Genomewide association study of lung lesions in cattle using sample pooling

Area of Science:

• Animal Genetics
• Veterinary Pathology
• Genomic Epidemiology

Background:

• Bovine respiratory disease complex (BRDC) is a major economic burden in the US beef industry, causing significant annual losses.
• BRDC leads to lung tissue damage and persistent lesions, negatively impacting cattle health and productivity.
• Severe lung lesions at slaughter are linked to reduced weight gain and increased clinical disease incidence in feedlot cattle.

Purpose of the Study:

• To identify single nucleotide polymorphisms (SNP) associated with severe lung lesions in feedlot cattle using a genomewide association study (GWAS).
• To understand the genetic architecture underlying susceptibility to BRDC-related lung damage.

Main Methods:

• A case-control GWAS was performed on 11,520 feedlot cattle using the Illumina Bovine HD array (~770,000 SNP).
• Lung samples (cases with lesions, controls without) were collected and pooled (60 case pools, 60 control pools, 96 animals/pool) for SNP analysis.
• Genomic DNA was extracted from pooled samples, and association analysis was conducted to identify significant SNP.

Main Results:

• Fourteen SNP reached genomewide significance (P ≤ 1.49 × 10⁻⁷) on 10 chromosomes.
• Eighty-five SNP on 28 chromosomes achieved a 5% false discovery rate (P ≤ 5.38 × 10⁻⁵).
• Significant SNP were located near genes involved in tissue repair, immunity, cell proliferation, and tumor suppression.

Conclusions:

• The genetic basis for severe lung lesions in cattle is complex, involving multiple genes and regulatory elements across the genome.
• This complex genetic footprint aligns with the multifactorial nature of BRDC, involving pathogens and environmental stressors.
• Identifying these associated SNP can facilitate genome-enhanced breeding strategies for improved BRDC resistance in cattle populations.