Genomewide association study of liver abscess in beef cattle

Area of Science:

• Animal Genetics
• Genomics
• Veterinary Science

Background:

• Liver abscesses affect 14% of U.S. cattle, reducing carcass value.
• Bacterial infections, often stemming from acidosis-induced rumen lesions, cause liver abscesses.
• Identifying genetic factors can help mitigate this significant economic issue in beef production.

Purpose of the Study:

• To identify single nucleotide polymorphisms (SNPs) associated with liver abscesses in beef cattle.
• To explore the genetic basis of susceptibility to liver abscesses for potential breeding applications.

Main Methods:

• Collected 2,304 lung samples from cattle with and without liver abscesses.
• Pooled lung tissue DNA into 24 pools (12 per phenotype) for BovineHD Bead Array analysis (777,962 SNPs).
• Analyzed pooling allele frequency (PAF) and total intensity (TI) to identify significant SNPs.

Main Results:

• Identified 15 significant SNPs for PAF and 20 for TI at a false discovery rate ≤ 5%.
• Genes near significant SNPs are involved in pH homeostasis, immune defense, and tissue repair.
• Detected 35 SNP associations, indicating polygenic variation in liver abscess incidence.

Conclusions:

• Significant genetic variation exists for liver abscess susceptibility in cattle.
• These findings support the potential for genetic selection to reduce acidosis and liver abscesses.
• Lung tissue is a viable DNA source for large-scale bovine genetic studies.