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Sheep are one of the most important livestock species in Croatia, found
mainly in the Mediterranean coastal and mountainous regions along the East
Adriatic coast, well adapted to the environment and mostly kept
extensively. Our main objective was therefore to map the positive
selection of the X-chromosome (18,983 SNPs that passed quality control),
since nothing is known about the adaptation genes on this chromosome for
any of the breeds from the Balkan cluster. Analyses were performed on a
sample of eight native Croatian breeds (101 females and 100 males)
representing the East Adriatic metapopulation and on 10 mouflons (five
females and males), all sampled in Croatia. Three classical
within-population approaches (extreme Runs of Homozygosity islands,
integration Haplotype Scores, and number of Segregating Sites by Length)
were applied along with our new approach called Haplotype Richness Drop
(HRiD), which uses only the information contained in male haplotypes. We
have also shown that phylogenetic analyses, such as the Median-joining
network, can provide additional information when performed with the
selection signals identified by HRiD. Our new approach identifies positive
selection signals by searching for genomic regions that exhibit a sudden
decline in haplotype richness. In total, we identified 14 positive
selection signals, 11 using the classical approach and three using the
HRiD approach, all together containing 34 annotated genes. High
repeatability (86%) of results was observed, as 12 identified selection
signals were also confirmed in other studies with sheep. HRiD offers an
interesting possibility to be used complementary to other approaches or
when only males are genotyped, which is often the case in genomic breeding
value estimations. These results highlight the importance of the
X-chromosome in the adaptive architecture of domestic ruminants, while our
novel HRiD approach opens new possibilities for research.
110 views reported since publication in 2022.