DOI: 10.5061/dryad.hdr7sqvkk
title: Data from: Identification of selection signals on the X-chromosome in East Adriatic sheep: a new complementary approach

description: 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.
description: All sampled sheep were raised in Croatia by registered breeders
 who provided information on their origin and the exact location of the
 farms. Sampling of close relatives (parents with offspring and full or
 half siblings) was avoided. Skin tissue samples from the ear were
 collected as part of the regular sampling of local autochthonous breeds by
 the National Gene Bank, from which DNA was isolated using a commercial kit
 (DNeasy Blood and Tissue Kits, Qiagene, Germany). Genotyping of 212
 individuals was performed using the Ovine Infinium® HD SNP BeadChip 600K
 (606 006 SNPs). This dataset includes 10 mouflons from Rab island and all
 native sheep breeds (8) from the East Adriatic part of Croatia: Istrian
 sheep (25), Cres Island sheep (20), Pag Island sheep (45), Krk Island
 sheep (20), Rab Island sheep (20), Lika Pramenka (20), Dalmatian Pramenka
 (26), and Dubrovnik Ruda (26). The following quality
 control steps were performed. Only SNPs of the X-chromosome according to
 the Oar v4.0 reference sheep genome were included. All SNPs with
 questionable quality (GenTrain score &lt;0.4, GenCall score
 &lt;=0.8, call rate &lt;90%, and SNPs that deviated from
 Hardy-Weinberg equilibrium with P&lt;10<sup>-7</sup>) and
 one Dalmatian Pramenka ram with call rate &lt;95% were excluded. The
 remaining data set included 18,983 SNPs genotyped in 201 sheep individuals
 (100 males and 101 females) and 10 mouflons.