Project Number: 8042-31000-104-22-I
Project Type: Interagency Reimbursable Agreement
Start Date: Oct 1, 2013
End Date: Aug 31, 2017
The objective of the project is to profile and compare the sperm methylomes of bulls that have high and low extreme daughter pregnancy rates (DPRs) using bisulphite sequencing (BS-seq). After experimental validations, ARS will study functional impacts of differentially methylated regions (DMRs). ARS plans to further identify functional epigenetic markers and epimutations associated with daughter pregnancy rates and develop an array-based methylation chip assay for semen quality control.
ARS scientists will implement a recently developed BS-seq protocol to provide genome-wide methylome map at a single nucleotide resolution. They will validate selected DNA methylations using targeted PCR-Sanger sequencing and the combined bisulfite restriction (CORBA) assay. Then they will study functional impacts of DMRs on genomic features including functional genes, control elements and common repeats and their associations with reproduction traits. Specifically, they will customize and optimize the existing human experimental and computational technologies to improve BS-seq data quality, to account for the draft nature of current cattle genome assemblies and to utilize the complex structure of cattle pedigrees.