Comparative transcriptome profile of embryos at different developmental stages derived from somatic cell nuclear transfer (SCNT) and In-vitro fertilization (IVF) in riverine buffalo (Bubalus bubalis)

Abstract Somatic cell nuclear transfer (SCNT) is a very important reproductive technology with many diverse applications, such as fast multiplication of elite animals, the production of transgenic animals and embryonic stem (ES) cells. However, low cloning efficiency, a low live birth rate and the abnormally high incidence of abnormalities in the offspring born are attributed to incomplete or aberrant nuclear reprogramming. In SCNT embryos, the aberrant expression pattern of the genes throughout embryonic development is responsible for the incomplete nuclear reprogramming. The present study was carried out to identify the differential gene expression (DEGs) profile of the SCNT and IVF embryos at different developmental stages (2 cells, 4 cells and blastocyst stages). In the present study, 1164 (2 cells), 1004 (8 cells) and 530 (blastocyst stage) DEGs were identified in the SCNT embryos as compared to IVF embryos. In addition, several genes such as ZEB1, GDF1, HSF5, PDE3B, VIM, TNNC, HSD3B1, TAGLN, ITGA4 and AGMAT were affecting the development of SCNT embryos as compared to IVF embryos. Different molecular functions, biological process, cellular component and molecular pathway affected the development of embryos throughout the different developmental stages in SCNT. Apart from this, q-PCR analysis of the GDF1, TMEM114, and IGSF22 genes were utilized to validate the RNA-seq data. These data sets offer the vital information regarding embryo development in SCNT embryos as compared to IVF embryos.