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Genome-wide expression quantitative trait loci (eQTL) analysis in maize

BACKGROUND: Expression QTL analyses have shed light on transcriptional regulation in numerous species of plants, animals, and yeasts. These microarray-based analyses identify regulators of gene expression as either cis-acting factors that regulate proximal genes, or trans-acting factors that functio...

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Autores principales: Holloway, Beth, Luck, Stanley, Beatty, Mary, Rafalski, J-Antoni, Li, Bailin
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2011
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3141675/
https://www.ncbi.nlm.nih.gov/pubmed/21718468
http://dx.doi.org/10.1186/1471-2164-12-336
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author Holloway, Beth
Luck, Stanley
Beatty, Mary
Rafalski, J-Antoni
Li, Bailin
author_facet Holloway, Beth
Luck, Stanley
Beatty, Mary
Rafalski, J-Antoni
Li, Bailin
author_sort Holloway, Beth
collection PubMed
description BACKGROUND: Expression QTL analyses have shed light on transcriptional regulation in numerous species of plants, animals, and yeasts. These microarray-based analyses identify regulators of gene expression as either cis-acting factors that regulate proximal genes, or trans-acting factors that function through a variety of mechanisms to affect transcript abundance of unlinked genes. RESULTS: A hydroponics-based genetical genomics study in roots of a Zea mays IBM2 Syn10 double haploid population identified tens of thousands of cis-acting and trans-acting eQTL. Cases of false-positive eQTL, which results from the lack of complete genomic sequences from both parental genomes, were described. A candidate gene for a trans-acting regulatory factor was identified through positional cloning. The unexpected regulatory function of a class I glutamine amidotransferase controls the expression of an ABA 8'-hydroxylase pseudogene. CONCLUSIONS: Identification of a candidate gene underlying a trans-eQTL demonstrated the feasibility of eQTL cloning in maize and could help to understand the mechanism of gene expression regulation. Lack of complete genome sequences from both parents could cause the identification of false-positive cis- and trans-acting eQTL.
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spelling pubmed-31416752011-07-23 Genome-wide expression quantitative trait loci (eQTL) analysis in maize Holloway, Beth Luck, Stanley Beatty, Mary Rafalski, J-Antoni Li, Bailin BMC Genomics Research Article BACKGROUND: Expression QTL analyses have shed light on transcriptional regulation in numerous species of plants, animals, and yeasts. These microarray-based analyses identify regulators of gene expression as either cis-acting factors that regulate proximal genes, or trans-acting factors that function through a variety of mechanisms to affect transcript abundance of unlinked genes. RESULTS: A hydroponics-based genetical genomics study in roots of a Zea mays IBM2 Syn10 double haploid population identified tens of thousands of cis-acting and trans-acting eQTL. Cases of false-positive eQTL, which results from the lack of complete genomic sequences from both parental genomes, were described. A candidate gene for a trans-acting regulatory factor was identified through positional cloning. The unexpected regulatory function of a class I glutamine amidotransferase controls the expression of an ABA 8'-hydroxylase pseudogene. CONCLUSIONS: Identification of a candidate gene underlying a trans-eQTL demonstrated the feasibility of eQTL cloning in maize and could help to understand the mechanism of gene expression regulation. Lack of complete genome sequences from both parents could cause the identification of false-positive cis- and trans-acting eQTL. BioMed Central 2011-06-30 /pmc/articles/PMC3141675/ /pubmed/21718468 http://dx.doi.org/10.1186/1471-2164-12-336 Text en Copyright ©2011 Holloway et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Holloway, Beth
Luck, Stanley
Beatty, Mary
Rafalski, J-Antoni
Li, Bailin
Genome-wide expression quantitative trait loci (eQTL) analysis in maize
title Genome-wide expression quantitative trait loci (eQTL) analysis in maize
title_full Genome-wide expression quantitative trait loci (eQTL) analysis in maize
title_fullStr Genome-wide expression quantitative trait loci (eQTL) analysis in maize
title_full_unstemmed Genome-wide expression quantitative trait loci (eQTL) analysis in maize
title_short Genome-wide expression quantitative trait loci (eQTL) analysis in maize
title_sort genome-wide expression quantitative trait loci (eqtl) analysis in maize
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3141675/
https://www.ncbi.nlm.nih.gov/pubmed/21718468
http://dx.doi.org/10.1186/1471-2164-12-336
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