Biology subjects

Enders, T. A.

Publications and source records attributed to Enders, T. A..

4 recordsLinked to original sources

bioRxiv2021

Applying cis-regulatory codes to predict conserved and variable heat and cold stress response in maize

Changes in gene expression are important for response to abiotic stress. Transcriptome profiling performed on maize inbred and hybrid genotypes subjected to heat or cold stress identifies many transcript abundance changes in response to these environmental conditions. Motifs that are enriched near differentially expressed genes were used to develop machine learning models to predict gene expression responses to heat or cold. The best performing models utilize the sequences both upstream and downstream of the transcription start site. Prediction accuracies could be improved using models developed for specific co-expression clusters compared to using all up- or down-regulated genes or by only using motifs within unmethylated regions. Comparisons of expression responses in multiple genotypes were used to identify genes with variable response and to identify cis- or trans-regulatory variation. Models trained on B73 data have lower performance when applied to Mo17 or W22, this could be improved by using models trained on data from all genotypes. However, the models have low accuracy for correctly predicting genes with variable responses to abiotic stress. This study provides insights into cis-regulatory motifs for heat- and cold-responsive gene expression and provides a framework for developing models to predict expression response to abiotic stress across multiple genotypes. One sentence summaryTranscriptome profiling of maize inbred and hybrid seedlings subjected to heat or cold stress was used to identify key cis-regulatory elements and develop models to predict gene expression responses.

plant biology↗

bioRxiv2020

Genetic and epigenetic contributions to variation in transposable element expression responses to abiotic stress in maize

O_LITransposable elements (TEs) pervade most eukaryotic genomes but the repetitive nature of TEs has complicated the analysis of their expression. Although the majority of TEs are silent, we document the activation of some TEs during abiotic stress. C_LIO_LITE expression was monitored in seedling leaf tissue of maize inbreds subjected to heat or cold stress conditions. DNA methylation profiles and comparative genomics were used to probe the variability of TE expression responses. C_LIO_LIAlthough there was no evidence for a genome-wide activation of TEs, a subset of TE families generate transcripts only in stress conditions. There is substantial variation for which TE families exhibit stress-responsive expression in the three genotypes. The stress-responsive activation of a TE family can often be attributed to a small number of elements in the family. These elements that are activated often contain small regions lacking DNA methylation, while fully methylated elements are rarely expressed. A comparison of the expression of specific TEs in different maize genotypes reveals high levels of variability that can be attributed to both genome content differences and epigenetic variation. C_LIO_LIThis study provides insights into the genetic and epigenetic factors that influence TE regulation in normal and stress conditions. C_LI

plant biology↗

bioRxiv2020

Utilizing top-down hyperspectral imaging for monitoring genotype and growth conditions in maize

There is significant enthusiasm about the potential for hyperspectral imaging to document variation among plant species, genotypes or growing conditions. However, in many cases the application of hyperspectral imaging is performed in highly controlled situations that focus on a flat portion of a leaf or side-views of plants that would be difficult to obtain in field settings. We were interested in assessing the potential for applying hyperspectral imaging to document variation in genotypes or abiotic stresses in a fashion that could be implemented in field settings. Specifically, we focused on collecting top-down hyperspectral images of maize seedlings similar to a view that would be collected in a typical maize field. A top-down image of a maize seedling includes a view into the funnel-like whorl at the center of the plant with several leaves radiating outwards. There is substantial variability in the reflectance profile of different portions of this plant. To deal with the variability in reflectance profiles that arises from this morphology we implemented a method that divides the longest leaf into 10 segments from the center to the leaf tip. We show that using these segments provides improved ability to discriminate different genotypes or abiotic stress conditions (heat, cold or salinity stress) for maize seedlings. We also found substantial differences in the ability to successfully classify abiotic stress conditions among different inbred genotypes of maize. This provides an approach that can be implemented to help classify genotype and environmental variation for maize seedlings that could be implemented in field settings. Significance StatementThis study describes the importance of using spatial information for the analysis of hyperspectral images of maize seedling. The segmentation of maize seedling leaves provides improved resolution for using hyperspectral variation to document genotypic and environmental variation in maize.

plant biology↗

bioRxiv2018

Classifying cold stress responses of inbred maize seedlings using RGB imaging

Increasing the tolerance of maize seedlings to low temperature episodes could mitigate the effects of increasing climate variability on yield. To aid progress toward this goal, we established a growth chamber-based system for subjecting seedlings of 40 maize inbred genotypes to a defined, temporary cold stress while collecting digital profile images over a 9-day time course. Image analysis performed with PlantCV software quantified shoot height, shoot area, 14 other morphological traits, and necrosis identified by color analysis. Hierarchical clustering of changes in growth rates of morphological traits and quantification of leaf necrosis over two time intervals resulted in three clusters of genotypes, which are characterized by unique responses to cold stress. For any given genotype, the set of traits with similar growth rates is unique. However, the patterns among traits are different between genotypes. Cold sensitivity was not correlated with the latitude where the inbred varieties were released suggesting potential further improvement for this trait. This work will serve as the basis for future experiments investigating the genetic basis of recovery to cold stress in maize seedlings.

plant biology↗