ABSTRACT: Bubalus bubalis Exome Sequencing: A framework for single nucleotide polymorphism discovery and its trait based clustering of low coverage sequencing data from three buffalo breeds.
Project description:The domestic buffalo (Bubalus bubalis) has presented an important role in the livestock industry, contributing to milk and meat production worldwide, especially in developing countries. However, little is known about its reproductive particularities. Studies regarding protein composition of buffalo SP are still limited and a complete mapping of buffalo SP proteins is still lacking in the literature. Hence, a comprehensive study of SP proteome is of great importance to better understand the mechanisms involved in male reproduction and to optimize the reproductive biotechnologies of farm animal species. Therefore, the aim of this study is to describe for the first time the Bubalus bubalis seminal plasma proteome using a label free shotgun HDMS approach. This type of analysis is interesting since it yields a high number of detected proteins, generating a dataset that is useful for further characterizing the buffalo SP.
Project description:Sperm carries information to the presumptive embryo upon fertilization in terms of epigenetic codes and transcripts along with the haploid genome. The epigenetic code includes DNA methylation and histone modifications. During spermatogenesis, the DNA of sperm undergoes overall methylation changes and this could have some role to play in fertilizing ability of the sperm. Many of the studies have shown that the altered methylation can cause sub fertility. In the present study we report the development of first comprehensive 4X180K buffalo (Bubalus bubalis) CpG island/promoter microarray for studying the global DNA methylation profile of buffalo sperm. The array has been developed by employing microarray based comparative genomic hybridization (aCGH) technique with bovine and buffalo DNA using bovine genome sequence as reference. The array represents 157084 features assembled from CDS, Promotor and CpG regions covering 2,967 unique genes. We also report the comparison of genome wide methylation differences in buffalo sperm from high fertile and sub fertile bulls which indicated profound discrepancies in their methylation status. A total of 96 individual genes along with another 55 genes covered under CpG islands were found differentially methylated and and were associated with different cellular functions and biological processes affecting germ cell development, spermatogenesis, capacitation and embryonic development.
