ArticlePlant physiology2016
eQTL Regulating Transcript Levels Associated with Diverse Biological Processes in Tomato.
Article in Plant physiology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers, 1 of them a synthesis that pooled it.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
36 citing papers in PubMed, 1 synthesis or guideline pooled it, 63 citations in OpenAlex.
- eQTL Meta-Analysis Reveals Conserved and Population-Specific Regulatory Variation Underlying Nutritional Trait Evolution and Domestication in Tomato.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Pooled it
- Article
- A nuclear receptor HR96-related gene underlies large trans-driven differences in detoxification gene expression in a generalist herbivore.Nature communications · 2023Article
- Diversity of tomato leaf form provides novel insights into breeding.Breeding science · 2023Article
- Plasticity of maternal environment-dependent expression-QTLs of tomato seeds.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2023Article
- Multi-omics analysis reveals the genetic basis of rice fragrance mediated by betaine aldehyde dehydrogenase 2.Journal of advanced research · 2022Article
- The time is ripe for eQTLs: Transcriptomic identification of a tomato fruit ripening regulator.Plant physiology · 2022Article
- A comparative transcriptomics and eQTL approach identifies SlWD40 as a tomato fruit ripening regulator.Plant physiology · 2022Article
- eQTLs are key players in the integration of genomic and transcriptomic data for phenotype prediction.BMC genomics · 2022Article
- Heinz-resistant tomato cultivars exhibit a lignin-based resistance to field dodder (Cuscuta campestris) parasitism.Plant physiology · 2022Article
- Genetic variants associated mRNA stability in lung.BMC genomics · 2022Article
- The genetics of gene expression in a Caenorhabditis elegans multiparental recombinant inbred line population.G3 (Bethesda, Md.) · 2021Article
- A combination of genome-wide and transcriptome-wide association studies reveals genetic elements leading to male sterility during high temperature stress in cotton.The New phytologist · 2021Article
- Leaf shape inEcology and evolution · 2020Article
- eQTL mapping of the 12S globulin cruciferin gene PGCRURSE5 as a novel candidate associated with starch content in potato tubers.Scientific reports · 2020Article
- Xylem systems genetics analysis reveals a key regulator of lignin biosynthesis inGenome research · 2020Article
- Cis- and Trans-Regulatory Variations in the Domestication of the Chili Pepper Fruit.Molecular biology and evolution · 2020Article
- Dissection of complex traits of tomato in the post-genome era.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2020Review
- Genetic dissection of the gene coexpression network underlying photosynthesis in Populus.Plant biotechnology journal · 2020Article
- Dissecting the eQTL Micro-Architecture inFrontiers in genetics · 2020Article
Corrections and comments
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Authors and funding
10 authors at 1 institution in 1 country.
Funding
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.
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Registered trials
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