ORIGINAL RESEARCH article
Front. Genet.
Sec. Livestock Genomics
Volume 16 - 2025 | doi: 10.3389/fgene.2025.1646127
Comaparative genome-wide analysis of Ovis aries of Saudi Arabia highlighting inbreeding and genetic isolation of Najdi sheep breed
Provisionally accepted
Abdulrahman K. Aldawish1,2,3
Mohanad A. Ibrahim3,4
Faisal M. Alsubaie1,2,3
QUAISER SAQUIB1
Mohammed Fahad Albeshr1*- 1Zoology Department, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Riyadh, Saudi Arabia
- 2National Livestock and Fisheries Development Program, Riyadh, Saudi Arabia
- 3Ministry of Environment, Water, and Agriculture (MEWA), Riyadh, Saudi Arabia
- 4Data Science Program, King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
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Sheep (Ovis aries) farming through traditional practices play vital role in the socioeconomic development of Kingdom of Saudi Arabia (KSA). Genetic relationships among KSA sheep breeds remain poorly characterized. In this study, we performed comparative genome-wide single-nucleotide polymorphism (SNPs) of three sheep breeds (Najdi, Naemi, Harri) to evaluate their genetic diversity. Blood samples from 95 individuals were genotyped using Ovine SNP50 BeadChip, generating 34026 highquality SNPs. Minor allele frequency (MAF) distribution revealed the highest genetic diversity in Naemi, followed by Harri and Najdi. ROH-based inbreeding coefficient (FROH) identified Najdi as the most inbred (FROH = 0.053), indicating its historical isolation, while Naemi displayed minimal recent inbreeding (FROH = 0.003).Heterozygosity-based inbreeding coefficient (FIS) was maxim for Najdi (FIS = 0.092) followed by Harri (FIS = 0.027) indicating greater level of inbreeding, while Naemi (FIS = -0.055) showed more outbreeding level. Principal Component (PC) and admixture distinctly separated Najdi from the other two breeds, reflecting its unique genetic identity. Wright's Fixation Index (FST) further affirmed genetic differentiation between Najdi and Naemi. Moreover, 336 high-FST SNPs were identified that were linked with breed-specific genetic signatures. Our study reveals genetic diversity among local breeds, and highlight the conservation efforts for Najdi sheep.
Keywords: Ovis aries, Najdi, naemi, harri, SNP genotyping, genetic diversity
Received: 12 Jun 2025; Accepted: 29 Jul 2025.
Copyright: © 2025 Aldawish, A. Ibrahim, Alsubaie, SAQUIB and Albeshr. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence: Mohammed Fahad Albeshr, Zoology Department, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Riyadh, Saudi Arabia
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