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.

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Publication Details

Journal
Communications Biology
Published
2025-12-03
DOI
https://doi.org/10.1038/s42003-025-09318-8
Primary Topic
Chromosomal and Genetic Variations
Type
article
Field-Weighted Citation Impact
0.00

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article

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

Quanzi Li, Guanzheng Qu, Wenxuan Liu, Zhijie Liu et al.
Communications Biology
Chromosomal and Genetic Variations
article

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

Quanzi Li, Guanzheng Qu, Wenxuan Liu, Zhijie Liu, Fuchun Li, Xingguo Lan, Yuting Wang, Yue Yu, Song Chen, Su Chen, Hanxi Li, Xuanchen Liu, Kanglei Li, Xinyu Wang
article en

Abstract

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.

Communications BiologyVol. 9(1)
Chinese Academy of Forestry (CN), Research Institute of Forestry (CN), Ministry of Agriculture and Rural Affairs (CN), Northeast Forestry University (CN)
China Postdoctoral Science Foundation, Natural Science Foundation of Heilongjiang Province
Openalex Percentile: Top 72%
Chromosomal and Genetic Variations
DOIOpen Access PDFOpenAlex
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