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 ne...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.展开更多
基金supported by the Biological Breeding-National Science and Technology Major Project(2023ZD04076)the Guangxi Key Research and Development Projects of China(GuikeAB21238004)the Agricultural Science and Technology Innovation Program.
文摘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.
