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Data from: Identification of selection signals on the X-chromosome in East Adriatic sheep: a new complementary approach

Citation

Shihabi, Mario et al. (2022), Data from: Identification of selection signals on the X-chromosome in East Adriatic sheep: a new complementary approach, Dryad, Dataset, https://doi.org/10.5061/dryad.hdr7sqvkk

Abstract

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.

Methods

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 <0.4, GenCall score <=0.8, call rate <90%, and SNPs that deviated from Hardy-Weinberg equilibrium with P<10-7) and one Dalmatian Pramenka ram with call rate <95% were excluded. The remaining data set included 18,983 SNPs genotyped in 201 sheep individuals (100 males and 101 females) and 10 mouflons.

Funding

Croatian Science Foundation, Award: IP-2018-01-8708

Operational Program for Competitiveness and Cohesion, Award: KK.01.1.1.04.0058