RT Journal Article
SR Electronic
T1 Allele expression biases in mixed-ploid sugarcane accessions
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2021.08.26.457296
DO 10.1101/2021.08.26.457296
A1 Fernando Henrique Correr
A1 Agnelo Furtado
A1 Antonio Augusto Franco Garcia
A1 Robert James Henry
A1 Gabriel Rodrigues Alves Margarido
YR 2021
UL http://biorxiv.org/content/early/2021/08/28/2021.08.26.457296.abstract
AB Allele-specific expression (ASE) represents differences in the magnitude of expression between alleles of the same gene. This is not straightforward for polyploids, especially autopolyploids, as knowledge about the dose of each allele is required for accurate estimation of ASE. This is the case for the genomically complex Saccharum species, characterized by high levels of ploidy and aneuploidy. We used a Beta-Binomial model to test for allelic imbalance in Saccharum, with adaptations for mixed-ploid organisms. The hierarchical Beta-Binomial model was used to test if allele expression followed the expectation based on genomic allele dosage. The highest frequencies of ASE occurred in sugarcane hybrids, suggesting a possible influence of interspecific hybridization in these genotypes. For all accessions, ASEGs were less frequent than those with balanced allelic expression. These genes were related to a broad range of processes, mostly associated with general metabolism, organelles, responses to stress and responses to stimuli. In addition, the frequency of ASEGs in high-level functional terms was similar among the genotypes, with a few genes associated with more specific biological processes. We hypothesize that ASE in Saccharum is largely a genotype-specific phenomenon, as a large number of ASEGs were exclusive to individual accessions.Competing Interest StatementThe authors have declared no competing interest.