Abstract
A pangenome encompasses the complete genetic diversity of a species, by assembling a range of representative individuals from various populations. This review describes the advances in plant pangenomics, tracing its evolution since the initial plant genome sequencing in 2000, and provides comprehensive best-practice advice to build a linear or graphical pangenome, delineating the strengths and limitations of different pangenome construction methods. The review also examines the challenges in pangenome data visualisation, the challenges of graph-based pangenomes and their utility in investigating the potential function of genome variation. Furthermore, we examine the application of pangenomes in plant breeding, including the identification of genetic diversity for crop improvement, and the integration of multi-omics data into pangenome databases to advance plant breeding.
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