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Genome engineering has greatly improved our understanding of functional genomics and gene regulation networks, and also holds great promise for crop and farm-animal breeding in agriculture.Toward these ends, development and application of new tools for genome engineering are of enormous value.Here we report the development and application of two approaches for genome engineering of model animals.In one study, we used site-specific nucleases, namely zinc-finger nucleases (ZFNs) and CRISPR-Cas system, to produce single or multiple gene mutant rats.We showed that knocking out the Mecp2 gene in rats by ZFNs could induce relevant phenotypes of Rett syndromes.And using the RNA-guided CRISPR-Cas system, multiple gene mutations could be simultaneously generated and successfully transmitted to next generation in rats.In the other study, we derived androgenetic haploid embryonic stem (ahES) cells in both mice and rats, and proved that they could serve as a new tool for genetic screening and genome engineering.The ahES cell lines can maintain haploidy and stable growth, express pluripotent markers, possess the ability to differentiate into all three germ layers in vitro and in vivo, and contribute to germlines of chimaeras when injected into blastocysts.Although epigenetically distinct from sperm cells, the ahES cells can produce viable and fertile progenies after intracytoplasmic injection into mature oocytes.Homozygous mutations can be efficiently introduced in ahES cells by large-scale gene trapping, and precise gene targeting methods including homologous recombination or the CRISPR-Cas system.Moreover, genetically modified mice and rats can be produced from ahES cells either by ES-cell-based germline transmission or the oocyte-injection procedure.Our findings facilitate the development and application of genome engineering approaches for functional genetic studies and production of transgenic animals.They may also shed new light on gene therapy and assisted reproduction.