Magnitude of modulation of gene expression in aneuploid maize depends on the extent of genomic imbalance. 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.

非整倍体（aneuploidy）对生物体具有深远影响，其效应通常远超多倍体（polyploidy），但二者产生这种差异的基础机制尚未完全阐明。本研究以玉米1号染色体长臂（chromosome arm 1L）的剂量系列材料为研究对象，对比不同类型、不同程度非整倍体的全基因组基因表达水平，以探究基因组失衡的严重程度以及亚倍体（hypoploidy）如何影响全局基因表达。过往的研究方法仅能针对性检测特定基因，而RNA测序（RNA sequencing）则可实现非整倍体样本中基因表达的全基因组全景分析。过往针对非整倍体全局效应的研究多聚焦于三体（trisomics），因为在多数模式遗传生物中，其他类型的非整倍体难以构建获得。玉米成熟的遗传操作体系可支持对多种倍性材料以及1至4个剂量的染色体臂进行研究。因此，相较于整倍体（euploid）对照，本研究可同时对亚倍体与超倍体（hyperploids）中变异染色体臂及基因组其他区域的表达变化进行细致分析。过往研究已发现反向反式效应（inverse trans effect）：即DNA剂量未发生改变的基因，其表达水平与发生剂量变异的染色体区域呈负相关关系。该效应同样是本研究中全局基因表达变化的主要类型。本研究还发现，非整倍体的效应呈渐进式特征：非整倍性程度越严重，其对基因表达的影响幅度越大。实验整体设计：本研究采用RNA测序（RNA sequencing）技术，对比玉米6种不同倍性状态下的基因表达水平，总计包含27个生物学重复样本。所有非整倍体样本的1号染色体长臂剂量均发生变异。第一组剂量系列包含17个生物学重复样本：4个二倍体（作为对照）、5个三体、3个四体、3个单倍体以及2个二体单倍体。第二组剂量系列包含10个生物学重复样本：4个单体、3个二倍体（作为对照）以及3个三体。