A comprehensive analysis of the impact of genomic imbalance on gene expression in a poplar aneuploidy population.

Alteration of chromosomal dosage severely affects the expressions of cis and trans genes in human and fruit fly. However, its effect on gene expression in plants needs to be further explored. Here, we generated 84 aneuploid lines with extra 1 to 16 chromosomes by crossing a female diploid poplar and a male triploid poplar. The chromosome compositions of the aneuploid population were dissected by DNA sequencing and cytogenetics. An RNA-seq analysis showed that cis genes were affected by both dosage and inverse effects, while trans genes were mainly affected by inverse effect. When the chromosomal dosage in an aneuploid line exceeds a threshold, the inverse effect may exceed the dosage effect on cis genes, causing dosage overcompensation. Interestingly, we found that even the genes located on the same chromosome may be subjected to different types of effect. These findings provided an important theoretical basis for analyzing the gene expression from the perspective of chromosomal dosage level.