Regulatory Hotspots Are Associated with Plant Gene Expression under Varying Soil Phosphorus Supply in Brassica rapa1[W][OA]
Gene expression is a quantitative trait that can be mapped genetically in structured populations to identify expression quantitative trait loci (eQTL). Genes and regulatory networks underlying complex traits can subsequently be inferred. Using a recently released genome sequence, we have defined cis...
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| Published in | Plant physiology (Bethesda) Vol. 156; no. 3; pp. 1230 - 1241 |
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| Main Authors | , , , , , , , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
Rockville
American Society of Plant Biologists
01.07.2011
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| Series | Focus Issue on Phosphorus Plant Physiology |
| Subjects | |
| Online Access | Get full text |
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| Abstract | Gene expression is a quantitative trait that can be mapped genetically in structured populations to identify expression quantitative trait loci (eQTL). Genes and regulatory networks underlying complex traits can subsequently be inferred. Using a recently released genome sequence, we have defined cis- and trans-eQTL and their environmental response to low phosphorus (P) availability within a complex plant genome and found hotspots of trans-eQTL within the genome. Interval mapping, using P supply as a covariate, revealed 18,876 eQTL. trans-eQTL hotspots occurred on chromosomes A06 and A01 within Brassica rapa; these were enriched with P metabolism-related Gene Ontology terms (A06) as well as chloroplast- and photosynthesis-related terms (A01). We have also attributed heritability components to measures of gene expression across environments, allowing the identification of novel gene expression markers and gene expression changes associated with low P availability. Informative gene expression markers were used to map eQTL and P use efficiency-related QTL. Genes responsive to P supply had large environmental and heritable variance components. Regulatory loci and genes associated with P use efficiency identified through eQTL analysis are potential targets for further characterization and may have potential for crop improvement. |
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| AbstractList | Gene expression is a quantitative trait that can be mapped genetically in structured populations to identify expression quantitative trait loci (eQTL). Genes and regulatory networks underlying complex traits can subsequently be inferred. Using a recently released genome sequence, we have defined cis- and trans-eQTL and their environmental response to low phosphorus (P) availability within a complex plant genome and found hotspots of trans-eQTL within the genome. Interval mapping, using P supply as a covariate, revealed 18,876 eQTL. trans-eQTL hotspots occurred on chromosomes A06 and A01 within
Brassica rapa
; these were enriched with P metabolism-related Gene Ontology terms (A06) as well as chloroplast- and photosynthesis-related terms (A01). We have also attributed heritability components to measures of gene expression across environments, allowing the identification of novel gene expression markers and gene expression changes associated with low P availability. Informative gene expression markers were used to map eQTL and P use efficiency-related QTL. Genes responsive to P supply had large environmental and heritable variance components. Regulatory loci and genes associated with P use efficiency identified through eQTL analysis are potential targets for further characterization and may have potential for crop improvement. Gene expression is a quantitative trait that can be mapped genetically in structured populations to identify expression quantitative trait loci (eQTL). Genes and regulatory networks underlying complex traits can subsequently be inferred. Using a recently released genome sequence, we have defined cis- and trans-eQTL and their environmental response to low phosphorus (P) availability within a complex plant genome and found hotspots of trans-eQTL within the genome. Interval mapping, using P supply as a covariate, revealed 18,876 eQTL. trans-eQTL hotspots occurred on chromosomes A06 and A01 within Brassica rapa; these were enriched with P metabolism-related Gene Ontology terms (A06) as well as chloroplast- and photosynthesis-related terms (A01). We have also attributed heritability components to measures of gene expression across environments, allowing the identification of novel gene expression markers and gene expression changes associated with low P availability. Informative gene expression markers were used to map eQTL and P use efficiency-related QTL. Genes responsive to P supply had large environmental and heritable variance components. Regulatory loci and genes associated with P use efficiency identified through eQTL analysis are potential targets for further characterization and may have potential for crop improvement. |
| Author | Welham, Sue J Broadley, Martin R Hammond, John P Love, Christopher G Spracklen, William P King, Graham J Bowen, Helen C Hayden, Rory M Wang, Jun White, Philip J Mayes, Sean Graham, Neil S |
| AuthorAffiliation | Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, United Kingdom (J.P.H., S.M., N.S.G., M.R.B.); Warwick HRI, University of Warwick, Wellesbourne, Warwick CV35 9EF, United Kingdom (H.C.B., R.M.H., W.P.S.); Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, United Kingdom (C.G.L., S.J.W., G.J.K.); James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom (P.J.W.); Centre for Haemato-Oncology, Barts Cancer Institute, Barts and London School of Medicine and Dentistry, London EC1M 6BQ, United Kingdom (J.W.) |
| AuthorAffiliation_xml | – name: Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, United Kingdom (J.P.H., S.M., N.S.G., M.R.B.); Warwick HRI, University of Warwick, Wellesbourne, Warwick CV35 9EF, United Kingdom (H.C.B., R.M.H., W.P.S.); Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, United Kingdom (C.G.L., S.J.W., G.J.K.); James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom (P.J.W.); Centre for Haemato-Oncology, Barts Cancer Institute, Barts and London School of Medicine and Dentistry, London EC1M 6BQ, United Kingdom (J.W.) |
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| Copyright | Copyright American Society of Plant Biologists Jul 2011 2011 American Society of Plant Biologists 2011 |
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| DOI | 10.1104/pp.111.175612 |
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| Notes | The author responsible for distribution of materials integral to the findings presented in this article in accordance with the policy described in the Instructions for Authors (www.plantphysiol.org) is: John P. Hammond (j.hammond@nottingham.ac.uk). www.plantphysiol.org/cgi/doi/10.1104/pp.111.175612 These authors contributed equally to the article. Present address: Southern Cross Plant Science, Southern Cross University, Lismore, NSW 2480, Australia. The online version of this article contains Web-only data. Open Access articles can be viewed online without a subscription. This work was supported by the United Kingdom Department for Environment, Food, and Rural Affairs (contract no. WQ0119 to J.P.H.), the United Kingdom Biotechnology and Biological Sciences Research Council (Industry Partnering Award no. BBG013969 to M.R.B., J.P.H., and G.J.K. and project no. BBE017797 to J.W.), and the Scottish Government Rural and Environment Research and Analysis Directorate (to P.J.W.). |
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| Snippet | Gene expression is a quantitative trait that can be mapped genetically in structured populations to identify expression quantitative trait loci (eQTL). Genes... |
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| SubjectTerms | Chromosomes Crop improvement Gene mapping Photosynthesis |
| Title | Regulatory Hotspots Are Associated with Plant Gene Expression under Varying Soil Phosphorus Supply in Brassica rapa1[W][OA] |
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