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Regulatory hotspots are associated with plant gene expression under varying soil phosphorus supply in Brassica rapa

Hammond, J. P., Mayes, S., Bowen, H. C., Graham, N. S., Hayden, R. M., Love, C. G., Spracklen, W. P., Wang, J., Welham, S. J., White, P. J., King, G. J. and Broadley, M. R. (2011) Regulatory hotspots are associated with plant gene expression under varying soil phosphorus supply in Brassica rapa. Plant Physiology, 156 (3). pp. 1230-1241. ISSN 1532-2548

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To link to this item DOI: 10.1104/pp.111.175612

Abstract/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.

Item Type:Article
Refereed:Yes
Divisions:Faculty of Life Sciences > School of Biological Sciences > Department of Bio-Engineering
No Reading authors. Back catalogue items
Interdisciplinary centres and themes > Centre for Food Security
Faculty of Life Sciences > School of Agriculture, Policy and Development > Biodiversity, Crops and Agroecosystems Division > Crops Research Group
Interdisciplinary centres and themes > Soil Research Centre
ID Code:33863
Uncontrolled Keywords:Regulatory hotspots plant gene expression soil phosphorus Brassica rapa phosphate eQTL genetical genomics QTL trait
Publisher:American Society of Plant Biologists

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