INRAE, ASSET, 97170, Petit-Bourg, France.
Institut National de la Recherche Agronomique de Tunisie, Laboratoire des Productions Animales et Fourragères, Université de Carthage, 2049, Ariana, Tunisia.
PLoS One. 2024 Aug 26;19(8):e0309411. doi: 10.1371/journal.pone.0309411. eCollection 2024.
Structural variants play an important role in evolutionary processes. Besides, they constitute a large source of inter individual genetic variation that might represent a major factor in the aetiology of complex, multifactorial traits. Their importance in adaptation is becoming increasingly evident in literature. Yet, the characterization of the genomic landscape of structural variants in local breeds remains scarce to date. Herein, we investigate patterns and gene annotation of structural variants in the Creole cattle from Guadeloupe breed using whole genome sequences from 23 bulls representative of the population. In total, we detected 32821 ascertained SV defining 15258 regions, representing ~ 17% of the Creole cattle genome. Among these, 6639 regions have not been previously reported in the Database of Genomic Variants archive. Average number of structural variants detected per individual in the studied population is in the same order of magnitude of that observed in indicine populations and higher than that reported in taurine breeds. We observe an important within-individual variability where approximately half of the detected structural variants have low frequency (MAF < 0.25). Most of the detected structural variants (55%) occurred in intergenic regions. Genic structural variants overlapped with 7793 genes and the predicted effect of most of them is ranked as "modifier". Among the structural variants that were predicted to have a high functional impact on the protein, a 5.5 Kb in length, highly frequent deletion on chromosome 2, affects ALPI, a gene associated with the interaction between gut microbiota and host immune system. The 6639 newly identified structural variants regions include three deletions and three duplications shared by more than 80% of individuals that are significantly enriched for genes related to tRNA threonylcarbamoyladenosine metabolic process, important for temperature adaptation in thermophilic organisms, therefore suggesting a potential role in the thermotolerance of Creole cattle from Guadeloupe cattle to tropical climate. Overall, highly frequent structural variants that are specific to the Creole cattle population encompass olfactory receptor and immunity genes as well as genes involved in muscle tone, muscle development and contraction. Beyond mapping and characterizing structural variants in the Creole cattle from Guadeloupe breed, this study provides valuable information for a better understanding of the potential role of chromosomal rearrangements in adaptive traits in cattle.
结构变异在进化过程中起着重要作用。此外，它们构成了个体间遗传变异的主要来源，可能是复杂多因素性状发病机制的主要因素。它们在适应中的重要性在文献中变得越来越明显。然而，迄今为止，地方品种结构变异的基因组景观特征仍然很少。在此，我们使用代表该种群的 23 头公牛的全基因组序列，研究了瓜德罗普克里奥尔牛的结构变异模式和基因注释。总共检测到 32821 个确定的 SV，定义了 15258 个区域，占克里奥尔牛基因组的约 17%。其中，6639 个区域以前未在基因组变异数据库中报道过。在所研究的种群中，每个个体检测到的结构变异数量与在印度牛种群中观察到的数量相当，高于在瘤牛品种中报告的数量。我们观察到个体内的重要变异性，大约一半的检测到的结构变异具有低频率（MAF<0.25）。大多数检测到的结构变异（55%）发生在基因间区域。基因结构变异与 7793 个基因重叠，其中大多数的预测效应被归类为“修饰剂”。在预测对蛋白质有高功能影响的结构变异中，2 号染色体上的一个 5.5 Kb 长度的高频缺失影响了 ALPI，该基因与肠道微生物群与宿主免疫系统的相互作用有关。新鉴定的 6639 个结构变异区域包括三个缺失和三个在超过 80%的个体中共享的重复，这些个体显著富集了与 tRNA 苏氨酰碳酰腺苷代谢过程相关的基因，这对于嗜热生物的温度适应很重要，因此表明在瓜德罗普克里奥尔牛对热带气候的耐热性方面可能具有潜在作用。总的来说，克里奥尔牛种群特有的高频结构变异包括嗅觉受体和免疫基因，以及涉及肌肉张力、肌肉发育和收缩的基因。除了对瓜德罗普克里奥尔牛的结构变异进行映射和特征描述外，这项研究还为更好地理解染色体重排在牛的适应性特征中的潜在作用提供了有价值的信息。
