@article {Ranjan040592, author = {Aashish Ranjan and Jessica M. Budke and Steven D. Rowland and Daniel H. Chitwood and Ravi Kumar and Leonela Carriedo and Yasunori Ichihashi and Kristina Zumstein and Julin N. Maloof and Neelima R. Sinha}, title = {eQTL in a Precisely Defined Tomato Introgression Population Reveal Genetic Regulation of Gene Expression Patterns Related to Physiological and Developmental Pathways}, elocation-id = {040592}, year = {2016}, doi = {10.1101/040592}, publisher = {Cold Spring Harbor Laboratory}, abstract = {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, and identified ~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 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 expression QTL analysis in tomato and their influence on plant phenotypes, which will be a valuable community resource for investigations on the genetic effects of eQTL on relevant phenotypes.}, URL = {https://www.biorxiv.org/content/early/2016/05/31/040592}, eprint = {https://www.biorxiv.org/content/early/2016/05/31/040592.full.pdf}, journal = {bioRxiv} }