Allele expression biases in mixed-ploid sugarcane accessions

Area of Science:

• Genetics
• Plant Biology
• Bioinformatics

Background:

• Allele-specific expression (ASE) quantifies expression differences between gene alleles.
• Accurate ASE estimation in polyploids, like *Saccharum* (sugarcane), requires allele dosage information due to high ploidy and aneuploidy.

Purpose of the Study:

• To develop and apply a Beta-Binomial model for accurate ASE testing in mixed-ploid *Saccharum* species.
• To investigate allele expression patterns and identify genes exhibiting allelic imbalance in diverse sugarcane genotypes.

Main Methods:

• Utilized a hierarchical Beta-Binomial model adapted for mixed-ploid organisms.
• Tested for allelic imbalance by comparing observed allele expression to expectations based on genomic allele dosage.

Main Results:

• Genes with allele-specific expression (ASEGs) were less frequent than balanced genes across all *Saccharum* accessions.
• Sugarcane hybrids exhibited the highest frequencies of ASE, indicating potential effects of interspecific hybridization.
• ASEGs were linked to general metabolism, stress responses, and stimuli, with similar frequencies across genotypes at high functional levels.

Conclusions:

• ASE in *Saccharum* appears to be a largely genotype-specific phenomenon, with many ASEGs unique to individual accessions.
• The findings provide insights into gene expression regulation in complex polyploid genomes, relevant for sugarcane breeding and improvement.