Limited allele-specific gene expression in highly polyploid sugarcane.

Area of Science:

• Plant genetics
• Genomics
• Molecular biology

Background:

• Polyploidy is common in plants, enabling differential gene expression.
• Allele-specific expression (ASE) allows varied gene activity across tissues and developmental stages.
• The prevalence and characteristics of ASE in polyploid genomes remain largely undefined.

Purpose of the Study:

• To analyze the frequency and patterns of allele-specific expression (ASE) across the entire genome of sugarcane.
• To investigate the relationship between allele dosage in the genome and gene expression levels in a highly polyploid organism.

Main Methods:

• High-depth whole-genome sequencing of sugarcane.
• High-depth RNA sequencing to analyze gene expression.
• Analysis of allele proportions in both genomic and expressed sequences.

Main Results:

• Strong correlation observed between allelic proportions in the genome and expressed sequences.
• Most genes expressed proportionally to their genomic allele frequency, with all allele doses represented.
• Rarer instances of ASE were enriched in defense-response and cell wall biosynthesis genes, often with functionally disruptive variants.

Conclusions:

• The low overall level of ASE in sugarcane may stem from its recent polyploid origin.
• Significant selection for disease resistance likely shapes the observed ASE patterns in sugarcane.
• ASE provides insights into gene regulation and adaptation in complex polyploid genomes.