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eQTL regulating transcript levels associated with diverse biological processes in tomato

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Title eQTL regulating transcript levels associated with diverse biological processes in tomato
 
Creator Ranjan, Aashish
Budke, Jessica
Rowland, Steven D.
Chitwood, Daniel H
Kumar, Ravi
Carriedo, Leonela G.
Ichihashi, Yasunori
Zumstein, Kristina
Maloof, Julin N.
Sinha, Neelima R.
 
Subject expression Quantitative Trait Loci
eQTL
Tomato
 
Description Accepted date: 11 July 2016
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 ~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 hotspots 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, and 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 expression QTL 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.
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.
 
Date 2016-07-18T08:45:18Z
2016-07-18T08:45:18Z
2016
 
Type Article
 
Identifier Plant Physiol., 172(1): 328-340
1532-2548
http://172.16.0.77:8080/jspui/handle/123456789/666
http://www.plantphysiol.org/content/early/2016/07/14/pp.16.00289.abstract
http:/​/​dx.​doi.​org/​10.​1104/​pp.​16.​00289
 
Language en_US
 
Publisher American Society of Plant Biologists