title: Regulatory hotspots are associated with plant gene expression under varying soil phosphorus supply in Brassica rapa.
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.
authors.affiliation: Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, United Kingdom. j.hammond@nottingham.ac.uk
authors.forename: John P
authors.initials: JP
authors.lastname: Hammond
authors.forename: Sean
authors.initials: S
authors.lastname: Mayes
authors.forename: Helen C
authors.initials: HC
authors.lastname: Bowen
authors.forename: Neil S
authors.initials: NS
authors.lastname: Graham
authors.forename: Rory M
authors.initials: RM
authors.lastname: Hayden
authors.forename: Christopher G
authors.initials: CG
authors.lastname: Love
authors.forename: William P
authors.initials: WP
authors.lastname: Spracklen
authors.forename: Jun
authors.initials: J
authors.lastname: Wang
authors.forename: Sue J
authors.initials: SJ
authors.lastname: Welham
authors.forename: Philip J
authors.initials: PJ
authors.lastname: White
authors.forename: Graham J
authors.initials: GJ
authors.lastname: King
authors.forename: Martin R
authors.initials: MR
authors.lastname: Broadley
mesh_terms: D029741:Brassica rapa / Q000187:drug effects* / Q000235:genetics*; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant / Q000187:drug effects*; D040582:Inheritance Patterns / Q000187:drug effects / Q000235:genetics; D020411:Oligonucleotide Array Sequence Analysis; D010758:Phosphorus / Q000494:pharmacology*; D018520:Plant Shoots / Q000187:drug effects / Q000235:genetics; D040641:Quantitative Trait Loci / Q000235:genetics; D019655:Quantitative Trait, Heritable; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D012987:Soil / Q000737:chemistry*; D014158:Transcription, Genetic / Q000187:drug effects
chemical_list: D012333:RNA, Messenger; D012987:Soil; D010758:Phosphorus