Pangenomics combined with artificial intelligence and precision breeding can accelerate crop improvement

Pangenomics significantly expands our understanding of genetic diversity in plants beyond single reference genomes by capturing extensive genomic variations. In this review, we discuss recent methodological breakthroughs in pangenomics, including advances in long-read sequencing, graph-based pangenome tools, artificial intelligence, and multiomics approaches that have collectively enabled pangenomes to become more accurate and prevalent. We review the broad applications of pangenomics in plant science, particularly focusing on crop breeding, including haplotype-based selection, improved prediction for genomic selection, multiomics guided marker discovery, precise identification of genome-editing targets, association of genes with agronomic traits, understanding transposable element dynamics, and providing valuable insights to guide crop improvement. Furthermore, we discuss current challenges and future directions for pangenomics studies.