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 photosynthesisrelated 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.

Genetical and Comparative Genomics of Brassica under Altered Ca Supply Identifies Arabidopsis Ca-Transporter Orthologs

“…The linkage map reported here, and used for eQTL analyses, is based on 134 gene expression markers (GEMs), selected from 3272 potential GEMs, and mapped for 85 individuals from the Brassica rapa IMB211 3 R500 Recombinant Inbred (BraIRRI) mapping population (Iniguez-Luy et al, 2009). This new map has a length of 811.6 centimorgan (cM), similar to that reported previously by Hammond et al (2011), which spanned 881.6 cM. Of the 134 GEMs in the current map, 121 have reported genomic locations consistent with their mapping positions.…”

“…Two parental lines of the B. rapa (2n = 2x = 20; A genome) BraIRRI population, IMB211 and R500 (Iniguez-Luy et al, 2009;Hammond et al, 2011), and the R-o-18 reference parent of the B. rapa TILLING population (Stephenson et al, 2010) were grown in a compost substrate in 9 3 9 3 8-cm pots (Desch Plantpak) in a controlled environment. The controlled environment was a walk-in high-specification growth room (Weiss-Gallenkamp) at Wellesbourne, UK, set to a 16-h photoperiod using metal halide lamps, giving a photon flux density between 400 and 700 nm (photosynthetically active radiation) of 250 µmol m 22 s 21 at plant height.…”

“…Recent developments in genetical genomics, also known as expression quantitative trait locus (eQTL) analysis, can now measure variation in global gene expression among individuals within mapping populations (Kliebenstein, 2009;Druka et al, 2010;Hammond et al, 2011;Holloway et al, 2011;Moscou et al, 2011;Cubillos et al, 2012;Ballini et al, 2013;Huang et al, 2013). Variation in gene expression can be linked to sequence polymorphisms in target genes or, perhaps more interestingly, inherited differences in cis-regulatory (proximal) or trans-regulatory (distal) regions.…”

eQTL Regulating Transcript Levels Associated with Diverse Biological Processes in Tomato

“…Closely related plant species often have little coding sequence divergence; nonetheless, the related species often develop unique physiological, metabolic, and developmental characteristics, indicating that patterns of gene expression are important in specieslevel phenotypic variation (Kliebenstein, 2009;Koenig et al, 2013). Phenotypic differences attributed to variations in gene expression patterns have been found to influence disease resistance, insect resistance, phosphate sensing, flowering time, circadian rhythm, and plant development (Kroymann et al, 2003;Werner et al, 2005;Clark et al, 2006;Zhang et al, 2006;Svistoonoff et al, 2007;Chen et al, 2010;Hammond et al, 2011).…”

A Systems Genetics Approach Identifies Gene Regulatory Networks Associated with Fatty Acid Composition in Brassica rapa Seed

“…Genome-wide mapping of gene transcripts in a segregating population was first proposed by Jansen and Nap (2001) and was named genetical genomics. Using genetical genomics, candidate genes were identified in B. rapa for flowering time and leaf development (Xiao et al, 2013(Xiao et al, , 2014, phytonutrient content (Pino Del Carpio et al, 2014), and phosphorus use efficiency (Hammond et al, 2011).…”