2012 Annual Report 1a.Objectives (from AD-416): The objective of this proposal is to optimally utilize the DNA sequencing and data analysis resources at USDA ARS Beltsville Agricultural Research Center (BARC) and Mississippi State University (MSU) through collaboration and utilization of complementary resources. 1b.Approach (from AD-416): MSU researchers will provide DNA templates and reagents as required to generate DNA sequence data and perform down-stream computational analysis. MSU will provide computational resources to annotate and display genomic data represented in the Bovine Genome Atlas. USDA ARS BARC will provide DNA sequencing services at cost. All of these activities will be considered true collaborations and thus, by definition, each party will be considered to have provided a true intellectual contribution consistent with authorship. 3.Progress Report: ARS Scientists at BARC and other locations continued to access and use the Illumina GAIIX/PEM next-generation sequence instrument and cBOT cluster station previously purchased by Mississippi State University (MSU). ARS scientists consulted in experimental design, generated sequence, and processed sequence data from MSU scientists in support of four different research projects, which resulted in one published manuscript and five meeting abstracts. ARS scientists also trained MSU scientists in use of the sequencing instrumentation. MSU purchased an Illumina miSeq sequence platform, which was installed and operational at BARC in June, 2012. This instrument provides flexibility for smaller sequencing projects, especially those related to microbial genomes. MSU scientists curated and maintained publicly availability of the Bovine Gene Atlas database through their AgBase website (http://bovineatlas.msstate.edu/), and continued to allow access for BARC scientists to MSU supercomputing facilities to do genome analysis studies in cattle. This research also supports one objective of the related in-house ARS project to develop biological resources and computational tools to enhance characterization of the bovine genome sequence (obj. #1).