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

Abstract

18Seed germination is characterized by a constant change of gene expression across different time points. These 19 changes are related to specific processes, which eventually determine the onset of seed germination. To get a better 20 understanding on the regulation of gene expression during seed germination, we performed a quantitative trait 21 locus mapping of gene expression (eQTL) at four important seed germination stages (primary dormant, after-22 ripened, six-hour after imbibition, and radicle protrusion stage) using Arabidopsis thaliana Bay x Sha recombinant 23 inbred lines (RILs). The mapping displayed the distinctness of the eQTL landscape for each stage. We found 24 several eQTL hotspots across stages associated with the regulation of expression of a large number of genes. 25Interestingly, an eQTL hotspot on chromosome five collocates with hotspots for phenotypic and metabolic QTLs 26 in the same population. Finally, we constructed a gene co-expression network to prioritize the regulatory genes for 27 two major eQTL hotspots. The network analysis prioritizes transcription factors DEWAX and ICE1 as the most 28 likely regulatory genes for the hotspot. Together, we have revealed that the genetic regulation of gene expression 29 is dynamic along the course of seed germination. 30 31

Plasticity of maternal environment dependent expression-QTLs of tomato seeds

“…mRNA abundances) in the seeds of a tomato RIL population that had matured in different maternal nutrient environments, we show that the maternal environment affects both regulation and the genetic architecture of gene expression in progeny seeds. Especially, trans eQTLs proved environment specific, which is comparable to other species [57,[63][64][65][66][67][72][73][74]. We found 3,833 genes (~26% of all detected expressed genes in the RILs), with an eQTL in HP and 6,815 genes (~46% of all expressed genes in the RILs) with an eQTL in LN.…”

“…Combining the wealth of information obtained by mapping eQTLs enables (re)construction of regulatory networks underlying plant traits [56,60,62]. In addition, comparison of eQTL profiles from multiple environments may aid our understanding of how genetic variation shapes the effects the environment has on the appearance of phenotypes [57,63,64]. In plant (Arabidopsis) and worm (Caenorhabditis elegans) model systems it has been shown that especially trans-eQTLs are dynamic and can be highly specific for a certain environment [57,[63][64][65][66][67][68].…”

The genetics of gene expression in a Caenorhabditis elegans multiparental recombinant inbred line population

“…Heritable variation in these molecular phenotypes often plays a role in heritable phenotypic variation ( Jimenez-Gomez et al 2010 ; Schmid et al 2015 ; Sterken et al 2017 ). Mapping expression QTLs (eQTLs) can provide insight into the transcriptional architecture of complex traits and have been conducted in model species such as Arabidopsis thaliana and C. elegans as well as several other taxa ( Li et al 2006 ; Keurentjes et al 2007 ; West et al 2007 ; Li et al 2010 ; Rockman et al 2010 ; Vinuela et al 2010 ; Snoek et al 2012 , 2017 ; Cubillos et al 2014 ; Ranjan et al 2016 ; Sterken et al 2017 , 2019 ; Hartanto et al 2020 ).…”

The genetics of gene expression in aC. elegansmulti parental recombinant inbred line population

“…Heritable variation in these molecular phenotypes often plays a role in heritable phenotypic variation [10,30,33]. Mapping expression QTLs (eQTLs) can provide insight into the transcriptional architecture of complex traits and have been conducted in model species such as Arabidopsis thaliana and C. elegans as well as several other taxa [26,[28][29][30][31][34][35][36][37][38][39][40][41].…”

“…Most eQTL studies have been done on populations of recombinant inbred lines (RILs) originating from a cross between two different parental genotypes [26,[28][29][30][31][34][35][36][37][38][39][40]. Inclusion of more than two parents can capture more genetic variation, increasing the number of detected QTLs, potentially allowing more precise mapping and therefore reducing the number of potential candidate causal genes to be verified [42].…”