Fig. 1: mRNA decay landscape in tetraploid Kronos.

a Schematic of determining mRNA stability in wheat by transcriptional arrest analysis with cordycepin treatment. b Hierarchical clustering of genes with different decay rates, based on the transcript abundance at the different time courses of transcription inhibition. The decay rate was determined using a mathematical modeling approach based on the maximum likelihood method applied to data obtained with the cordycepin inhibitor method³⁰. The genes with a fast decay rate and low RNA abundance are shown in light blue, while the genes with a slow decay rate and high RNA abundance are shown in dark blue. The heatmap displays fold changes in RNA abundance (RPM) at each time point relative to 0 min. The relative decay rate at 0 min is set to 1. c TaSWEET13e, and TaSWEET17e from the same gene family with different decay rates are shown as an example. The bar plot represents the steady-state relative mRNA abundance (error bars indicating ± SEM (standard error of the mean), n_{replicate samples} = 3; ^***p < 0.001, p = 4.7e-06 by one-sided student’s t-test), while the line plot shows the degradation trend of the gene pair (error bars indicating ± SEM, n_{replicate samples} = 3; p = 7.05e-09 by one-sided repeated measures ANOVA test). d The distribution of mRNA half-lives at the genome-wide level. The mean half-life in Kronos is 6.15 h. e RNA abundance curves for transcripts from the whole transcriptome, miRNA target, and intronless genes, respectively (error bars indicating ± SEM, n_{replicate samples} = 3). f–h The correlation between decay rates and RNA abundance (f: r = −0.28, p < 2.2e-16; g r = −0.304, p < 2.2e-16; h r = −0.299, p < 2.2e-16, two-sided Pearson correlation test). i The correlation between decay rates and RNA abundance for functional gene categories (significant: p < 0.05, by two-sided Pearson correlation test).