Project Number: 1245-32000-093-00
Project Type: Appropriated

Start Date: Oct 11, 2011
End Date: Oct 10, 2016

Objective:
Objective 1. Develop genomic tools for small ruminants to study structural and functional genetic variation. A de novo goat genome assembly will be constructed using next-generation sequencing technologies. Single-nucleotide polymorphisms in small ruminant genomes will be analyzed and their utility in genome-wide association studies will be established. Objective 2. Characterize genetic variation in small ruminants to develop selection tools for host resistance to parasites and their pathogenic effects. Genes and QTL in small ruminant genomes that influence host resistance to gastrointestinal nematodes will be identified. Objective 3. Investigate the ruminant host transcriptome and immune responses to identify similarities and differences in response to parasitic infection across ruminants. Inter- and intra-species and breed differences in parasite-induced changes in the host transcriptome will be analyzed, and biological pathways underlying host resistance and their regulatory processes will be characterized.

Approach:
The project will focus on using integrated approaches to develop genomic tools in ruminants and information to better understand how to implement selection for parasite tolerance while also increasing meat and milk production. The studies will attempt to better understand livestock biology of parasite resistance through a combination of quantitative genetics, marker-assisted selection, genome annotation, and gene expression analyses. First, studies will focus on the development of genomic tools for small ruminants to study structural and functional genetic variation, including the construction of a de novo goat reference genome assembly and identification of approximately 45 million single-nucleotide polymorphisms (SNP) to facilitate genetic analysis. Additionally, the project will use combined linkage and linkage disequilibrium (LD) mapping in small ruminant resource populations to identify previously unidentified genes and QTL for parasite tolerance. Finally, efforts will be made to investigate the ruminant host transcriptome and immune responses to identify similarities and differences in host immunity, growth characteristics and nutrient utilization in response to parasitic infection across ruminants.