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ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » Animal Genomics and Improvement Laboratory » Research » Research Project #436110

Research Project: Pan-genome and structural variation analyses in dozens of de novo assembled diploid cattle genomes

Location: Animal Genomics and Improvement Laboratory

Project Number: 8042-31000-001-010-I
Project Type: Interagency Reimbursable Agreement

Start Date: Apr 1, 2019
End Date: Mar 31, 2022

Objective:
1. Detect and phase structural variations in a near-complete, haplotype-aware manner in diploid cattle genomes using a combination of selected third-generation sequencing and mapping platforms; 2. Compare with existing structural variation datasets and validate selected events by experimental approaches; 3. Test functional impacts of cattle structural variations on animal production and health and prepare a resource collection of structural variations.

Approach:
Using a combination of selected third-generation genomic platforms, including 10X Genomics linked read and Oxford Nanopore long read sequencing, ARS scientists propose to map and phase structural variation in cattle genomes. We aim to identify near-complete, haplotype-resolved structural variations to explore and enhance the diploid cattle genome assemblies. After comparing with existing datasets and validating selected events, we will further associate them with production and health traits and initialize a resource collection of structural variations.