Chromosome painting in plants: history and future perspectives

Abstract Chromosome painting was developed in mammalian species nearly four decades ago and rapidly became a powerful tool for chromosome identification, comparative cytogenetics, and evolutionary genome analysis. Comparative chromosome painting among diverse mammals generated much of the foundational knowledge of chromosome structure, chromosomal rearrangements, and karyotype evolution before the advent of whole-genome sequencing. Although chromosome painting was first demonstrated in plants in 2001, its applications remained largely restricted to a few plant lineages until the development of oligonucleotide (oligo)-based chromosome painting in 2015. During the last decade, oligo-based chromosome painting has transformed plant cytogenetics, enabling many investigations that were previously impossible. These studies have provided new insights into meiotic chromosome pairing, crossover formation, chromosome fusion, karyotype stability, and chromosome evolution across diverse plant lineages. This review summarizes the history of technological development of chromosome painting in plants, highlights major discoveries enabled by oligo-based chromosome painting, and discusses future opportunities, particularly the integration of chromosome painting with three-dimensional chromosome and genome biology.