Fig. 5: Stability-associated RNA structural motifs may have evolved during wheat domestication and be altered in the EMS-induced mutants.

a The correlations of RNA abundances between A and B subgenomes of the homoeologous gene pairs containing the subgenomic preferred sRSMs in Kronos, durum wheat. The differential steady-state RNA abundances of those homoeologous gene pairs are dramatically reduced in both domesticated emmer and wild emmer wheat accessions (DEW: B086 and WEW: B028), where the SNVs disrupted the subgenomic preferred sRSMs. The bar plot represents the average differential expressions between subgenomes (error bars indicating ± SEM, n_{replicate samples} = 3). b In the 3’ UTR of TRITD4Av1G006890 in Kronos, there is one SNV, C749 inside the sRSM1 that forms a CG base pair (marked with red asterisks). This C-type changes to U-type in the 3’ UTR of TRITD4Bv1G167230, resulting in the disruption of the sRSM1. c The proportions of the C-type and U-type present in the 3’ UTR of TRITD4Av1G006890 in the WEW, DEW, and DW assessions as reported². d–h The corresponding RNA stability measured by qRT-PCR across accessions with different types of SNVs. The line plots depict the degradation trend of the gene pair (error bars indicating ± SEM, n_{replicate samples} = 3, d p = 1.83e-03, e p = 5.85e-04, f p = 2.34e-03, g p = 0.421, h p = 0.424, one-sided repeated measures ANOVA test). i This SNV alone was capable of altering mRNA stability. The RNA decay rates of the fused 3’ UTR regions containing only this C-type or U-type SNV with the dual-luciferase reporter gene were measured by qRT-PCR (error bars indicating ± SEM, n_{replicate samples} = 3, p = 1.25e-05 by one-sided repeated measures ANOVA test). j–l The RNA decay rates of the gene pair were measured by qRT-PCR across three EMS-mutagenized mutants of Kronos (Kronos3532, Kronos4597, and Kronos3484, error bars indicating ± SEM, n_{replicate samples} = 3, j p = 0.408, k p = 1.55e-04, l p = 3.49e-03, one-sided repeated measures ANOVA test).