Our objective is to contribute for the development of high-quality, safe and secure livestock products by breeding techniques using genomic information. In a cell of mammals, about 25,000 genes are located on the genomic DNA. We cooperated in the International Swine Genome Sequencing Consortium and we have also independently decoded more than 15,000 expressed genes (full length cDNAs) in pigs. As a result of various genome analysis researches, sequencing of genomic DNA has been completed in many livestock animals and poultry such as cow, pig and chicken. Genetic factors of individual difference in such as meat quality and growth performance are thought to be derived from polymorphisms in DNA sequences. The accumulation of polymorphisms in genomic DNA has been proceeded in each livestock animal and poultry, and DNA polymorphisms associated with phenotypes can be elucidated. In pigs, we are now proceeding with the identification of important genomic regions responsible for meat quality and productivity by whole genome association study with SNP chip contains 60,000 SNP. If DNA polymorphisms which is responsible for useful phenotypes are identified, they can be used as DNA markers for animal breeding. In addition to the genome analysis, we performed transcriptome and proteome analyses for products of gene expression, and also metabolome analysis for metabolic products in vivo. With the multiple omics analysis for DNA, mRNA, protein and metabolite, we are searching the factors causing the differences of performance as livestock animals and developing novel techniques for animal breeding.