Tensor decomposition reveals <i>trans</i>-regulated gene modules in maize drought response

Jiawen Lu; Yuxin Xie; Chunhui Li; Jinliang Yang; Junjie Fu

doi:10.1016/j.jgg.2024.10.011

Volume 52 Issue 6

Jun. 2025

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Tensor decomposition reveals trans-regulated gene modules in maize drought response

doi: 10.1016/j.jgg.2024.10.011

a. State Key Laboratory of Crop Gene Resources and Breeding, National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China;
b. Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA

Funds:

We thank Riliang Gu and Feng Qin for their suggestions about manuscript reviewing. This work was supported by the Biological Breeding-National Science and Technology Major Project (2023ZD04076), the Guangxi Key Research and Development Projects of China (GuikeAB21238004), and the Agricultural Science and Technology Innovation Program.

Received Date: 2024-05-29
Accepted Date: 2024-10-24
Rev Recd Date: 2024-10-22

Available Online: 2025-07-11

Publish Date: 2024-11-08

Abstract

Abstract

When plants respond to drought stress, dynamic cellular changes occur, accompanied by alterations in gene expression, which often act through trans-regulation. However, the detection of trans-acting genetic variants and networks of genes is challenged by the large number of genes and markers. Using a tensor decomposition method, we identify trans-acting expression quantitative trait loci (trans-eQTLs) linked to gene modules, rather than individual genes, which were associated with maize drought response. Module-to-trait association analysis demonstrates that half of the modules are relevant to drought-related traits. Genome-wide association studies of the expression patterns of each module identify 286 trans-eQTLs linked to drought-responsive modules, the majority of which cannot be detected based on individual gene expression. Notably, the trans-eQTLs located in the regions selected during maize improvement tend towards relatively strong selection. We further prioritize the genes that affect the transcriptional regulation of multiple genes in trans, as exemplified by two transcription factor genes. Our analyses highlight that multidimensional reduction could facilitate the identification of trans-acting variations in gene expression in response to dynamic environments and serve as a promising technique for high-order data processing in future crop breeding.
- Maize,
- Drought stress,
- Tensor decomposition,
- Gene expression,
- trans-eQTL

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