Characterizing linkage disequilibrium in pig populations

Area of Science:

• Animal Genetics
• Population Genetics
• Quantitative Genetics

Background:

• Linkage disequilibrium (LD) is crucial for gene localization, selection identification, and genetic resource management in animal populations.
• Understanding LD extent and range is vital for genetic studies.

Purpose of the Study:

• Evaluate LD measures (r(2) and D') and their adjustments in commercial pig populations.
• Estimate the extent of LD in pig populations using SNP data.
• Provide recommendations for SNP spacing in pig genome-wide association studies.

Main Methods:

• Genotyped over 6,000 pigs from six commercial lines using ~4,500 autosomal SNPs.
• Evaluated two LD measures, r(2) and D', including permutation-based adjustments.
• Estimated LD extent based on SNP map distance and allele frequencies.

Main Results:

• Permutation adjustments partially corrected D' dependency on allele frequency; r(2) proved more robust.
• LD extent decreased with increasing map distance between SNPs.
• Average r(2) was 0.1 for SNPs approximately 3 centiMorgans (cM) apart.

Conclusions:

• r(2) is a reliable LD measure for pig populations.
• Recommended SNP spacing of 0.1–1 cM for whole genome association studies in pigs.
• Observed LD levels in these populations are lower than previously suggested by microsatellite data.