Network Analysis Prioritizes DEWAX and ICE1 as the Candidate Genes for Major eQTL Hotspots in Seed Germination of Arabidopsis thaliana

Margi Hartanto*, Ronny V.L. Joosen, Basten L. Snoek, Leo A.J. Willems, Mark G. Sterken, Dick de Ridder, Henk W.M. Hilhorst, Wilco Ligterink, Harm Nijveen*

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

Abstract

Seed germination is characterized by a constant change of gene expression across different time points. These changes are related to specific processes, which eventually determine the onset of seed germination. To get a better understanding on the regulation of gene expression during seed germination, we performed a quantitative trait locus mapping of gene expression (eQTL) at four important seed germination stages (primary dormant, after-ripened, six-hour after imbibition, and radicle protrusion stage) using Arabidopsis thaliana Bay x Sha recombinant inbred lines (RILs). The mapping displayed the distinctness of the eQTL landscape for each stage. We found several eQTL hotspots across stages associated with the regulation of expression of a large number of genes. Interestingly, an eQTL hotspot on chromosome five collocates with hotspots for phenotypic and metabolic QTLs in the same population. Finally, we constructed a gene co-expression network to prioritize the regulatory genes for two major eQTL hotspots. The network analysis prioritizes transcription factors DEWAX and ICE1 as the most likely regulatory genes for the hotspot. Together, we have revealed that the genetic regulation of gene expression is dynamic along the course of seed germination.
Original languageEnglish
Pages (from-to)4215-4226
JournalG3 : Genes Genomes Genetics
Volume10
Issue number11
DOIs
Publication statusPublished - Nov 2020

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