Transposable elements are associated with genome-specific gene expression in bread wheat

Area of Science:

• Genomics
• Molecular Biology
• Plant Science

Background:

• Transposable elements (TEs) are key drivers of genetic variation in wheat, comprising ~85% of its genome.
• Their role in shaping gene structure and function in bread wheat remains incompletely understood.

Purpose of the Study:

• To investigate the impact of transposable element (TE) insertions within gene bodies on gene expression variation in bread wheat homoeologs.
• To identify specific TE families associated with gene expression regulation and stress responses.

Main Methods:

• Integration of publicly available RNA-Seq databases for bread wheat.
• Identification of TE insertions within gene bodies (exons/introns) of homoeolog gene groups.
• Analysis of gene expression levels in relation to TE insertion presence/absence and location.

Main Results:

• Approximately 36% of analyzed genes contained at least one TE insertion within their gene body.
• TE insertions in homoeologs were associated with both balanced expression and expression bias.
• Specific TE superfamilies and subfamilies showed significant correlations with the suppression of single homoeolog genes and stress-related gene expression.

Conclusions:

• Transposable elements (TEs) play a significant role in regulating gene expression in a genome-specific manner in bread wheat.
• TEs contribute to functional variation by influencing homoeolog expression, particularly in genes involved in stress responses.