Transposable elements as modulators of homoeologous gene expression in bread wheat: lessons from the...

Area of Science:

• Plant genetics
• Genomics
• Molecular biology

Background:

• Bread wheat (Triticum aestivum L.) is an allohexaploid with complex gene regulation due to its three ancestral subgenomes.
• Homoeolog expression bias, the relative expression balance among homoeologous gene copies, is crucial for polyploid evolution and adaptation.
• Recent advances in genomics and transcriptomics reveal extensive cultivar-specific transcriptional diversity.

Purpose of the Study:

• To synthesize evidence linking transposable elements (TEs) to subgenome asymmetry in bread wheat.
• To propose a unifying framework where TEs modulate homoeolog expression.
• To discuss challenges and future strategies for leveraging TE-associated regulatory diversity in wheat breeding.

Main Methods:

• Review and synthesis of recent pan-genomic and transcriptomic evidence.
• Genome-wide association studies linking TE insertions to genome-specific expression.
• Analysis of TE mechanisms including cis-regulatory sequences, chromatin states, small RNAs, and structural variation.

Main Results:

• Transposable elements (TEs) constitute over 80% of the wheat genome and are key drivers of transcriptional diversity.
• TEs modulate homoeolog expression through diverse mechanisms, contributing to subgenome asymmetry.
• Evidence suggests a strong association between TE insertions and genome-specific gene expression.

Conclusions:

• Transposable elements play a central role in shaping homoeolog expression bias and transcriptional diversity in bread wheat.
• Understanding TE-mediated regulation offers potential for targeted wheat improvement.
• Future research should focus on establishing causality and functional validation of TE roles in gene regulation for breeding applications.