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Integration of developing countries into international agricultural markets requires animal production systems to be competitive and this will demand to increase efficiency of animal production. Conventional selection schemes have been useful to increase productivity in livestock (milk, beef, wool, eggs) by using quantitative genetics and many changes in the productive systems. The animals that have the best combination of genes for a given trait has been accomplished by using pedigree information (parents, grandparents, cousins, and/or offspring). Nevertheless, the use of animal breeding schemes is difficult in many production systems because no pedigree information exists and the improvement under the quantitative model in many important traits (ie resistance to disease, traits with low heritability, traits limited to one sex; longevity, etc.) was not stimulant. The molecular and technological development in the last three decades became most of us astonished. Thomas H. Roderick in 1986 coined genomics as the discipline that studies the genome. The development of genomics was prompted by the availability of the human genome sequence and since then, the genome sequence of most livestock species is available. The new paradigm quantitative-molecular in animal breeding was growing and expanding the opportunities of using molecular techniques. As an example, the bovine genome has a minimum of 22000 genes, of which 14345 are orthologues shared among different mammalian species. The estimated size of the bovine genome is 2.87 Gigabases. The availability of high throughput sequencing techniques not only enabled the …