College of Animal Science and Technology, Hunan Agricultural University, Changsha, China.
Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, Changsha, China.
Mol Ecol Resour. 2023 Oct;23(7):1656-1672. doi: 10.1111/1755-0998.13818. Epub 2023 May 31.
Understanding the genetic variations of the horse (Equus caballus) genome will improve breeding conservation and welfare. However, genetic variations in long segments, such as structural variants (SVs), remain understudied. We de novo assembled 10 chromosome-level three-dimensional horse genomes, each representing a distinct breed, and analysed horse SVs using a multi-assembly approach. Our findings suggest that SVs with the accumulation of mammalian-wide interspersed repeats related to long interspersed nuclear elements might be a horse-specific mechanism to modulate genome-wide gene regulatory networks. We found that olfactory receptors were commonly loss and accumulated deleterious mutations, but no purge of deleterious mutations occurred during horse domestication. We examined the potential effects of SVs on the spatial structure of chromatin via topologically associating domains (TADs). Breed-specific TADs were significantly enriched by breed-specific SVs. We identified 4199 unique breakpoint-resolved novel insertions across all chromosomes that account for 2.84 Mb sequences missing from the reference genome. Several novel insertions might have potential functional consequences, as 519 appeared to reside within 449 gene bodies. These genes are primarily involved in pathogen recognition, innate immune responses and drug metabolism. Moreover, 37 diverse horses were resequenced. Combining this with public data, we analysed 97 horses through a comparative population genomics approach to identify the genetic basis underlying breed characteristics using Thoroughbreds as a case study. We provide new scientific evidence for horse domestication, an understanding of the genetic mechanism underlying the phenotypic evolution of horses, and a comprehensive genetic variation resource for further genetic studies of horses.
理解马（Equus caballus）基因组的遗传变异将提高其繁殖保护和福利。然而，长片段的遗传变异，如结构变异（SVs），仍未得到充分研究。我们从头组装了 10 个染色体水平的三维马基因组，每个基因组代表一个不同的品种，并使用多组装方法分析了马的 SVs。我们的研究结果表明，积累了与长散布核元件相关的哺乳动物广泛散布重复的 SVs 可能是调节全基因组基因调控网络的马特异性机制。我们发现嗅觉受体通常会丢失和积累有害突变，但在马驯化过程中没有清除有害突变。我们通过拓扑关联域（TAD）检查了 SVs 对染色质空间结构的潜在影响。品种特异性 TADs 被品种特异性 SVs 显著富集。我们在所有染色体上鉴定了 4199 个独特的断点解析新插入，这些插入共占参考基因组缺失的 2.84 Mb 序列。一些新的插入可能具有潜在的功能后果，因为 519 个似乎位于 449 个基因体内。这些基因主要参与病原体识别、先天免疫反应和药物代谢。此外，我们对 37 匹不同的马进行了重测序。结合公共数据，我们通过比较群体基因组学方法分析了 97 匹马，以确定以纯血马为例的品种特征的遗传基础。我们为马的驯化提供了新的科学证据，为理解马表型进化的遗传机制提供了依据，并为进一步的马遗传研究提供了全面的遗传变异资源。
