Genome-wide scan for runs of homozygosity identifies potential candidate genes associated with local adaptation in Valle del Belice sheep
Résumé
Background: Because 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.
Results: We 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.
Conclusions: These 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.
Domaines
Sciences du Vivant [q-bio]
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Origine : Publication financée par une institution
Origine : Publication financée par une institution
Origine : Publication financée par une institution
Origine : Publication financée par une institution
Origine : Publication financée par une institution