The translational landscape of bread wheat during grain development

The dynamics of gene expression in crop grains has typically been investigated at the transcriptional level. However, this approach neglects translational regulation, a widespread mechanism that rapidly modulates gene expression to increase the plasticity of organisms. Here, we performed ribosome profiling and polysome profiling to obtain a comprehensive translatome data set of developing bread wheat (Triticum aestivum) grains. We further investigated the genome-wide translational dynamics during grain development, revealing that the translation of many functional genes is modulated in a stage-specific manner. The unbalanced translation between subgenomes is pervasive, which increases the expression flexibility of allohexaploid wheat. In addition, we uncovered widespread previously unannotated translation events, including upstream open reading frames (uORFs), downstream open reading frames (dORFs), and open reading frames (ORFs) in long noncoding RNAs, and characterized the temporal expression dynamics of small ORFs. We demonstrated that uORFs act as cis-regulatory elements that can repress or even enhance the translation of mRNAs. Gene translation may be combinatorially modulated by uORFs, dORFs, and microRNAs. In summary, our study presents a translatomic resource that provides a comprehensive and detailed overview of the translational regulation in developing bread wheat grains. This resource will facilitate future crop improvements for optimal yield and quality.

Automated summary

In this study, ribosome profiling and polysome profiling were used to investigate the translational regulation in developing bread wheat grains. The results showed that the translation of many functional genes is stage-specific and unbalanced between subgenomes, increasing the expression flexibility of wheat. Additionally, previously unannotated translation events, such as upstream open reading frames and downstream open reading frames, as well as temporal expression dynamics of small open reading frames, were identified. It was demonstrated that upstream open reading frames can act as cis-regulatory elements to modulate mRNA translation. Overall, this study provides a comprehensive resource for understanding translational regulation in wheat grains and will contribute to future crop improvements.