Liu Jiaxin, Shi Yilong, Mo Dongxin, Luo Lingyun, Xu Songsong, Lv Fenghua
Frontiers Science Center for Molecular Design Breeding (MOE); State Key Laboratory of Animal Biotech Breeding; College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
J Anim Sci Biotechnol. 2024 Oct 5;15(1):132. doi: 10.1186/s40104-024-01092-7.
Unveiling genetic diversity features and understanding the genetic mechanisms of diverse goat phenotypes are pivotal in facilitating the preservation and utilization of these genetic resources. However, the total genetic diversity within a species can't be captured by the reference genome of a single individual. The pan-genome is a collection of all the DNA sequences that occur in a species, and it is expected to capture the total genomic diversity of the specific species.
We constructed a goat pan-genome using map-to-pan assemble based on 813 individuals, including 723 domestic goats and 90 samples from their wild relatives, which presented a broad regional and global representation. In total, 146 Mb sequences and 974 genes were identified as absent from the reference genome (ARS1.2; GCF_001704415.2). We identified 3,190 novel single nucleotide polymorphisms (SNPs) using the pan-genome analysis. These novel SNPs could properly reveal the population structure of domestic goats and their wild relatives. Presence/absence variation (PAV) analysis revealed gene loss and intense negative selection during domestication and improvement.
Our research highlights the importance of the goat pan-genome in capturing the missing genetic variations. It reveals the changes in genomic architecture during goat domestication and improvement, such as gene loss. This improves our understanding of the evolutionary and breeding history of goats.
揭示遗传多样性特征并了解不同山羊表型的遗传机制对于促进这些遗传资源的保护和利用至关重要。然而，单个个体的参考基因组无法涵盖一个物种内的全部遗传多样性。泛基因组是一个物种中出现的所有DNA序列的集合，有望捕获特定物种的全部基因组多样性。
我们基于813个个体构建了一个山羊泛基因组，其中包括723只家山羊和90个来自其野生近缘种的样本，这些样本具有广泛的区域和全球代表性。总共鉴定出146 Mb序列和974个基因在参考基因组（ARS1.2；GCF_001704415.2）中缺失。我们通过泛基因组分析鉴定出3190个新的单核苷酸多态性（SNP）。这些新的SNP能够恰当地揭示家山羊及其野生近缘种的种群结构。存在/缺失变异（PAV）分析揭示了驯化和改良过程中的基因丢失和强烈的负选择。
我们的研究突出了山羊泛基因组在捕获缺失遗传变异方面的重要性。它揭示了山羊驯化和改良过程中基因组结构的变化，如基因丢失。这增进了我们对山羊进化和育种历史的理解。
