The extent of linkage disequilibrium in the ancient Ukrainian grey cattle breed

Abstract

Mekki Boussaha, Rabia Letaief, Nikolay Yudin, Mikhail Voevoda and Dominique Rocha

We present here the first genome-wide characterization of linkage disequilibrium (LD) in the Ukrainian Grey (UKR) cattle breed, a very ancient beef breed. The aim of our study was to assess the pattern and extent of LD in Ukraine. We used a sample of 48 animals and 37,576 single nucleotide polymorphisms (SNPs) covering all cattle autosomes. The squared correlation of the alleles at two loci (r 2 ) was used as a measure of LD. The analysis of adjacent marker pairs revealed that the level of LD decreases rapidly with physical distance between SNPs. Overall mean r 2 was 0.218 (±0.261). Strong LD (r 2 > 0.8) and useful LD (measured as r 2 > 0.2) were observed within genomic regions of up to 534 kb and 2 Mb, respectively. Unexpectedly, our results indicate that LD extent found in UKR is comparable to LD measures in modern breeds, particularly in beef breeds, suggesting a bottleneck during conservation herd and/or breed formation. In addition, LD mapping of phenotypic traits in the UKR population should be feasible with an optimized medium-density SNP panel or using high-density genome-wide genotyping tools.