Genomic Diversity and Footprints of Selection in Hamdani Sheep

This study aimed to characterize the genomic diversity, population structure, and candidate regions consistent with selection in Hamdani (HAM) sheep using high-density SNP generated by double-digest restriction site-associated DNA sequencing (ddRADseq). A total of 20 animals were sampled, and after quality filtering, 310,663 SNPs from 18 individuals were retained for downstream analyses. Genetic diversity parameters indicated a relatively high level of genomic variation within the breed (H_O = 0.323 ± 0.01 and H_E = 0.326 ± 0.01) and low levels of inbreeding (F_HOM = 0.029 ± 0.02 and F_ROH = 0.008 ± 0.01), suggesting that the population has maintained substantial genetic diversity and has not experienced recent intensive inbreeding. Population structure analyses revealed that HAM sheep form a distinct genetic cluster separated from Turkish fat-tailed breeds, reflecting their unique genetic background and breeding history. Footprints of selection analyses based on runs of homozygosity (ROH) and integrated haplotype score (iHS) identified preliminary candidate genomic regions consistent with selection. After FDR correction, 12 of the 34 trait-chromosome combinations tested for the iHS-derived regions and three of the eight combinations tested for the ROH-derived regions were significantly enriched. Functional annotation highlighted biologically relevant candidate genes involved in reproductive performance (TSHR, FSHR, and LHCGR), lipid metabolism (ABCG1 and LPIN1), and environmental adaptation (LACC1 and MBOAT7). This ddRADseq-based genome-wide characterization provides preliminary information on genetic variability and candidate genomic regions consistent with selection in HAM sheep. Therefore, further studies focusing on a larger sampling strategy across multiple different sheep breeds are needed to design conservation, breeding, and future genomic selection programs.