Genome-wide selection signatures in Ramlıç sheep identified by complementary ROH and iHS analyses.
- 1Department of Animal Science, Faculty of Veterinary Medicine, Afyon Kocatepe University, Afyonkarahisar, Türkiye.
- 2Department of Medical Biology and Genetics, Faculty of Veterinary Medicine, Afyon Kocatepe University, Afyonkarahisar, Türkiye.
Abstract
Introduction
Ramlıç is a composite sheep breed developed in Türkiye through crossbreeding between Rambouillet and Dağlıç sheep followed by selection for economically important traits. This study aimed to characterize genomic autozygosity and identify putative selection signatures in Ramlıç sheep by integrating runs of homozygosity (ROH) and integrated haplotype score (iHS) analyses.Methods
A total of 96 animals were genotyped using the Illumina OvineSNP50K BeadChip, and 44,171 autosomal SNPs were retained after quality control.Results
Overall, 1,956 ROH segments were identified, with an average of 20.38 ROH per individual and a mean ROH-based genomic inbreeding coefficient (FROH of 4.57%). Short-to-intermediate ROH predominated, with segments of 2-<8 Mb accounting for approximately 78% of all detected ROH. Genome-wide analysis identified 66 ROH islands, with the highest maximum ROH incidence observed on OAR6. Haplotype-based analysis identified 48 candidate 500-kb windows containing at least three SNPs exceeding the empirical top 1% |iHS| threshold. Integrating both approaches revealed 15 concordant ROH-iHS regions on OAR1, OAR2, OAR6, and OAR11. The most prominent concordance was observed on OAR6 at 36.5-38.0 Mb, where the ROH island with the highest maximum incidence coincided with a cluster of extreme |iHS| signals and encompassed candidate genes including ABCG2, SPP1, MEPE, LAP3, and NCAPG, which have previously been associated with economically relevant traits in sheep.Discussion
These findings provide new insights into genomic autozygosity and the potential selection history of Ramlıç sheep and highlight candidate regions that warrant further investigation in larger populations using higher-resolution genomic data and functional validation.
Related
- Genomic signatures of selection in Dazu Black goat (Capra hircus) revealed by whole-genome resequencing
- Genome-wide scans between two honeybee populations reveal putative signatures of human-mediated selection
- Genomic inbreeding and selection signatures analyses in the Doberman Pinscher breed
- Genome-wide selection signatures in Turkish Awassi sheep: uncovering the genetic basis of production traits and adaptation.
- Whole-genome sequencing reveals divergent and shared selection signatures of heat stress adaptation in indigenous Ethiopian zebu cattle from dry-hot and humid-hot environments
BibTeX
@article{eser2026genomewide,
title = {{Genome-wide selection signatures in Ramlıç sheep identified by complementary ROH and iHS analyses.}},
author = {Orhan Eser and Mustafa Tekerli and Mustafa Demirtaş and Samet Çinkaya and Eda Demirtaş and Metin Erdoğan and Koray Çelikeloğlu},
journal = {Frontiers in veterinary science},
year = {2026},
month = oct,
doi = {10.3389/fvets.2026.2009151},
url = {https://europepmc.org/article/MED/42948655},
note = {CC BY},
}
RIS
TY - JOUR
TI - Genome-wide selection signatures in Ramlıç sheep identified by complementary ROH and iHS analyses.
AU - Orhan Eser
AU - Mustafa Tekerli
AU - Mustafa Demirtaş
AU - Samet Çinkaya
AU - Eda Demirtaş
AU - Metin Erdoğan
AU - Koray Çelikeloğlu
PY - 2026
DA - 2026/10/13
JO - Frontiers in veterinary science
DO - 10.3389/fvets.2026.2009151
UR - https://europepmc.org/article/MED/42948655
AB - Introduction Ramlıç is a composite sheep breed developed in Türkiye through crossbreeding between Rambouillet and Dağlıç sheep followed by selection for economically important traits. This study aimed to characterize genomic autozygosity and identify putative selection signatures in Ramlıç sheep by integrating runs of homozygosity (ROH) and integrated haplotype score (iHS) analyses.Methods A total of 96 animals were genotyped using the Illumina OvineSNP50K BeadChip, and 44,171 autosomal SNPs were retained after quality control.Results Overall, 1,956 ROH segments were identified, with an average of 20.38 ROH per individual and a mean ROH-based genomic inbreeding coefficient (FROH of 4.57%). Short-to-intermediate ROH predominated, with segments of 2-<8 Mb accounting for approximately 78% of all detected ROH. Genome-wide analysis identified 66 ROH islands, with the highest maximum ROH incidence observed on OAR6. Haplotype-based analysis identified 48 candidate 500-kb windows containing at least three SNPs exceeding the empirical top 1% |iHS| threshold. Integrating both approaches revealed 15 concordant ROH-iHS regions on OAR1, OAR2, OAR6, and OAR11. The most prominent concordance was observed on OAR6 at 36.5-38.0 Mb, where the ROH island with the highest maximum incidence coincided with a cluster of extreme |iHS| signals and encompassed candidate genes including ABCG2, SPP1, MEPE, LAP3, and NCAPG, which have previously been associated with economically relevant traits in sheep.Discussion These findings provide new insights into genomic autozygosity and the potential selection history of Ramlıç sheep and highlight candidate regions that warrant further investigation in larger populations using higher-resolution genomic data and functional validation.
SN - 2297-1769
ER -