(3,668 citation statements)

References 2 publications

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“…The intervals for the QTL were defined by comparing the position of the significant markers on the consensus and physical maps. Map graphics were drawn using the R package ggplot 2 (Wickham, 2016).…”

Section: Genome Wide Association Analysismentioning

confidence: 99%

Novel Alleles for Combined Drought and Heat Stress Tolerance in Wheat

et al. 2020

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Drought and heat waves commonly co-occur in many wheat-growing regions causing significant crop losses. The identification of stress associated quantitative trait loci, particularly those for yield, is problematic due to their association with plant phenology and the high genetic × environment interaction. Here we studied a panel of 315 diverse, spring type accessions of bread wheat (Triticum aestivum) in pots in a semi-controlled environment under combined drought and heat stress over 2 years. Importantly, we treated individual plants according to their flowering time. We found 134 out of the 145 identified loci for grain weight that were not associated with either plant phenology or plant height. The majority of loci uncovered here were novel, with favorable alleles widespread in Asian and African landraces providing opportunities for their incorporation into modern varieties through breeding. Using residual heterozygosity in lines from a nested association mapping population, we were able to rapidly develop near-isogenic lines for important target loci. One target locus on chromosome 6A contributed to higher grain weight, harvest index, thousand kernel weight, and grain number under drought and heat stress in field conditions consistent with allelic effects demonstrated in the genome-wide association study.

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Section: Genome Wide Association Analysismentioning

confidence: 99%

Novel Alleles for Combined Drought and Heat Stress Tolerance in Wheat

et al. 2020

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“…The silhouette and CSV, moreover, are obtained by the kmed package [30]. While the neighborhood graph is visualized via the flexclust [17]- [18] package, a function, created with the assistance of the ggplot2 [31] and geomnet [32] packages, visualizes the MSV network graph.…”

Section: Resultsmentioning

confidence: 99%

Medoid-based shadow value validation and visualization

Budiaji¹

2019

Preprint

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A silhouette index is a well-known measure of an internal criteria validation for the clustering algorithm results. While it is a medoid-based validation index, a centroid-based validation index that is called a centroid-based shadow value (CSV) has been developed. Although both are similar, the CSV has an additional unique property where an image of a 2-dimensional neighborhood graph is possible. A new internal validation index is proposed in this article in order to create a medoid-based validation that has an ability to visualize the results in a 2-dimensional plot. The proposed index behaves similarly to the silhouette index and produces a network visualization, which is comparable to the neighborhood graph of the CSV. The network visualization has a multiplicative parameter (c) to adjust its edges visibility. Due to the medoid-based, in addition, it is more an appropriate visualization technique for any type of data than a neighborhood graph of the CSV.

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“…Data visualisations were performed using the ggplot2 ver. 3.2.1 (Wickham, 2016) package in R ver. 3.6.1 (R Core Team, 2019).…”

Section: Discussionmentioning

confidence: 99%

Oxidative stress delays development and alters gene function in the agricultural pest moth,Helicoverpa armigera

Apirajkamol

James

Walsh

et al. 2020

Preprint

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Stress is a widespread phenomenon that all organisms must endure. Common in nature is oxidative stress, which can interrupt cell homeostasis to cause cell damage and may be derived from respiration or from environmental exposure thought diet. As a result of the routine exposure from respiration, many organisms can mitigate the effects of oxidative stress, but less is known about responses to oxidative stress from other sources. Helicoverpa armigera is a major agricultural pest moth that causes significant damage to crops worldwide.Here, we examined the effects of oxidative stress on H. armigera by chronically exposing individuals to paraquat -a free radical producer -and measuring changes in development (weight, developmental rate, lifespan), and gene expression.We found that oxidative stress strongly affected development in H. armigera, with stressed samples spending more time as caterpillars than control samples (>24 vs. ~15 days, respectively) and living longer overall. We found 1,618 up-and 761 down-regulated genes, respectively, in stressed vs. control samples. In the up-regulated gene set were genes associated with cell senescence and apoptosis and an over-representation of biological processes related to cuticle and chitin development, glycine metabolism, and oxidationreduction.Oxidative stress clearly impacts physiology and biochemistry in H. armigera and the interesting finding of an extended lifespan in stressed individuals could demonstrate hormesis, the process whereby toxic compounds can actually be beneficial at low doses. Collectively, our findings provide new insights into genomic responses to oxidative stress in invertebrates.

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Data Analysis

Cited by 9,448 publications

References 2 publications

Novel Alleles for Combined Drought and Heat Stress Tolerance in Wheat

Novel Alleles for Combined Drought and Heat Stress Tolerance in Wheat

Medoid-based shadow value validation and visualization

Oxidative stress delays development and alters gene function in the agricultural pest moth,Helicoverpa armigera

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