Abstract
Key message
This study provided important insights into the genetic architecture of variations in A. thaliana leaf ionome in a cell-type-specific manner.
Abstract
The functional interpretation of traits associated variants by expression quantitative trait loci (eQTL) analysis is usually performed in bulk tissue samples. While the regulation of gene expression is context-dependent, such as cell-type-specific manner. In this study, we estimated cell-type abundances from 728 bulk tissue samples using single-cell RNA-sequencing dataset, and performed cis-eQTL mapping to identify cell-type-interaction eQTL (cis-eQTLs(ci)) in A. thaliana. Also, we performed Genome-wide association studies (GWAS) analyses for 999 accessions to identify the genetic basis of variations in A. thaliana leaf ionome. As a result, a total of 5,664 unique eQTL genes and 15,038 unique cis-eQTLs(ci) were significant. The majority (62.83%) of cis-eQTLs(ci) were cell-type-specific eQTLs. Using colocalization, we uncovered one interested gene AT2G25590 in Phloem cell, encoding a kind of plant Tudor-like protein with possible chromatin-associated functions, which colocalized with the most significant cis-eQTL(ci) of a Mo-related locus (Chr2:10,908,806:A:C; P = 3.27 × 10–27). Furthermore, we prioritized eight target genes associated with AT2G25590, which were previously reported in regulating the concentration of Mo element in A. thaliana. This study revealed the genetic regulation of ionomic variations and provided a foundation for further studies on molecular mechanisms of genetic variants controlling the A. thaliana ionome.
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Data availability
We provide the R script needed to reproduce the processed scRNA-seq datasets results of ct-eQTL, and as for supplementary tables, please visit the database linking page (https://github.com/Jasonxu0109/ct-eQTL).
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Acknowledgements
We appreciate anonymous reviewers and the editor for the insightful comments and valuable suggestions. This work was financially supported by the Natural Science Foundation of China (NSFC) (31870581, 32171740, 31570586), and the National Key Research and Development Program of China (2017YFC0506102).
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Xu, C., Song, LY., Zhou, Y. et al. Integration of eQTL and GWAS analysis uncovers a genetic regulation of natural ionomic variation in Arabidopsis. Plant Cell Rep 42, 1473–1485 (2023). https://doi.org/10.1007/s00299-023-03042-5
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DOI: https://doi.org/10.1007/s00299-023-03042-5