Akademik Veri Yönetim Sistemi
Small Ruminant Research, cilt.257, 2026 (SCI-Expanded, Scopus)
The detection of genetic variants that lead to differentiation in terms of morphological, psychological, and behavioral traits within a specific population enables the design of comprehensive characterization, conservation, and selection strategies in livestock. This study aimed to evaluate the usefulness of genetic data obtained from the double digest restriction-site associated DNA sequencing (ddRADseq) technique in the discovery of genetic variants at three levels of depth of coverage (DP), including 2, 5, and 10. Via genotyping 21 animals belonging to Pırlak sheep, a higher number of single nucleotide polymorphisms (SNPs) (ranging from 869,471 to 1204,553) than insertion–deletions (InDels) (varying between 73,762 and 88,327) were identified in the sheep genome depending on the DP criterion. Despite the high number of genetic variants identified across the genome, the annotation survey validated that a small percentage of variants (ranging from 0.009 in DP2 and 0.001 in DP5 and DP10) were of high functional impact on phenotype. Moreover, 544,154 SNPs were novel at DP 10, indicating that ddRADseq is promising for screening population-specific variants in sheep. Further analyses validated that 44 SNPs categorized as high functional impact overlapped with 43 genes, which were previously reported to be associated with reproduction (TRNAC-GCA, ATG10, TRNAS-GGA, and ANKRD31) and milk traits (SLC50A1, THSD7B, and VPS37C) in various mammalian species. Moreover, genetic diversity parameters showed observed heterozygosity (HO = 0.333) slightly higher than expected heterozygosity (HE = 0.328), with an inbreeding coefficient of FIS = -0.018. Compared to whole genome sequencing and array technologies, the ddRADseq was shown to be an alternative technique to identify genetic variants for further genomic studies due to its specific advantages, such as being cost-efficient and not having bias for the detection of population-specific variants. Genetic variants identified by the ddRADseq technique are promising to improve ongoing molecular characterization, conservation, and breeding programs via various genomic studies, such as genetic variability, genome-wide association studies, and selection signatures.