Abstract
BackgroundThe recent availability of sheep genome-wide SNP panels allows providing background information concerning genome structure in domestic animals. The aim of this work was to investigate the patterns of linkage disequilibrium (LD), the genetic diversity and population structure in Valle del Belice, Comisana, and Pinzirita dairy sheep breeds using the Illumina Ovine SNP50K Genotyping array.ResultsAverage r2 between adjacent SNPs across all chromosomes was 0.155 ± 0.204 for Valle del Belice, 0.156 ± 0.208 for Comisana, and 0.128 ± 0.188 for Pinzirita breeds, and some variations in LD value across chromosomes were observed, in particular for Valle del Belice and Comisana breeds. Average values of r2 estimated for all pairwise combinations of SNPs pooled over all autosomes were 0.058 ± 0.023 for Valle del Belice, 0.056 ± 0.021 for Comisana, and 0.037 ± 0.017 for Pinzirita breeds. The LD declined as a function of distance and average r2 was lower than the values observed in other sheep breeds. Consistency of results among the several used approaches (Principal component analysis, Bayesian clustering, FST, Neighbor networks) showed that while Valle del Belice and Pinzirita breeds formed a unique cluster, Comisana breed showed the presence of substructure. In Valle del Belice breed, the high level of genetic differentiation within breed, the heterogeneous cluster in Admixture analysis, but at the same time the highest inbreeding coefficient, suggested that the breed had a wide genetic base with inbred individuals belonging to the same flock. The Sicilian breeds were characterized by low genetic differentiation and high level of admixture. Pinzirita breed displayed the highest genetic diversity (He, Ne) whereas the lowest value was found in Valle del Belice breed.ConclusionsThis study has reported for the first time estimates of LD and genetic diversity from a genome-wide perspective in Sicilian dairy sheep breeds. Our results indicate that breeds formed non-overlapping clusters and are clearly separated populations and that Comisana sheep breed does not constitute a homogenous population. The information generated from this study has important implications for the design and applications of association studies as well as for development of conservation and/or selection breeding programs.Electronic supplementary materialThe online version of this article (doi:10.1186/s12863-014-0108-5) contains supplementary material, which is available to authorized users.
Highlights
The recent availability of sheep genome-wide single nucleotide polymorphism (SNP) panels allows providing background information concerning genome structure in domestic animals
In order to examine the decay of linkage disequilibrium (LD) with physical distance, SNP pairs on autosomes were sorted into bins based on their inter-marker distance and average values of r2 were calculated for each bin
Previous studies in five populations of domestic sheep based on microsatellite markers [6] and in wild sheep based on dense panel of SNPs [15] showed LD extends over long distance (r2 = 0.192 ± 0.131 for markers separated by 5–10 cM, and high levels of LD observed over 4 Mb, respectively)
Summary
The recent availability of sheep genome-wide SNP panels allows providing background information concerning genome structure in domestic animals. Average values of r2 estimated for all pairwise combinations of SNPs pooled over all autosomes were 0.058 ± 0.023 for Valle del Belice, 0.056 ± 0.021 for Comisana, and 0.037 ± 0.017 for Pinzirita breeds. The application of recently developed genomic technology, such as high-density single nucleotide polymorphism (SNP) arrays, has great potential to increase our understanding on the genetic architecture of complex traits, to improve selection efficiency in domestic animals through genomic selection [1], and to conduct association studies [2]. With availability of high-density SNP arrays, genetic diversity can be estimated accurately in the absence of pedigree information [9]
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