Kusza Szilvia, Badaoui Bouabid, Wanjala George
Faculty of Agricultural and Food Sciences and Environmental Management, Centre for Agricultural Genomics and Biotechnology, University of Debrecen, Egyetem tér 1., 4032, Debrecen, Hungary.
Faculty of Sciences, Centre de Biotechnologies Végétales et Microbiennes, Biodiversité et Environnement, Mohammed V University in Rabat, Rabat, Morocco.
Sci Rep. 2024 Jul 17;14(1):16515. doi: 10.1038/s41598-024-67558-w.
Numerous studies have indicated that Morocco's indigenous sheep breeds are genetically homogenous, posing a risk to their survival in the challenging harsh climate conditions where they predominantly inhabit. To understand the genetic behind genetic homogeneity through the lens of runs of homozygosity (ROH), we analyzed the whole genome sequences of five indigenous sheep breeds (Beni Guil, Ouled Djellal, D'man, Sardi, Timahdite and Admixed).The results from principal component, admixture, Fst, and neighbour joining tree analyses consistently showed a homogenous genetic structure. This structure was characterized by an average length of 1.83 Mb for runs of homozygosity (ROH) segments, with a limited number of long ROH segments (24-48 Mb and > 48 Mb). The most common ROH segments were those ranging from 1-6 Mb. The most significant regions of homozygosity (ROH Islands) were mostly observed in two chromosomes, namely Chr1 and Chr5. Specifically, ROH Islands were exclusively discovered in the Ouled Djellal breed on Chr1, whereas Chr5 exhibited ROH Islands in all breeds. The analysis of ROH Island and iHS technique was employed to detect signatures of selection on Chr1 and Chr5. The results indicate that Chr5 had a high level of homogeneity, with the same genes being discovered across all breeds. In contrast, Chr1 displays some genetic variances between breeds. Genes identified on Chr5 included SLC39A1, IL23A, CAST, IL5, IL13, and IL4 which are responsible for immune response while genes identified on Chr1 include SOD1, SLAMF9, RTP4, CLDN1, and PRKAA2. ROH segment profile and effective population sizes patterns suggests that the genetic uniformity of studied breeds is the outcome of events that transpired between 250 and 300 generations ago. This research not only contributes to the understanding of ROH distribution across breeds but helps design and implement native sheep breeding and conservation strategies in Morocco. Future research, incorporating a broader sample size and utilizing the pangenome for reference, is recommended to further elucidate these breeds' genomic landscapes and adaptive mechanisms.
众多研究表明，摩洛哥本土绵羊品种在基因上具有同质性，这对它们在主要栖息的具有挑战性的恶劣气候条件下的生存构成了风险。为了通过纯合子连续片段（ROH）来理解基因同质性背后的遗传学原理，我们分析了五个本土绵羊品种（贝尼吉尔、乌尔德杰拉尔、德芒、萨尔迪、蒂马赫迪特和混合品种）的全基因组序列。主成分分析、混合分析、Fst分析和邻接树分析的结果一致显示出基因结构的同质性。这种结构的特征是纯合子连续片段（ROH）的平均长度为1.83兆碱基，长ROH片段数量有限（24 - 48兆碱基和>48兆碱基）。最常见的ROH片段是1 - 6兆碱基范围的那些。纯合性最显著的区域（ROH岛）大多出现在两条染色体上，即1号染色体和5号染色体。具体而言，仅在乌尔德杰拉尔品种的1号染色体上发现了ROH岛，而5号染色体在所有品种中都显示有ROH岛。采用ROH岛分析和iHS技术来检测1号染色体和5号染色体上的选择特征。结果表明，5号染色体具有高度同质性，在所有品种中发现了相同的基因。相比之下，1号染色体在品种间显示出一些基因差异。在5号染色体上鉴定出的基因包括SLC39A1、IL23A、CAST、IL5、IL13和IL4，它们负责免疫反应，而在1号染色体上鉴定出的基因包括SOD1、SLAMF9、RTP4、CLDN1和PRKAA2。ROH片段图谱和有效种群大小模式表明，所研究品种的基因一致性是250至300代之前发生的事件的结果。这项研究不仅有助于理解ROH在各品种间的分布，还有助于设计和实施摩洛哥本土绵羊的育种和保护策略。建议未来的研究纳入更广泛的样本量并利用泛基因组作为参考，以进一步阐明这些品种的基因组景观和适应机制。
