随着大规模基因组研究的进展,已经发现,单个参考基因组模式不能代表物种水平的遗传多样性。虽然家畜往往有复杂的起源和迁徙路线,这表明当前参考基因组中可能遗漏了一些群体特异性序列。相反,pangenome是一个物种的所有DNA序列的集合,包含所有个体共有的序列(核心基因组),并且还能够显示每个个体独特的序列信息(可变基因组)。人类pangenome研究的进展,植物和家畜已经证明,缺失的遗传成分和大型结构变异(SV)的鉴定可以通过全基因组研究来探索。许多个体特异性序列已被证明与生物适应性有关,表型和重要经济性状。第三代测序等技术和方法的成熟,端粒到端粒基因组,图形基因组,无参考组装将进一步促进pangenome的发展。在未来,pangenome结合长读数据和多组学将有助于解决大型SV及其与驯养动物感兴趣的主要经济性状的关系,为动物驯化提供更好的见解,进化和繁殖。在这次审查中,我们主要讨论pangenome分析如何揭示家畜(绵羊,牛,猪,鸡)及其对表型的影响,以及这如何有助于理解物种多样性。此外,我们还讨论了牲畜和家禽pangenome研究的潜在问题和未来前景。
As large-scale genomic studies have progressed, it has been revealed that a single reference genome pattern cannot represent genetic diversity at the species level. While domestic animals tend to have complex routes of origin and migration, suggesting a possible omission of some population-specific sequences in the current reference genome. Conversely, the
pangenome is a collection of all DNA sequences of a species that contains sequences shared by all individuals (core genome) and is also able to display sequence information unique to each individual (variable genome). The progress of
pangenome research in humans, plants and domestic animals has proved that the missing genetic components and the identification of large structural variants (SVs) can be explored through pangenomic studies. Many individual specific sequences have been shown to be related to biological adaptability, phenotype and important economic traits. The maturity of technologies and methods such as third-generation sequencing, Telomere-to-telomere genomes, graphic genomes, and reference-free assembly will further promote the development of pangenome. In the future,
pangenome combined with long-read data and multi-omics will help to resolve large SVs and their relationship with the main economic traits of interest in domesticated animals, providing better insights into animal domestication, evolution and breeding. In this
review, we mainly discuss how
pangenome analysis reveals genetic variations in domestic animals (sheep, cattle, pigs, chickens) and their impacts on phenotypes and how this can contribute to the understanding of species diversity. Additionally, we also go through potential issues and the future perspectives of
pangenome research in livestock and poultry.