Linkage Disequilibrium and Persistence of Phase in Holstein–Friesian, Jersey and Angus Cattle

TLDR

Linkage disequilibrium between a marker and a QTL can differ across populations, including changes in phase. The study aimed to compare the extent of LD and persistence of LD phase across multiple cattle populations. LD measures r and r² were calculated for syntenic marker pairs using genome‑wide SNPs genotyped in Dutch and Australian Holstein‑Friesian bulls, Australian Angus cattle, and New Zealand Friesian and Jersey cows. Average r² values ranged from ~0.35 at 10 kb to ~0.06 at 1000 kb, implying that genomic selection within breeds with r² ≥ 0.20 would need ~50,000 SNPs, while cross‑breed LD correlations drop with distance and divergence, suggesting ~300,000 markers are required to identify QTL‑linked markers across HF, Jersey, and Angus.

Abstract

When a genetic marker and a quantitative trait locus (QTL) are in linkage disequilibrium (LD) in one population, they may not be in LD in another population or their LD phase may be reversed. The objectives of this study were to compare the extent of LD and the persistence of LD phase across multiple cattle populations. LD measures r and r(2) were calculated for syntenic marker pairs using genomewide single-nucleotide polymorphisms (SNP) that were genotyped in Dutch and Australian Holstein-Friesian (HF) bulls, Australian Angus cattle, and New Zealand Friesian and Jersey cows. Average r(2) was approximately 0.35, 0.25, 0.22, 0.14, and 0.06 at marker distances 10, 20, 40, 100, and 1000 kb, respectively, which indicates that genomic selection within cattle breeds with r(2) >or= 0.20 between adjacent markers would require approximately 50,000 SNPs. The correlation of r values between populations for the same marker pairs was close to 1 for pairs of very close markers (<10 kb) and decreased with increasing marker distance and the extent of divergence between the populations. To find markers that are in LD with QTL across diverged breeds, such as HF, Jersey, and Angus, would require approximately 300,000 markers.