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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...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2011
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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. |
format | Online Article Text |
id | pubmed-3141675 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2011 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
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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