Biomathematics & Statistics Scotland
Genetical genomics is an exciting new research area in which microarray expression data are combined with marker data from a genetic linkage map to locate the genetic factors (expression quantitative trait loci, or eQTLs) controlling the levels of expression.
As mapping populations need to be large, an efficient use of resources is to pair offspring from the population on two-colour arrays. The information for QTL mapping can be maximised by pairing the offspring so that they differ for as many markers as possible. The ratio of the expression data of the offspring is then modelled as a function of the marker genotypes of the pair, to identify the markers with the largest effects.
This approach was applied to study resistance to leaf rust Puccinia hordei in 144 doubled haploid offspring from the barley cross Steptoe x Morex, using an Agilent barley array with more than 15,000 genes. At least one eQTL was identified for over 9,000 of the genes. Of particular interest were the genes whose expression was highly correlated with rust scores, and with eQTLs in regions where QTLs for rust resistance have been previously located. The figure shows the profile of the percentage variation explained along chromosome 2H for rust scores and for three such genes.
Linkage map of barley chromosome 2H, showing the profile of %R2 for rust resistance and the expression of three candidate genes.
Further details from: Christine Hackett
