Linkage disequilibrium levels and allele frequency distribution in Blanco Orejinegro and Romosinuano Creole cattle using medium density SNP chip data

Abstract

The linkage disequilibrium (LD) between molecular markers affects the accuracy of genome-wide association studies and genomic selection application. High-density genotyping platforms allow identifying the genotype of thousands of single nucleotide polymorphisms (SNPs) distributed throughout the animal genomes, which increases the resolution of LD evaluations. This study evaluated the distribution of minor allele frequencies (MAF) and the level of LD in the Colombian Creole cattle breeds Blanco Orejinegro (BON) and Romosinuano (ROMO) using a medium density SNP panel (BovineSNP50K_v2). The LD decay in these breeds was lower than those reported for other taurine breeds, achieving optimal LD values (r2 ≥ 0.3) up to a distance of 70 kb in BON and 100 kb in ROMO, which is possibly associated with the conservation status of these cattle populations and their effective population size. The average MAF for both breeds was 0.27 ± 0.14 with a higher SNP proportion having high MAF values (≥ 0.3). The LD levels and distribution of allele frequencies found in this study suggest that it is possible to have adequate coverage throughout the genome of these breeds using the BovineSNP50K_v2, capturing the effect of most QTL related with productive traits, and ensuring an adequate prediction capacity in genomic analysis.

Diversity analysis, runs of homozygosity and genomic inbreeding reveal recent selection in Blanco Orejinegro cattle

“…In the current study, BON cattle presented an r 2 > 0.30 at an average distance of 98.38 kb, which, for a genome size of 2,512,085.51 kb, is equivalent to a genotyping density of 25,534 SNPs that can be covered by medium‐density genotyping chips. This result differs from another study with Colombian creole breeds that reported an r 2 > 0.30 at an average distance of 70 kb in BON and 100 kb in Romosinuano (Bejarano et al., 2018). Other taurine breeds such as Angus, Holstein and Brown Swiss exhibited r 2 levels > 0.30 at distances of 40 to 50 kb (Pérez O'Brien et al., 2014).…”

“…In Figure 1a, the red line represents the average r 2 up to 1Mb (0.21). The LD value of the current study calculated with the PLINK v1.90 software agreed with the results reported for the Colombian breeds, BON and Romosinuano (Bejarano et al., 2018). In BON, at a distance of 1 Mb, the r 2 was 0.19 and in Romosinuano, it was 0.23.…”

Genetic Background and Inbreeding Depression in Romosinuano Cattle Breed in Mexico

“…Such observed decay in as the distance between markers increases is a typical trend found in other populations [ 50 , 51 ]. Decay in level was also studied for Romosinuano beef cattle in Colombia by Bejarano et al [ 52 ]. These authors analyzed decay up to 200 and 500 kb and reported larger values than those found for the same distances between SNP in the present study.…”

Organic farming - Deep genotyping reveals specific selection footprints in barley populations

“…Based on these assumptions, the estimate of linkage disequilibrium (LD) is not only dependent on linkage, but also on selection in these populations, as the estimation of LD is based on the distribution of respective allele frequencies. The expected value of LD at equilibrium decreases in the presence of selection 54,55 . Consequently, an even moderate but continuous selection over consecutive generations will reduce the allele frequency variation and subsequently LD ( Figure 3).…”