Genome-wide Effects on Gene Expression Between Parental and Filial Generation of Trisomy 11 and 12 of Rice

Aneuploidy is a major source of gene dosage imbalance due to copy number alterations, with severe phenotypic consequences. It has rarely been reported whether this consequence has a certain response pattern by the alternation of generations. Whole-genome sequencing analysis using asexual reproduction rice (Oryza sativa L.) primary trisomy 11 and 12, same type of filial generation primary trisomy and the plant with normal chromosome numbers in their filial generation was studied. We systematically summarize the changes in gene expression patterns that occur on extra chromosomes (cis) and on the rest of the genome (trans) between parental and filial. The ratio of gene expression on the extra chromosome both showed dosage compensation in parental and filial as well as inverse trans-effect on other chromosomes, maybe due to more genes being downregulated. Further quantity dysregulated genes were calculated in filial with normal chromosomes stains, and there are still aneuploid-sensitive genes differentially expressed within their genomes, indicating that the effect of aneuploidy is far-reaching and could not be easily eliminated. In addition, among these differentially expressed genes, low expression level genes were more likely to be up-regulated, medium and high expression level genes down-regulated. For the different types of rice aneuploid, up-regulated expressed genes were involved in similar pathways, down-regulated genes were largely unrelated. Together, our results indicate that the effects of different single chromosome additions on genome-wide gene expression and summarize the pattern of aneuploidy effects transmitted to the progeny, which bear implications to further understanding the genetics and evolution of the aneuploidy genome of rice.