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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Bibliographic Details
Published inPlant physiology (Bethesda) Vol. 156; no. 3; pp. 1230 - 1241
Main Authors Hammond, John P, Mayes, Sean, Bowen, Helen C, Graham, Neil S, Hayden, Rory M, Love, Christopher G, Spracklen, William P, Wang, Jun, Welham, Sue J, White, Philip J, King, Graham J, Broadley, Martin R
Format Journal Article
LanguageEnglish
Published Rockville American Society of Plant Biologists 01.07.2011
SeriesFocus Issue on Phosphorus Plant Physiology
Subjects
Chromosomes
Crop improvement
Gene mapping
Photosynthesis
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Summary: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.
Bibliography: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.
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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.).
ISSN:0032-0889
1532-2548
DOI:10.1104/pp.111.175612