Genes/ term eQTLs observed Col up-regulated alleles Cvi up-regulated alleles P-value (directional allelic effect) 8 0 1 0 5 0 0.00002 0.02 0.03 0.03 0.04 0.05 Page 8 of 12 Cubillos et al. BMC Genomics 2012, 13:117 http://www.biomedcentral.com/1471-2164/13/117 Table 2 Directional allelic effect in CviCol GO term defense response response to far-red light plant-type hypersensitive response response to fungus response to oxidative stress response to hypoxia 582 42 37 35 231 20 58 8 11 7 23 6 50 8 10 7 18 6 GO terms showing a significant directional allelic effect. The number of genes per term, eQTLs observed and number of up-regulating allele from each parent is shown, as well as the P value associated with the allelic bias probabilistic way of classifying eQTLs into their mode of action. We observed that, albeit the two crosses shared a common accession, the eQTL distribution among these types is very dissimilar. The BurCol set shows three times more distant than local eQTLs. At the same FDR, the CviCol set has a very different balance, with an equivalent number of both types of eQTLs (50% distant and 50% local, Figure 1c) and a lower number of hot- spots (Figure 3) encompassing 44.2% of the trans eQTLs. Nevertheless, the distribution pattern of local eQTLs on each chromosome was conserved between crosses, likely due to a strong correlation with gene den- sity and chromosome structural features. Also, we found that local eQTLs were overrepresented at higher signifi- cance in all crosses (Figure 1c-d), explaining a greater phenotypic variance per trait compared to distant eQTLs. Our result agrees with another study in Mouse, where many highly significant local-eQTLs and moder- ately significant trans-acting associations were observed [29]. Furthermore, the BurCol recombinant population exhibited a higher number of distant eQTLs, concentrat- ing 75% of them in 24 bins classified as hotspots (Figure 3). One of the most interesting intervals was the hotspot at bin #8, which contained the highest number of genes whose function is related to the regulation of transcrip- tion (52 genes), including the strong candidate GIGAN- TEA [30], a gene known to be involved in diverse developmental processes [31]. It is difficult to guess whether a hotspot could be the expression of a locus actually controlling the transcription of many genes, or that of a major (for example, developmental) player that has indirect effects on many genes’ expression (as sec- ondary consequences of a strong phenotype for exam- ple). The presence of pleiotropic hotspots affecting the expression of many transcripts has already been described in yeast [14], where no more than 200 trans- eQTLs explained transcript variation for 1,716 traits. Similarly, many trans-hotspots were described in pre- vious A. thaliana studies [3,10]. In agreement with these studies, the hotspots detected here explained approximately 10% of the individual traits’ variation, demonstrating their milder effect on transcript abun- dance compared to local eQTLs [11]. Interestingly, only ~7% of the hotspots overlapped between crosses, sug- gesting either alternative master regulators or little con- servation in complex regulatory networks [14]. These conserved regions could also suggest the presence of polymorphisms in Col-0 as major contributors for the large number of trans eQTLs within these shared regions. To increase the power in detecting eQTLs and identify milder genetic variations, we have utilised the bayesian framework VBQTL, a model designed to dissect gene expression variation in order to account for confounding factors [24]. The implementation of this model in the CviCol set allowed us to detect twice as many eQTLs compared to the standard approach (Figure 4), without affecting the ratio of local versus distant eQTLs. Subse- quently, we used this extended set and focused the pos- terior analyses on local eQTLs since they likely represent independent alleles, only affecting a single transcript and explaining a greater phenotypic variance, in contrast to distant eQTLs that may affect many genes and show minor phenotypic effects. The use of this new set of local eQTLs allowed us to look for potential traces of selection where Col alleles were overexpressed in a set of genes with related function. Assuming neu- trality, no over-representation of either up-regulated or down-regulated alleles from the same accession is expected within a cluster of genes, unless a directional allelic drift has occurred, which may represent selection [32]. We detected an overrepresentation of eQTLs in several GO functional categories and a significant skew within GO terms (Table 1, 2). The accumulation of local regulatory polymorphisms up-regulating Col alleles in all cases, suggests dissimilar patterns of responses to the environment and an advantage in a particular niche [5] or, else, a specific lack of cost in loosing this response. For example, one of the clusters of genes glob- ally up-regulated in Col with respect to Cvi relates to