From genome editing to chromosome engineering in plants

Engineering large genomic segments is rapidly expanding the scope of plant genome manipulation from individual genes to chromosome-scale redesign. Recent advances in double-strand break-, prime-editing-, recombinase-, and transposase-based technologies now enable programmable deletion, insertion, replacement, duplication, inversion, and translocation of DNA fragments ranging from kilobases to megabases. In this review, we summarize the major strategies for large-fragment genome engineering in plants, compare their strengths and limitations, and discuss their applications in both fundamental plant biology and crop breeding. We further highlight that the integration of artificial intelligence is catalyzing the rapid optimization of large-fragment genome engineering. The ongoing transition from genome editing to chromosome engineering promises to revolutionize crop breeding and plant synthetic biology, ultimately enabling rational design of plant genomes.