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.
Highlights
Gene alleles which are physically close in a chromosome are inherited in an interconnected manner by inheritance properties, and these are not passed to the offspring independently but as blocks of alleles or haplotypes provided by each parent (Ardlie et al, 2002; Pérez O’Brien et al, 2014a)
This condition creates a level of correlation among the alleles that is known as linkage disequilibrium (LD), and this concept can be extended to any nucleotide in the genome, as well as to any type of genetic molecular marker, such as single nucleotide polymorphisms (SNP)
Knowledge of the LD decay magnitude and pattern along the bovine genome has important implications on a large number of methodologies based on genomic data that are currently used in genetics and animal breeding, as the genome-wide association studies (GWAS) (Ardlie et al, 2002), prediction and genomic selection (Meuwissen et al, 2001; The Bovine Genome Sequencing and Analysis Consortium et al, 2009), genomic markers imputation (Piccoli et al, 2014), marker-assisted selection (MAS), quantitative trait loci (QTL) mapping, parentage testing, genomic markers-based disease testing, among others
Summary
Gene alleles which are physically close in a chromosome are inherited in an interconnected manner by inheritance properties, and these are not passed to the offspring independently but as blocks of alleles or haplotypes provided by each parent (Ardlie et al, 2002; Pérez O’Brien et al, 2014a). Knowledge of the LD decay magnitude and pattern along the bovine genome has important implications on a large number of methodologies based on genomic data that are currently used in genetics and animal breeding, as the genome-wide association studies (GWAS) (Ardlie et al, 2002), prediction and genomic selection (Meuwissen et al., 2001; The Bovine Genome Sequencing and Analysis Consortium et al, 2009), genomic markers imputation (Piccoli et al, 2014), marker-assisted selection (MAS), quantitative trait loci (QTL) mapping, parentage testing, genomic markers-based disease testing, among others Most of these tools are routinely applied in animal breeding programs, and their implementation success is inherently dependent on the LD levels present between markers, and between markers and their surrounding genomic regions (Pérez O’Brien et al, 2014a)
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