PT - JOURNAL ARTICLE AU - Aashish Ranjan AU - Jessica M. Budke AU - Steven D. Rowland AU - Daniel H. Chitwood AU - Ravi Kumar AU - Leonela Carriedo AU - Yasunori Ichihashi AU - Kristina Zumstein AU - Julin N. Maloof AU - Neelima R. Sinha TI - eQTL in a Precisely Defined Tomato Introgression Population Reveal Genetic Regulation of Gene Expression Patterns Related to Physiological and Developmental Pathways AID - 10.1101/040592 DP - 2016 Jan 01 TA - bioRxiv PG - 040592 4099 - http://biorxiv.org/content/early/2016/02/22/040592.short 4100 - http://biorxiv.org/content/early/2016/02/22/040592.full AB - Variation in gene expression, in addition to sequence polymorphisms, is known to influence developmental, physiological and metabolic traits in plants. Genetical genomics approaches on genetic mapping populations have facilitated the 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 desert-adapted 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 through differential gene expression analysis, and identified ~7,200 eQTL regulating the expression of 5,300 genes. Barnes-Hut t-distributed stochastic neighbor embedding clustering identified 42 modules revealing novel associations between gene expression patterns and biological processes. The results showed a complex genetic architecture of global gene expression pattern in tomato. Several genetic hotspots regulating a large number of gene expression patterns relating to diverse biological processes such as plant defense and photosynthesis were identified. We identified important eQTL regulating gene expression patterns related to leaf number and complexity, and hypocotyl length. Genes associated with leaf development showed an inverse correlation with photosynthetic gene expression but their regulation was dispersed across the genome. This is the first comprehensive insight into the global regulation of transcript abundance in tomato and its influence on plant phenotypes, which sets the stage for identifying gene/s underlying these regulatory loci.Summary: Genetical genomics approach in tomato identified genetic hotspots that regulate gene expression patterns relating to diverse biological processes such as plant development, photosynthesis and defense.Footnotes: Funding information: This work is supported through a National Science Foundation grant (IOS-0820854) awarded to NRS and JNM. DHC was a fellow of the Life Sciences Research Foundation funded through the Gordon and Betty Moore Foundation. JMB is a recipient of Katherine Esau Postdoctoral Fellowship at UC Davis.Research area: Genes, Development and Evolution