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

Abstract

BackgroundThe 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.ResultsMean 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 demonstrated moderate to strong persistence of phase at all distances (RH,B = 0.53 to 0.97). The largest phase correlations were found in the 0 to 50 Kb bins (RH,B = 0.92 to 0.97). Estimated LD decreased rapidly with increasing distance between SNP, however, useful linkage for GWAS and GS (r2 > 0.2) was found spanning to ~50 Kb.ConclusionsPanels 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.

Linkage disequilibrium and within-breed genetic diversity in Iranian Zandi sheep

“…The average of r 2 varied across autosomes (ranging from 0.16 in OAR26 to 0.34 in OAR10 for the pairwise distance of < 10 kb), which is in line with previous reports in sheep (Liu et al, 2017;Prieur et al, 2017;Zhao et al, 2014), beef cattle (Bohmanova et al, 2010;Edea et al, 2015), and dairy cattle (Qanbari et al, 2010). This phenomenon can be due to variation in the recombination rate in different autosomes, natural or artificial selection, and genetic drift (Liu et al, 2017;Mastrangelo et al, 2017;Qanbari et al, 2010).…”

“…The level of LD in Zandi sheep was less than it is in cattle (Biegelmeyer et al, 2016;Bohmanova et al, 2010;Jasielczuk et al, 2016) and pigs (Grossi et al, 2017) but close to the level of LD reported for other sheep breeds (Al-Mamun et al, 2015;García-Gámez et al, 2012;Liu et al, 2017). For example, Qanbari et al (2010) reported r 2 of 0.20±0.24 for SNPs within 50-75 kb in German Holstein dairy cattle.…”

“…Moreover, the average r 2 for inter-marker distance < 10 kb in Hereford and Bradford beef cattle breeds was reported at 0.49 and 0.43, respectively (Biegelmeyer et al, 2016). We found that for a very short inter-marker distance (< 10 kb), the calculated r 2 in Zandi sheep was 0.26 ± 0.30.…”

Tag SNP selection for prediction of tick resistance in Brazilian Braford and Hereford cattle breeds using Bayesian methods

“…It should be mentioned that the Hereford and Braford population studied here is evaluated and selected as a single breed-type with common breeding objectives and variance components by the Delta G Connection Breeding Program [24]. Moreover, as demonstrated by Biegelmeyer et al [25], correlation of marker phase between these two breeds was estimated at 0.92 for SNPs less than 50 kb apart, which further supports the assumption that the initial detection analyses based on the 50 K SNP panel was suitable [18]. Therefore, we carried out a joint analysis that accounted for breed differences and heterosis to calculate DEBV.…”

Positive selection ofIL‐33 in adaptive immunity of domestic Chinese goats

“…with the phenotypic changes. The excess of polymorphism in genome sequence data (Nez et al, 2016) has provided a valuable inventive tool in the search for traces of the most recent selection in the genome, for example, (Biegelmeyer et al, 2016).…”