Prediction of barley gene position based on linkage analysis of mRNA abundance. A – Scattergram of the LRS value distributions of 324 eQTLs with genetic positions of the underlying genes determined using SNP- or RFLP-based linkage mapping. B – Cumulative (%) distribution of the LRS values for cis- (blue line graph) and trans- (red line graph) eQTLs. C – Scatterplots showing the distribution of high (> 30) and low (< 30) LRS class eQTLs across the barley genetic map (x-axes) relative to the position of their putative rice orthologs. Each diagram shows only the comparison to rice chromosome 1 which exhibits considerable conservation of synteny with barley 3H (y-axes). On the x-axis the eQTL positions of barley orthologs of genes on rice chromosome 1 are ordered according to their location on the barley genetic map (tip of barley 1HS to bottom of 7HL), but barley map distances are not taken into account. As expected, barley 3H exhibits strong synteny with rice 1. This is particularly obvious when considering the eQTLs with LRS > 30, suggesting that this class of eQTLs is generally cis- acting. The eQTLs with LRS < 30 show a less obvious (but still apparent) association between rice 1 and barley 3H. In these comparisons all genes reported by 22,840 Barley1 GeneChip probe sets were analysed.