Transposons are important contributors to gene expression variability under selection in rice populations

Area of Science:

• Genomics
• Molecular Biology
• Plant Science

Background:

• Transposable elements (TEs) are significant contributors to genome variability.
• Understanding TE roles in gene expression is crucial for crop improvement.

Purpose of the Study:

• To investigate the impact of transposable element insertions on gene expression variability in rice.
• To identify specific genes affected by TEs during rice domestication and breeding.

Main Methods:

• Utilized transposable element insertion polymorphism (TEIP) expression quantitative trait locus (eQTL) mapping.
• Analyzed gene expression data from 208 rice varieties (indica and japonica subspecies).

Main Results:

• TE insertions are linked to expression changes in numerous genes targeted by rice domestication and breeding.
• A substantial portion of identified TE insertions were present in wild rice ancestors and differentially selected.
• TE-induced expression changes in signal transduction genes were observed.

Conclusions:

• Transposable elements significantly contribute to gene expression variability in rice.
• Differential selection of TEs played a role in the divergence of indica and japonica rice subspecies.
• TEs influenced the domestication and adaptation of rice through subtle gene expression modifications.