Linkage disequilibrium and persistence of phase in Holstein-Friesian, Jersey and Angus cattle

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.

Figure 1.—

Average linkage disequilibrium (r²) as a function of average genomic distance for Dutch black-and-white Holstein–Friesian bulls (HF_NLD), Dutch red-and-white Holstein–Friesian bulls (RW_NLD), Australian Holstein–Friesian bulls (HF_AUS), Australian Angus animals (ANG_AUS), New Zealand Friesian cows (HF_NZL), and New Zealand Jersey cows (JER_NZL) for distances between 0 and 100 kb. Each data point was based on 200 marker pairs, resulting in standard errors ≤0.03.

Figure 2.—

Average linkage disequilibrium (r²) as a function of average genomic distance for Dutch black-and-white Holstein–Friesian bulls (HF_NLD), Dutch red-and-white Holstein–Friesian bulls (RW_NLD), Australian Holstein–Friesian bulls (HF_AUS), Australian Angus animals (ANG_AUS), New Zealand Friesian cows (HF_NZL), and New Zealand Jersey cows (JER_NZL) for distances between 100 and 1000 kb. Each data point was based on 400 marker pairs, resulting in standard errors ≤0.01.

Figure 3.—

Relationship between r in Australian Holstein–Friesian bulls (HF_AUS) and New Zealand Friesian cows (HF_NZL) for marker pairs with distance between 77 and 108 kb, averaging 93 kb (n = 400).

Figure 4.—

Correlation of r between populations as a function of genomic distance, for Dutch black-and-white Holstein–Friesian bulls (HF_NLD), Dutch red-and-white Holstein–Friesian bulls (RW_NLD), Australian Holstein–Friesian bulls (HF_AUS), Australian Angus animals (ANG_AUS), New Zealand Friesian cows (HF_NZL), and New Zealand Jersey cows (JER_NZL). Each data point was based on 400 marker pairs, resulting in standard errors of 0.02, 0.03, and 0.05 for correlations around 0.9, 0.8, and 0.2, respectively.

Figure 5.—

Correlation of r between groups of Dutch black-and-white Holstein–Friesian animals as a function of genomic distance, for progeny-tested bulls born before 1995 (Pre95), progeny-tested bulls born after 1997 (Post97), and calves born in 2006 (Calf), using maternal (extension “_m”) or paternal (extension “_p”) haplotypes. Each data point was based on 400 marker pairs, resulting in standard errors of 0.02, 0.03, and 0.05 for correlations around 0.9, 0.8, and 0.2, respectively.

Figure 6.—

Effective population size along the population history, estimated from the average r² at different marker distances, for Dutch black-and-white Holstein–Friesian bulls (HF_NLD), Dutch red-and-white Holstein–Friesian bulls (RW_NLD), Australian Holstein–Friesian bulls (HF_AUS), Australian Angus animals (ANG_AUS), New Zealand Friesian cows (HF_NZL), and New Zealand Jersey cows (JER_NZL). Data points were based on at least 400 marker pairs.

Figure 7.—

Expected and realized correlation of r as a function of genomic distance (c) between Australian Holstein–Friesian bulls and Australian Angus animals, with expected correlation following exp(−2Tc) with T = 364.

Figure 8.—

Expected and realized correlation of r as a function of genomic distance (c) between New Zealand Friesian cows and New Zealand Jersey cows, with expected correlation following exp(−2Tc) with T = 191.