2010 Annual Report 1a.Objectives (from AD-416) Produce 6000 single nucleotide polymorphism (SNP) markers for channel catfish. 1b.Approach (from AD-416) Genomic DNA from multiple individuals will be pooled and sequenced using next-generation sequencing technology. SNP loci will be identified using computational methods. 3.Progress Report The project is designed for large scale identification of single nucleotide polymorphisms (SNP) in the channel catfish genome, and the development of a high-throughput genotyping platform for applications in catfish genetics and selective breeding. Three-generation reference families useful for the production of a high-resolution genetic map were produced in spring 2010 by matings of pedigreed broodstock. To maximize the probability of ascertaining polymorphisms that will be useful in a wide range of genetic backgrounds, genomic DNA libraries were produced from restriction enzyme digestion fragments from multiple individuals of multiple commercial and research strains. Second generation DNA sequencing technology and state of the art bioinformatic methodologies will be used to identify specific polymorphisms. The ADODR worked collaboratively with the Auburn University through telephone and email correspondence to design and initiate the project.