Genotyping of Arabidopsis ecotypes

Large-scale screening studies carried out to date to elucidate the causal mechanism of an allelic imbalance are generally limited to descriptions of allele-specific differences in expression detected in vivo and to linking them to differences in cis- and trans-regulatory changes. Although such gene surveys for regulatory variation leave the underlying mechanisms unexplored, they are a first step in identifying the specific nucleotide changes that govern gene expression differences. We describe a quantitative genetics approach to distinguish between cis- and trans-regulatory changes at a genome-wide scale and, hence, to detect cis-regulatory variation. For this purpose, we took advantage of diallel designs that are often used in plant breeding programs in which the goal is the estimation of general combining abilities (GCAs) of specific inbred lines and the identification of high yielding hybrid combinations of parents based on their specific combining abilities (SCAs). We show that in a context of gene expression, empirical estimates of GCA and SCA are valid parameters to distinguish between cis- and trans-regulatory changes and, hence, to detect cis-regulatory variation. By using this approach, we identified a considerable number of genes that showed evidence of cis-regulated allele-specific expression in a total of 10 diploid Arabidopsis hybrids. The method can also be used to explore naturally occurring cis-regulatory variation among inbred lines for laboratory animals, such as mouse and rat. This experiment covers data from 10 pairs of reciprocal hybrid samples, referred to as Hx.y where x=1...10 and y=1,2; The related data from 20 Recombinant Inline Line samples is submitted as experiment : - VIB Plant Systems Biology "RIL")