RESEARCH ARTICLE Open Access Linkage disequilibrium, persistence of phase and effective population size

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 (RH,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 (r2), 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 r2 was> 0.2 and 0.3, respectively, for 34 and 25 % of adjacent markers in Herefords, and 26 and 17 % in Brafords. Estimated Ne for Brafords and Herefords at the current generation was 220 and 153 individuals, respectively. The two breeds demonstrate