eQTL Regulating Transcript Levels Associated with Diverse Biological Processes in Tomato

Abstract

Variation in gene expression, in addition to sequence polymorphisms, is known to influence developmental, physiological, and metabolic traits in plants. Genetic mapping populations have facilitated identification of expression quantitative trait loci (eQTL), the genetic determinants of variation in gene expression patterns. We used an introgression population developed from the wild desertadapted Solanum pennellii and domesticated tomato (Solanum lycopersicum) to identify the genetic basis of transcript level variation. We established the effect of each introgression on the transcriptome and identified approximately 7,200 eQTL regulating the steady-state transcript levels of 5,300 genes. Barnes-Hut t-distributed stochastic neighbor embedding clustering identified 42 modules revealing novel associations between transcript level patterns and biological processes. The results showed a complex genetic architecture of global transcript abundance pattern in tomato. Several genetic hot spots regulating a large number of transcript level patterns relating to diverse biological processes such as plant defense and photosynthesis were identified. Important eQTL regulating transcript level patterns were related to leaf number and complexity as well as hypocotyl length. Genes associated with leaf development showed an inverse correlation with photosynthetic gene expression, but eQTL regulating genes associated with leaf development and photosynthesis were dispersed across the genome. This comprehensive eQTL analysis details the influence of these loci on plant phenotypes and will be a valuable community resource for investigations on the genetic effects of eQTL on phenotypic traits in tomato.

Allele‐specific expression and genetic determinants of transcriptomic variations in response to mild water deficit in tomato

“…On the contrary, trans-acting eQTLs mostly presented low to moderate effects varying with watering conditions. Ranjan et al (2016) also identified in an interspecific progeny of tomato a majority of trans-acting eQTL.…”

“…Several transcriptomic analyses have revealed the evolution of gene expression levels along tomato fruit development (Tomato Genome Consortium, 2012) or in different fruit tissues (Carrari et al, 2006;Mounet et al, 2009;Matas et al, 2011;Pattison et al, 2015;Zhang et al, 2016). The genetic bases of these variations have been addressed for the first time by Ranjan et al (2016), revealing 7225 loci that regulate the steady-state transcript levels of 5289 genes using an introgression line population derived from the wild relative species S. pennellii. More recently, Zhu et al (2018) performed transcriptome-based association mapping in a collection of 399 diverse tomato genotypes and identified 2566 cis eQTLs and 93 587 trans eQTLs involved in the expression level variations of 3465 genes.…”

Lignin-based resistance toCuscuta campestrisparasitism in Heinz resistant tomato cultivars

“…Therefore, in order to understand the relationships between the candidate genes and their targets, we conducted DGE analysis with ANOVA and selected 9776 DEGs with FDR less than 0.1 (Table S6). Next, we used Barnes-Hut t-distributed stochastic neighbor embedding (BH-SNE) 20 to generate gene clusters based on gene expression patterns (Data S4) (23). Among the 85 gene clusters generated (Table S7), four clusters were selected based on their GO (Gene Ontology) enrichment terms ( Fig.…”

A new advanced backcross tomato population enables high resolution leaf QTL mapping and gene identification

“…Together these two clusters contained the majority of the literature-curated leaf development genes used for the candidate gene search (Ichihashi et al 2014;Ranjan et al 2016). The IRanges R/Bioconductor package (Lawrence et al 2013) was used to find the overlaps between the IL trans-eQTL and the BIL epistatic QTL.…”