Embryo development can be affected by genetic material and growth environment. Embryo genetic abnormalities, which originate from paternal, maternal or embryonic genome, may increase the risk of implantation failures and human infertility. Next generation sequencing technologies have been applied in many fields including reproductive and developmental sciences. The characters of NGS, high throughputs and accuracy at base-pair resolution, can help us to know not only the key molecular events during early embryo development, but also the factors correlated with infertility and miscarriage. In Part I of this thesis, single cells were isolated from four groups of developing embryos，two groups of androgenetic and two groups of parthenogenetic embryos at four embryonic stages. Their genome and transcriptome were investigated using single cell whole genome and transcriptome sequencing based on NGS technologies. Our results implied that parent-of-origin effects played a predominant role after the major wave of embryonic genome activation (EGA) during embryo development. In Part II and III of this thesis, low-pass whole genome sequencing was successfully used to detect seemingly balanced chromosomal abnormalities (BCAs) in recurrent miscarriage population and normal population from 1000 genomes project. Comparing with traditional chromosome analysis, lowpass WGS also can identify cryptic rearrangements and provided important information for complex chromosome rearrangements in blind. Additionally, combined with RNA expression analysis, it shown that the expression levels of some genes in breakpoints areas were not changed, which indicated that the clinical interpretation for balanced chromosome abnormality (BCA) would be better if combined with RNA expression analysis. These results show that lowpass WGS is a highly cost-effective approach to detect BCA events. Taken together, NGS has wide applications in reproductive and developmental sciences, from basic research in embryo development to clinical applications for abnormal chromosome identification.