Genomic imbalance modulates transposable element expression in maize  

作　　者：Hua Yang Xiaowen Shi Chen Chen Jie Hou Tieming Ji Jianlin Cheng James A.Birchler 

机构地区：[1]Division of Biological Sciences,University of Missouri,Columbia,MO 65211,USA [2]Department of Electrical Engineering and Computer Science,University of Missouri,Columbia,MO 65211,USA [3]Department of Statistics,University of Missouri,Columbia,MO 65211,USA [4]College of Agriculture and Biotechnology,Zhejiang University,Hangzhou 310058,China

出　　处：《Plant Communications》2023年第2期214-226,共13页植物通讯（英文）

基　　金：supported by National Science Foundation USA grant IOS-1545780;Computation for this work was performed on the highperformance computing infrastructure provided by Research Computing Support Services and in part by the National Science Foundation USA under grant number CNS-1429294 at the University of Missouri,Columbia,MO,https://doi.org/10.32469/10355/69802.

摘　　要：Genomic imbalance refers to the more severe phenotypic consequences of changing part of a chromosome compared with the whole genome set.Previous genome imbalance studies in maize have identified prevalent inverse modulation of genes on the unvaried chromosomes(trans)with both the addition or subtraction of chromosome arms.Transposable elements(TEs)comprise a substantial fraction of the genome,and their reaction to genomic imbalance is therefore of interest.Here,we analyzed TE expression using RNA-seq data of aneuploidy and ploidy series and found that most aneuploidies showed an inverse modulation of TEs,but reductions in monosomy and increases in disomy and trisomy were also common.By contrast,the ploidy series showed little TE modulation.The modulation of TEs and genes in the same experimental group were compared,and TEs showed greater modulation than genes,especially in disomy.Class Ⅰ and Ⅱ TEs were differentially modulated in most aneuploidies,and some superfamilies in each TE class also showed differential modulation.Finally,the significantly upregulated TEs in three disomies(TB-7Lb,TB9Lc,and TB-10L19)did not increase the proportion of adjacent gene expression when compared with non-differentially expressed TEs,indicating that modulations of TEs do not compound the effect on genes.These results suggest that the prevalent inverse TE modulation in aneuploidy results from stoichiometric upset of the regulatory machinery used by TEs,similar to the response of core genes to genomic imbalance.

关 键 词：genome imbalance transposable element expression ANEUPLOIDY POLYPLOIDY ClassⅠandⅡTEs 

分 类 号：S513[农业科学—作物学]