Pangenome analysis of transposable element insertion polymorphisms reveals features underlying cold tolerance in rice

Area of Science:

• Genetics and Genomics
• Plant Biology
• Epigenetics

Background:

• Transposable elements (TEs) are crucial sources of genetic and epigenetic variation in plants.
• TEs influence gene expression and adaptive evolution, particularly under environmental stress.
• Understanding TE architecture is key to crop improvement.

Purpose of the Study:

• To investigate the role of transposable element (TE) architecture in rice cold tolerance.
• To identify specific TEs and their associated genes involved in cold stress response.
• To provide a resource for breeding cold-tolerant rice varieties.

Main Methods:

• Pangenome graph analysis and resequencing of 165 rice accessions.
• Identification of transposable element insertion polymorphism (TIP) sites and polymorphic TEs (pTEs).
• Analysis of H3K27me3 enrichment, transcriptome data, and TIP-genome-wide association studies (TIP-GWAS).

Main Results:

• Identified 30,316 TIP sites and significant diversity among polymorphic TEs (pTEs).
• Observed increased H3K27me3 enrichment in pTEs, suggesting epigenetic regulatory roles under cold stress.
• Discovered 26,914 cold-responsive TEs and identified OsCACT and OsPTR as key cold tolerance genes.

Conclusions:

• Polymorphic TEs play a significant role in the epigenetic regulation of cold response in rice.
• OsCACT and OsPTR are critical genes for cold tolerance, validated through genetic manipulation.
• The identified TEs and genes offer valuable targets for developing climate-resilient rice cultivars.