2012 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: Our main focus to to analyze the diversity of genees that have function in the Brassica napus genome and assess changes to these genes during the course of gene banking. Our focus has been to look to loci that are involved in fatty acid biosynthesis because there genes have been well characterized and because they underpin the traits that our B. rapa collection is primarily used for. To this end we have identified 80 candidate loci and are pairing this set down to ~15 loci that are 1.) involved in the biosynthetic patty way of fatty acids in both Arabidopsis thaliana and Brassica napus and 2.) are present in Brassica rapa in single copy. We are currently sequencing these loci and looking for allelic variation. In addition we have been given access to a set of 48 SSR markers specific to B rapa from Agri Canada. Using these markers we have been able to assess variation within and among U.S. accessions. Our intent to compare these variation estimates made from SSR markers to those derived from functionally important loci.