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

By Peng Zhou, Tara A Enders, Zachary A. Myers, Erika Magnusson, Peter Alexander Crisp, Jaclyn M. Noshay, Fabio A. Gomez Cano, Zhikai Liang, Erich Grotewold, Katie Greenham, Nathan Springer

Posted 17 Jan 2021
bioRxiv DOI: 10.1101/2021.01.15.426829

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.

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