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
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. MSU purchased and placed both an Illumina GAIIX/PEM next generation sequence instrument and cBOT cluster station to support DNA sequencing at MSU and BARC. ARS scientists consulted in experimental design, generated sequence, and processed sequence data of MSU scientists in support of 6 different research projects. ARS scientists at BARC and at other locations also accessed this equipment and infrastructure in support of multiple research projects. MSU scientists curated and maintained publicly availability of the Bovine Gene Atlas database through their AgBase website (http://bovineatlas.msstate.edu/), and through access to MSU supercomputing facilities are hosting bovine SNP discovery reanalysis using nearly 600 billion bases of cattle sequence data. Monitoring activities associated with this project included regular email correspondence and conference calls. 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).