Abstract
BackgroundBecause very large numbers of single nucleotide polymorphisms (SNPs) are now available throughout the genome, they are particularly suitable for the detection of genomic regions where a reduction in heterozygosity has occurred and they offer new opportunities to improve the accuracy of inbreeding (F) estimates. Runs of homozygosity (ROH) are contiguous lengths of homozygous segments of the genome where the two haplotypes inherited from the parents are identical. Here, we investigated the occurrence and distribution of ROH using a medium-dense SNP panel to characterize autozygosity in 516 Valle del Belice sheep and to identify the genomic regions with high ROH frequencies.ResultsWe identified 11,629 ROH and all individuals displayed at least one ROH longer than 1 Mb. The mean value of F estimated from ROH longer than1 Mb was 0.084 ± 0.061. ROH that were shorter than 10 Mb predominated. The highest and lowest coverages of Ovis aries chromosomes (OAR) by ROH were on OAR24 and OAR1, respectively. The number of ROH per chromosome length displayed a specific pattern, with higher values for the first three chromosomes. Both number of ROH and length of the genome covered by ROH varied considerably between animals. Two hundred and thirty-nine SNPs were considered as candidate markers that may be under directional selection and we identified 107 potential candidate genes. Six genomic regions located on six chromosomes, corresponding to ROH islands, are presented as hotspots of autozygosity, which frequently coincided with regions of medium recombination rate. According to the KEGG database, most of these genes were involved in multiple signaling and signal transduction pathways in a wide variety of cellular and biochemical processes. A genome scan revealed the presence of ROH islands in genomic regions that harbor candidate genes for selection in response to environmental stress and which underlie local adaptation.ConclusionsThese results suggest that natural selection has, at least partially, a role in shaping the genome of Valle del Belice sheep and that ROH in the ovine genome may help to detect genomic regions involved in the determinism of traits under selection.
Highlights
Because very large numbers of single nucleotide polymorphisms (SNPs) are available throughout the genome, they are suitable for the detection of genomic regions where a reduction in heterozygosity has occurred and they offer new opportunities to improve the accuracy of inbreeding (F) estimates
Among several alternative methods to estimate inbreeding, F estimated from runs of homozygosity (ROH) (FROH) is considered as the most powerful and makes it possible to distinguish between recent and ancient inbreeding [2]
We found that only the ROH on OAR2 partially overlapped with a region under climate-associated selection, which spanned two genes (MELK and GNE) [42] and with a selection signature detected in the Comisana
Summary
Because very large numbers of single nucleotide polymorphisms (SNPs) are available throughout the genome, they are suitable for the detection of genomic regions where a reduction in heterozygosity has occurred and they offer new opportunities to improve the accuracy of inbreeding (F) estimates. We investigated the occurrence and distribution of ROH using a medium-dense SNP panel to characterize autozygosity in 516 Valle del Belice sheep and to identify the genomic regions with high ROH frequencies. The current availability of very large numbers of single nucleotide polymorphisms (SNPs) throughout the genome makes these markers suitable for the detection of genomic regions where a reduction in heterozygosity has occurred and offers the opportunity to estimate F more precisely at the genome level. We investigated the occurrence and the distribution of ROH in Valle del Belice sheep using a medium-density SNP genotyping array, in order to characterize autozygosity and identify the genomic regions with high ROH frequencies, namely ROH islands or ROH hotspots
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