Genetic Regulation of Gene Expression During Shoot Development in Arabidopsis

DeCook, Rhonda; Lall, Sonia; Nettleton, Dan; Howell, Stephen H.

doi:10.1534/genetics.105.042275

Cited by 129 publications

(92 citation statements)

References 29 publications

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“…0.3). These results contrast to studies that were based on smaller population sizes in which large phenotypic effect cis-eQTL were prevalent (Schadt et al 2003;DeCook et al 2006). Studies based on small sizes in combination with population structures that do not maximize recombination events reduce QTL resolution and lead to sampling bias when detecting eQTL/QTL of larger phenotypic effect (Beavis 1998;Bogdan and Doerge 2005;de Koning and Haley 2005;Gibson and Weir 2005).…”

Section: à14mentioning

confidence: 75%

“…Recent studies in a limited number of organisms indicate that the levels of transcripts are heritable and can be under multigenic control (Brem et al 2002;Schadt et al 2003;Yvert et al 2003;Kirst et al 2004;Brem and Kruglyak 2005;Bystrykh et al 2005;Chesler et al 2005;Hubner et al 2005;DeCook et al 2006). Global eQTL analyses in yeast, mice, and humans have detected significant levels of cis polymorphism controlling individual genes, as well as evidence for clustered trans-eQTL that simultaneously regulate a large fraction of the transcriptome (Brem et al 2002;Schadt et al 2003;Morley et al 2004).…”

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confidence: 99%

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Global eQTL Mapping Reveals the Complex Genetic Architecture of Transcript-Level Variation in Arabidopsis

et al. 2007

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The genetic architecture of transcript-level variation is largely unknown. The genetic determinants of transcript-level variation were characterized in a recombinant inbred line (RIL) population (n ¼ 211) of Arabidopsis thaliana using whole-genome microarray analysis and expression quantitative trait loci (eQTL) mapping of transcript levels as expression traits (e-traits). Genetic control of transcription was highly complex: one-third of the quantitatively controlled transcripts/e-traits were regulated by cis-eQTL, and many trans-eQTL mapped to hotspots that regulated hundreds to thousands of e-traits. Several thousand eQTL of large phenotypic effect were detected, but almost all (93%) of the 36,871 eQTL were associated with small phenotypic effects (R 2 , 0.3). Many transcripts/e-traits were controlled by multiple eQTL with opposite allelic effects and exhibited higher heritability in the RILs than their parents, suggesting nonadditive genetic variation. To our knowledge, this is the first large-scale global eQTL study in a relatively large plant mapping population. It reveals that the genetic control of transcript level is highly variable and multifaceted and that this complexity may be a general characteristic of eukaryotes.

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Section: à14mentioning

confidence: 75%

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confidence: 99%

Global eQTL Mapping Reveals the Complex Genetic Architecture of Transcript-Level Variation in Arabidopsis

et al. 2007

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“…The eQTLs investigated in a population provide the necessary information required for identifying genes or loci that control quantitative traits. In plants, global eQTL analyses of gene expression have been applied to detect cis-polymorphisms controlling individual genes as well as to identify transeQTLs that regulate individual genes from remote loci (DeCook et al, 2006;Keurentjes et al, 2007;Potokina et al, 2008;West et al, 2007). Initial observations from ysis was performed with the backcross (BC1) model set independently for the female parent, 'Okitsu-46' (A255) and male parent, .…”

Section: Rna Extraction and Quantification Of Expression Levelsmentioning

confidence: 99%

Expression Quantitative Trait Loci Analysis of Carotenoid Metabolism-related Genes in Citrus

Sugiyama

Omura

Shimada

et al. 2014

J. Japan. Soc. Hort. Sci.

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The expression profiles of carotenoid metabolism pathway genes are one of the important factors that regulate carotenoid content and composition in the fruit of Citrus cultivars. To identify regulatory factors of gene expressions in the carotenoid pathway, expression quantitative trait loci (eQTL) analysis was applied using a hybrid population. In the analyzed population, significant eQTLs for phytoene synthase (PSY), phytoene desaturase (PDS), z-carotene desaturase (ZDS), b-ring hydroxylase (HYb), and zeaxanthin epoxidase (ZEP) were detected. Among these eQTLs, eQTLs for HYb and ZEP were located on their responsible gene loci, respectively. This result indicates that the expression level of HYb and ZEP was influenced by cis-elements in their up-stream regions. Conversely, eQTLs for PDS and ZDS were located in different loci from those of the responsible genes, indicating that the loci were trans-regulating factors. It also suggested that expression levels of PDS and ZDS were regulated by a common transcription factor because their eQTLs were co-localized. Significant eQTL of lycopene b-cyclase (LCYb) and 9-cis-epoxycarotenoid dioxygenase (NCED) were not detected in this population. The major factors to control gene expression depend on each carotenoid metabolism gene, and their combination might cause complex carotenoid metabolism and extend the variation of content and composition in citrus varieties. eQTL analysis was demonstrated as a powerful tool to identify cis-or trans-regulation for carotenoid metabolism genes, as well as in generating functionally defined markers for marker-assisted selection to increase the carotenoid content of citrus in breeding programs.

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“…QTL have traditionally been statistically analyzed by comparison between the genotypes of marker genes and the occurrence of the trait among naturally occurring genetic variants [5,11,27,59]. Recently, transcripotmic information has been used for QTL, which is referred to as expression QTL (eQTL), thereby clarifying the genes directly related to metabolism, such as those coding for enzymes and transporters, and the regulator genes such as the transcription factors [16,40,53,55,56,86]. In addition to transcriptomic data, metabolomic data may be capable of application to QTL analysis.…”

Section: Future Prospectsmentioning

confidence: 99%

Rice Metabolomics

Oikawa

Mizutani

Kusano

et al. 2008

Rice

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Metabolomics is a recently developed technology for comprehensive analysis of metabolites in organisms. Plant metabolites that are produced for the growth, development, and chemical defense of plants against climatic alterations or natural predators are also useful to us as nutrients or medicines; hence, it is important to comprehend the amounts and varieties of plant metabolites. Besides providing an understanding of the metabolic state in plants under various circumstances, metabolomic techniques are applicable to the clarification of the functions of unknown genes by using natural variants or mutants of the target plants. Furthermore, a metabolomic approach might be useful in the breeding of crops, since valuable plant traits such as taste and yield are closely related to metabolic conditions. Here, we describe the methodology of metabolomics including sample extraction and preparation, metabolite detection, and data processing and analysis, and introduce the application of metabolomic studies to rice.

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Genetic Regulation of Gene Expression During Shoot Development in Arabidopsis

Cited by 129 publications

References 29 publications

Global eQTL Mapping Reveals the Complex Genetic Architecture of Transcript-Level Variation in Arabidopsis

Global eQTL Mapping Reveals the Complex Genetic Architecture of Transcript-Level Variation in Arabidopsis

Expression Quantitative Trait Loci Analysis of Carotenoid Metabolism-related Genes in Citrus

Rice Metabolomics

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