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Only in recent years,the draft sequences for several agricultural animals have been assembled.Assembling an individual animals entire genome sequence or specific region(s) of interest is increasingly important for agricultural researchers to perform genetic comparisons between animals with different performance.We review the current status for several sequenced agricultural species and suggest that next generation sequencing (NGS) technology with decreased sequencing cost and increased speed of sequencing can benefit agricultural researchers.By taking advantage of advanced NGS technologies,genes and chromosomal regions that are more labile to the influence of environmental factors could be pinpointed.A more long term goal would be addressing the question of how animals respond at the molecular and cellular levels to different environmental models (e.g.nutrition).Upon revealing important genes and gene-environment interactions,the rate of genetic improvement can also be accelerated.It is clear that NGS technologies will be able to assist animal scientists to efficiently raise animals and to better prevent infectious diseases so that overall costs of animal production can be decreased.