Elimination of a Retrotransposon for Quenching Genome Instability in Modern Rice

Area of Science:

• Genomics
• Plant Biology
• Evolutionary Biology

Background:

• Transposable elements (TEs) are abundant in plant genomes and influence evolution and crop domestication.
• The selective pressures on TEs themselves during crop domestication remain largely unknown.

Purpose of the Study:

• To investigate whether transposable elements are selected during rice domestication.
• To identify specific TEs that may have been targeted by selection.

Main Methods:

• Comparative genomics analysis of rice accessions, archaeological grains, landraces, and modern varieties.
• Investigation of the activity and genomic insertion preferences of the identified retrotransposon (HUO).
• Analysis of gene silencing mechanisms (RNA-directed DNA methylation) and impact on genome-wide DNA methylation, small RNA biogenesis, and gene expression.

Main Results:

• An active long terminal repeat (LTR) retrotransposon, named HUO, was identified as a potential target of selection.
• HUO is present in wild rice and ancient grains but largely absent in modern varieties, indicating its elimination during domestication and breeding.
• HUO is silenced via RNA-directed DNA methylation and its elimination correlates with improved genomic stability, disease resistance, and yield.

Conclusions:

• Negative selection of active retrotransposons like HUO may be crucial for enhancing genome stability during crop domestication and breeding.
• Understanding TE dynamics provides insights into crop improvement strategies.