Linkage disequilibrium, persistence of phase and effective population size estimates in Hereford and Braford cattle.

Background: The existence of moderate to high levels of linkage disequilibrium (LD) between genetic markers and quantitative trait loci (QTL) affecting traits of interest is fundamental for the success of genome-wide association (GWAS) and genomic selection (GS) studies. Knowledge about the extent and the pattern of LD in livestock populations is essential to determine the density of single nucleotide polymorphisms (SNP) required for accurate GWAS and GS. Moreover, observed LD is related to historical effective population sizes (Ne), and can provide insights into the genetic diversity history of populations. Estimates of the consistency of linkage phase across breeds (R H,B ) can be used to determine if there is sufficient relationship to use pooled reference populations in multi-breed GS programs. The objective of this study was to estimate LD levels, persistence of phase and effective population size in Hereford and Braford cattle populations sampled in Brazil.

Results: Mean LD estimates, measured using the squared correlation of alleles at two loci (r (2)), obtained between adjacent SNP across all chromosomes were 0.21 ± 0.27 for Herefords (391 samples with 41,241 SNP) and 0.16 ± 0.22 for Brafords (2044 samples and 41,207 SNP). Estimated r(2) was > 0.2 and 0.3, respectively, for 34 and 25% of adjacent markers in Herefords, and 26 and 17% in Brafords. Estimated N e for Brafords and Herefords at the current generation was 220 and 153 individuals, respectively. The two breeds demonstrated moderate to strong persistence of phase at all distances (R H,B  = 0.53 to 0.97). The largest phase correlations were found in the 0 to 50 Kb bins (R H,B = 0.92 to 0.97). Estimated LD decreased rapidly with increasing distance between SNP, however, useful linkage for GWAS and GS (r(2) > 0.2) was found spanning to ~50 Kb.

Conclusions: Panels containing about 50,000 and 150,000 SNP markers are necessary to detect minimal levels of LD between adjacent markers that would be useful for GWAS and GS studies to Hereford and Braford breeds, respectively. Markers are expected to be linked to the same QTL alleles in distances < 50 Kb in both populations due to observed high persistence of phase levels.