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.
Highlights
Gene expression is a quantitative trait that can be mapped genetically in structured populations to identify expression quantitative trait loci
Sequence polymorphisms in regulatory genes such as transcription factors, which do not colocate with the physical position of the gene, can result in allelic variation at trans-expression quantitative trait loci (eQTL)
The transcriptional profiling of B. rapa recombinant inbred lines (RILs) grown in different environments has enabled us to characterize the genetic architecture of plant adaptation to low P availability
Summary
Gene expression is a quantitative trait that can be mapped genetically in structured populations to identify expression quantitative trait loci (eQTL). Expression quantitative trait loci (eQTL) are genetic regions associated with variation in gene expression among individuals (Kliebenstein, 2009) This variation can arise due to sequence polymorphisms in target genes, their cis-regulatory (proximal) or trans-regulatory (distal) regions, leading to phenotypic differences. Several trans-eQTL hotspots have been identified in plants, in which loci are associated with variation in the expression level of many hundreds or even thousands of genes, and these are thought to represent master regulatory loci with potentially pleiotropic effects (Kliebenstein, 2009). The statistical significance of associations between genetic loci and trans-eQTL are less than cis-eQTL, potentially due to the complex nature of regulatory gene networks. The identification of eQTL under abiotic stress has not yet been reported
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
