Prediction of conserved and variable heat and cold stress response in maize using cis-regulatory information

Abstract

Changes in gene expression are important for responses to abiotic stress. Transcriptome profiling of heat- or cold-stressed maize genotypes identifies many changes in transcript abundance. We used comparisons of expression responses in multiple genotypes to identify alleles with variable response to heat or cold stress and to distinguish examples of cis- or trans-regulatory variation for stress-responsive expression changes. We used motifs enriched near the transcription start sites for thermal stress-responsive genes to develop predictive models of gene expression responses. Prediction accuracies can be improved focusing only on motifs within unmethylated regions near the transcription start site and vary for genes with different dynamic responses to stress. Models trained on expression responses in a single genotype and promoter sequences provided lower performance when applied to other genotypes but this could be improved by using models trained on data from all three genotypes tested. The analysis of genes with cis-regulatory variation provides evidence for structural variants that result in presence/absence of transcription factor binding sites in creating variable responses. This study provides insights into cis-regulatory motifs for heat- and cold-responsive gene expression and defines a framework for developing models to predict expression responses across multiple genotypes.

Metabolic Insight into Cold Stress Response in Two Contrasting Maize Lines

“…B144 depicted up-accumulation of several metabolites, viz., flavonoids, lipids, amino acids, alkaloids, and phenolic acids under induced cold stress. Several studies have suggested genotype-dependent regulatory responses under abiotic stresses [61][62][63][64]. Survival strategies under a stress environment highly depend on vegetative growth regulation and hormonal distribution [65].…”

Conserved and variable responses of the HEAT SHOCK FACTOR transcription factor family in maize and Setaria viridis

“…With a clearer picture of the composition of the SvHSF gene family, we proceeded to assess whether orthologous HSF TFs would respond similarly to heat stress. To address this, we conducted RNA-seq experiments on control and heat stressed Setaria seedlings, matching growth, stress, and sampling conditions with a previously published maize dataset (Zhou et al ., 2021). We identified 1,941 upregulated and 986 downregulated genes in response to a one-hour, 10°C increase over ambient heat stress (Figure 2A-B, Table S2).…”

“…Several of these examples show evidence for a heat response in maize but it was not statistically significant (Figure S6). A prior study monitoring heat responses in maize (Zhou et al ., 2021) generated unreplicated time-course data for responses to heat stress and included a 30-minute time point. Three of the maize genes ( HSFA2b, HSFA2d , and HSFB2a ) from sub-families classified as having Setaria -specific responses exhibit striking up-regulation in response to heat stress at 30 minutes, but the response has largely subsided by 1 hour and the genes are not detected as significant at 1 hour.…”

Recent Advances in the Analysis of Cold Tolerance in Maize

“…This study highlighted the importance of miRNAs in the maize response to cold stress. Combined with large-scale bioinformatic analysis, Zhou et al ( 2022 ) examined the transcriptome changes in seedlings of the inbred lines B73, Mo17, and W22 and the F 1 hybrids with all three combinations (B73xMo17, W22xB73, and W22xMo17) in response to cold or heat stress. They identified many stress-related DEGs among the different maize genotypes and assigned these expression changes to cis-or trans-regulatory mechanisms using the F 1 hybrid data.…”