"THE AVAILABILITY OF COMPLETE GENOMES HAS DRAMATICALLY IMPROVED THE CHARACTERIZATION OF BIODIVERSITY AND SELECTION FOOTPRINTS IN CROP AND LIVESTOCK SPECIES, AND HAS POTENTIALLY MANY APPLICATIONS IN PRACTICAL BREEDING AS WELL. NEXT GENERATION SEQUENCING (NGS) HAS CERTAINLY DEMOCRATIZED GENOMICS BUT, NOT UNEXPECTEDLY, THE DRAMATIC INCREASE IN COMPLETE GENOME SEQUENCES HAS RESULTED IN A BOTTLENECK ON HOW TO OPTIMALLY ANALYZE THESE VAST DATASETS. THIS PROJECT AIMS AT PROVIDING METHODS AND EASY-TO-USE SOFTWARE (DNASP) TO ANALYZE SEQUENCE DATA AT THE POPULATION LEVEL (WORK PACKAGES WP 1 AND 2). THE USE OF NGS DATA FOR GENOMIC SELECTION, IN COMPARISON TO ASCERTAINED SNP ARRAYS, WILL BE ALSO EVALUATED BY SIMULATION IN SEVERAL SCENARIOS (WP 3). FINALLY, SOME PORCINE DATASETS OF RELEVANCE TO THE INDUSTRY AND TO THE STUDY OF THE EFFECTS OF DOMESTICATION AND ARTIFICIAL SELECTION WILL BE ANALYZED (WP 4). THE DNASP SOFTWARE WILL DIRECTLY HANDLE ALIGNED BAM FILES AND WILL ACCOUNT FOR SEQUENCING ERRORS AND INCOMPLETE DATA, TYPICAL FEATURES OF NGS DATASETS. IT WILL REPORT CLASSICAL AND NEW STATISTICS USED IN POPULATION GENETICS, E.G., TO DETECT SELECTIVE EVENTS. IT WILL BE PROGRAMMED IN A FULLY SCALABLE MANNER SUCH THAT NEW FUNCTIONALITIES, E.G., ASSOCIATION ANALYSES OR GENOMICS SELECTION COULD BE ADDED EASILY IN THE FUTURE. IT WILL BE PUBLICLY AVAILABLE. IN WP3, A SIMULATION STUDY WILL BE CARRIED OUT TO EVALUATE WHETHER NGS WOULD OUTPERFORM DENSE GENOTYPING AND, IF SO, UNDER WHAT CONDITIONS. THE EFFECTS OF THE DEMOGRAPHIC MODEL, GENOTYPING DENSITY VS. NGS COVERAGE AND QTL GENETIC ARCHITECTURE WILL BE ADDRESSED. IN WP4, SEVERAL COMPLEMENTARY ANALYSES ON A SET OF OVER 130 PIG GENOMES AVAILABLE WILL BE CARRIED OUT TO CHARACTERIZE POLYMORPHISM GENOME WIDE AND SPECIES WIDE. WE WILL STUDY AS WELL THE GENETIC BASES OF DOMESTICATION AND OF MODERN SELECTION. THESE ANALYSES WILL PROMPT US TO UTILIZE NEW CONCEPTS, IN PARTICULAR, WE AIM AT INCORPORATING FUNCTIONAL INFORMATION ON THE GENOME, SUCH AS PATHWAY OR METABOLIC DATABASES. AS A PROOF OF CONCEPT, DATA FROM THE INDUSTRY OF FEED EFFICIENCY WILL BE ANALYZED. "