Cloning by somatic cell nuclear transfer is an important technology, but remains limited due to poor rates of success. Identifying genes supporting clone development would enhance our understanding of basic embryology, improve applications of the technology, support greater understanding of establishing pluripotent stem cells, and provide new insight into clinically important determinants of oocyte quality. For the first time, a systems genetics approach was taken to discover genes contributing to the ability of an oocyte to support early cloned embryo development. This identified a primary locus on mouse chromosome 17 and potential loci on chromosomes 1 and 4. A combination of oocyte transcriptome profiling data, expression correlation analysis, and functional and network analyses yielded a short list of likely candidate genes in two categories. The major category-including two genes with the strongest genetic associations with the traits (Epb4.1l3 and Dlgap1)-encodes proteins associated with the subcortical cytoskeleton and other cytoskeletal elements such as the spindle. The second category encodes chromatin and transcription regulators (Runx1t1, Smchd1, and Chd7). Smchd1 promotes X chromosome inactivation, whereas Chd7 regulates expression of pluripotency genes. Runx1t1 has not been associated with these processes, but acts as a transcriptional repressor. The finding that cytoskeleton-associated proteins may be key determinants of early clone development highlights potential roles for cytoplasmic components of the oocyte in supporting nuclear reprogramming. The transcriptional regulators identified may contribute to the overall process as downstream effectors.T HE oocyte is a remarkable cell. It harbors essential stored mRNAs, proteins, and other macromolecules to sustain and direct normal development until embryonic gene expression commences and until external nutrient supplies become available. The oocyte also has the unique ability to reprogram somatic cell nuclei to a totipotent state, a capacity that reflects its unique role during normal embryogenesis of uniting the two gamete genomes and converting them into an embryonic genome. A variety of approaches since the late 1800s investigated the nuclear reprogramming capacity of oocytes by manipulating the ooplasm-nucleus dialog, using blastomere ligature experiments, embryo splitting, embryonic cell nuclear transfer, and ultimately somatic cell nuclear transfer (SCNT). These methodologies have also been useful in determining the timing and mechanisms underlying other processes such as cell-fate restriction and lineage determination in the early embryo. Cloning studies can thus provide unique insight into the early formative processes that are essential to creating each new individual.Ooplasmic components must mediate a myriad of key events to make cloned embryogenesis possible, and observing the execution of these events in cloned embryos can reveal previously unappreciated aspects of normal development. The first step of the cloning process entai...