CHARACTERIZATION OF DNA METHYLOME BY WHOLE GENOME SEQUENCING

• Sponsoring Institution: Agricultural Research Service/USDA
• Project Status: ACTIVE
• Funding Source: USDA COOPERATIVE AGREEMENT
• Reporting Frequency: Annual
• Accession No.: 0429747
• Project Start Date: Jan 27, 2016
• Project End Date: Mar 31, 2016
• Program Code: [(N/A)]- (N/A)

Recipient Organization
Novogene Corporation
602 Rockwood Road
Wilmington,DE 19802

Performing Department
(N/A)

Non Technical Summary
(N/A)

Animal Health Component

50%

Research Effort Categories

Basic

50%

Applied

50%

Developmental

0%

Classification

Knowledge Area (KA)	Subject of Investigation (SOI)	Field of Science (FOS)	Percent
303	3410	1080	10%
304	3820	1040	10%
303	3399	1040	80%

Knowledge Area
303 - Genetic Improvement of Animals; 304 - Animal Genome;

Subject Of Investigation
3820 - Goats, meat, and mohair; 3410 - Dairy cattle, live animal; 3399 - Beef cattle, general/other;

Field Of Science
1040 - Molecular biology; 1080 - Genetics;

Keywords

dna

methylation

whole

genome

sequencing

differentially

methylated

region

fertility

Goals / Objectives
The objective of this cooperative research project is to characterize over 20 representative sperm DNA methylomes of cattle with high or low male fertility traits using whole genome sequencing.

Project Methods
ARS will isolate genomic DNA and generate over 20 NGS libraries. Novogene will sequence them using 30 lanes on HiSeq 2500 with the V4 PE125 chemistry (paired-end reads of 125bp). For each lane, Novogene will guarantee at least 60 Gb raw data with greater than 85% of bases above Q30. These genomic data will be analyzed to characterize differentially methylated regions (DMRs) on genomic features including genes, control elements and common repeats.