ArticlePlant cell reports2023
Integration of eQTL and GWAS analysis uncovers a genetic regulation of natural ionomic variation in Arabidopsis.
Article in Plant cell reports, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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Who cites it
5 citing papers in PubMed, 10 citations in OpenAlex.
- Single-Cell Omics in Legumes: Research Trends and Applications.Plants (Basel, Switzerland) · 2025Review
- Functional Study ofPlants (Basel, Switzerland) · 2025Article
- Trans-regulatory loci shape natural variation of gene expression plasticity in Arabidopsis.Genetics · 2025Article
- The origin and evolution of cultivated rice and genomic signatures of heterosis for yield traits in super-hybrid rice.BMC biology · 2025Article
- Genome-wide association study reveals genetic loci for ten trace elements in foxtail millet (Setaria italica).TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2024Article
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Authors and funding
10 authors at 2 institutions in 1 country.
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Abstract
key messageThis study provided important insights into the genetic architecture of variations in A. thaliana leaf ionome in a cell-type-specific manner. 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
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