The Potential Role of RNA Structure in Crop Molecular Breeding

Abstract

The continually growing human population creates a concomitantly increasing demand for nutritious crops with high yields. Advances in high throughput sequencing technologies have revealed the genetic architecture of major crops. This includes extensive information enabling comprehensive genetic markers for breeding selection, new gene discoveries, and novel gene regulatory strategies for crop editing. RNA structure is an important type of genetic feature, essential for post-transcriptional regulation of gene expression. Here, we summarize recent advances in genome-wide RNA structure studies in crops and review the associated RNA structure-mediated regulation of gene expression. We also discuss the functional importance of those single nucleotide variations that induce large RNA structure disparities. Lastly, we discuss the potential role of RNA structure in crop molecular breeding.

Keywords: RNA structure; crop improvement; molecular breeding; riboSNitches; translation.

Figure 1

The gene functions of wheat homoeologous pairs preferring RNA structure-mediated translational subgenome asymmetry and the evolved riboSNitch during wheat domestication. (A) The detailed gene functions of wheat homoeologous pairs have significant correlation coefficients between subgenomic RNA structural and subgenomic translational differences (Yang et al., 2021). The green circles highlight the functions related to the responses to stimulus; the gray circles highlight the functions related to the intracellular anatomical structures; the red circles highlight the functions related to the binding functions; the rose fog circles highlight the functions related to the regulation of gene expression. The circle size represents correlation coefficients where the bigger circle size means the higher correlation coefficient. (B) Schematic of the differentiated riboSNitch at position 41 in the 5'UTR of the homoeologous pair TRITD2Av1G193730 and TRITD2Bv1g159660. In the A subgenome homoeolog, the riboSNitch denotes the sequence of Cytosine (C41) in blue, while in the B subgenome homoeolog it denotes the sequence of Adenine (A41) in red. Small purple circles represent small ribosomal subunits, whilst big purple circles indicate large ribosomal subunits.

Figure 2

Schematic of the diversity among phenotypes, genome sequences, RNA structures, and translational levels across natural varieties. Red squares represent the sequence variations. Small blue circles represent small ribosomal subunits, whilst big blue circles indicate large ribosomal subunits.