2009 Annual Report 1a.Objectives (from AD-416) The objectives of this cooperative research agreement are to:. 1)validate a set of polymorphic markers (SSR or SNPs) located around candidate genes or gene networks important in adaptive differentiation; and. 2)assess variation in these loci across inventories of diverse Brassica accessions. 1b.Approach (from AD-416) The first part of the project makes use of the extensive genomic annotation in Arabidopsis thaliana and looks for homologous loci within Brassica species. These objectives dovetail with ongoing work that includes identifying key functional loci and assessing allelic variation at these loci in progeny of crosses phenotyped in controlled environment. We will begin development of genotyping approaches at these loci in a wider pool of accession that have undergone multiple rounds of regeneration. 3.Progress Report We have initiated a number of studies with Brassica. Our main focus has been finding the Brassica genomic regions homologous to Arabidopsis WUE QTL by utilizing the synteny across genera between Arabidopsis and Brassica and taking advantage of data from the B. rapa genome, which is currently being sequenced. For 10 Arabidopsis QTL we have indentified homologous regions in Brassica, using available synteny maps to localize Arabidopsis QTL to genomic regions of Brassica napus. To date we have focused on regions with the fewest number of copies, ones that exist only 2 to 4 times in B. napus. The goal is to find several low copy sets of regions that will be used in further experiments. We have genotyped these regions of interest using 4 varieties of B. rapa and 19 lines of B. napus, representing both spring and winter varieties. SSR markers are being used to identify polymorphisms associated with the regions of interest. Thus far, we are genotyping 8 locations in the Brassica genome using 20 markers. Several markers have revealed polymorphisms among the varieties that we have tested. Based on these results we will be able to utilize available mapping populations to segregate different locations and examine the functional importance of these different regions for drought tolerance, water-use efficiency, and yield.