title: 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 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 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.
authors.affiliation: Department of Plant Biology, University of California, Davis, California 95616.
authors.forename: Aashish
authors.identifier: 0000-0003-3447-4442
authors.initials: A
authors.lastname: Ranjan
authors.affiliation: Department of Plant Biology, University of California, Davis, California 95616.
authors.forename: Jessica M
authors.initials: JM
authors.lastname: Budke
authors.affiliation: Department of Plant Biology, University of California, Davis, California 95616.
authors.forename: Steven D
authors.initials: SD
authors.lastname: Rowland
authors.affiliation: Department of Plant Biology, University of California, Davis, California 95616.
authors.forename: Daniel H
authors.identifier: 0000-0003-4875-1447
authors.initials: DH
authors.lastname: Chitwood
authors.affiliation: Department of Plant Biology, University of California, Davis, California 95616.
authors.forename: Ravi
authors.initials: R
authors.lastname: Kumar
authors.affiliation: Department of Plant Biology, University of California, Davis, California 95616.
authors.forename: Leonela
authors.identifier: 0000-0002-9260-4770
authors.initials: L
authors.lastname: Carriedo
authors.affiliation: Department of Plant Biology, University of California, Davis, California 95616.
authors.forename: Yasunori
authors.initials: Y
authors.lastname: Ichihashi
authors.affiliation: Department of Plant Biology, University of California, Davis, California 95616.
authors.forename: Kristina
authors.identifier: 0000-0001-9516-8081
authors.initials: K
authors.lastname: Zumstein
authors.affiliation: Department of Plant Biology, University of California, Davis, California 95616.
authors.forename: Julin N
authors.identifier: 0000-0002-9623-2599
authors.initials: JN
authors.lastname: Maloof
authors.affiliation: Department of Plant Biology, University of California, Davis, California 95616 nrsinha@ucdavis.edu.
authors.forename: Neelima R
authors.identifier: 0000-0002-1494-7065
authors.initials: NR
authors.lastname: Sinha
mesh_terms: D001686:Biological Phenomena / Q000235:genetics*; D016000:Cluster Analysis; D020869:Gene Expression Profiling / Q000379:methods; D018507:Gene Expression Regulation, Developmental; D018506:Gene Expression Regulation, Plant; D063990:Gene Ontology; D018546:Hypocotyl / Q000235:genetics / Q000254:growth & development; D018551:Solanum lycopersicum / Q000235:genetics* / Q000254:growth & development; D010641:Phenotype; D018515:Plant Leaves / Q000235:genetics / Q000254:growth & development; D018520:Plant Shoots / Q000254:growth & development; D040641:Quantitative Trait Loci / Q000235:genetics*; D032322:Solanum / Q000235:genetics / Q000254:growth & development; D013045:Species Specificity