GSE134936
Magnitude of modulation of gene expression in aneuploid maize depends on the extent of genomic imbalance
Aneuploidy has profound effects on an organism, typically more so than polyploidy, and the basis of this contrast is not fully understood. A dosage series of maize chromosome arm 1L was used to compare relative global gene expression in different types and degrees of aneuploidy to gain insight into how the magnitude of genomic imbalance as well as hypoploidy affect global gene expression. While previously available methods required a selective examination of specific genes, RNA sequencing provides a whole-genome view of gene expression in aneuploids. Most studies of global aneuploid effects have concentrated on trisomics because other types of aneuploids are difficult to produce in most model genetic organisms. The genetic toolkit of maize allows the examination of multiple ploidies and 1-4 doses of chromosome arms. Thus, a detailed examination of expression changes both on the varied chromosome arm and elsewhere in the genome is possible, in both hypoploids and hyperploids, compared with euploid controls. Previous studies observed the inverse trans effect, in which genes not varied in DNA dosage are expressed in a negative relationship to the varied chromosomal region. This response was also the major type of change found globally in this study. It was also found that the effects of aneuploidy are progressive, with more severe aneuploids producing effects of greater magnitude. Overall design: RNA-seq was used to compare gene expression in 6 different ploidy states in maize, with 27 biological replicates in total. All aneuploids are varied in dosage for the long arm of chromosome 1. The first dosage series includes 17 biological replicates: 4 diploids (used as control), 5 trisomics, 3 tetrasomics, 3 haploids, and 2 disomic haploids. The second dosage series includes 10 biological replicates: 4 monosomics, 3 diploids (used as control), and 3 trisomics.