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当前位置: 首页 > 文章 > A review of the pangenome: how it affects our understanding of genomic variation, selection and breeding in domestic animals? 畜牧与生物技术杂志(英文版) 2023,14 (1)
Position: Home > Articles > A review of the pangenome: how it affects our understanding of genomic variation, selection and breeding in domestic animals? Journal of Animal Science and Biotechnology 2023,14 (1)

A review of the pangenome: how it affects our understanding of genomic variation, selection and breeding in domestic animals?

作  者：
Ya‐Jun Gong;Yefang Li;Xuexue Liu;Yue Ma;Lin
单  位：
Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China;Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China;Centre d’Anthropobiologie et de Génomique de Toulouse, Université Paul Sabatier, Toulouse, France;Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, Chin
关键词：
Breeding;Domestic animals;Pangenome;Structural variation
摘  要：
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.

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