All nonhomologous chromosomes and rearrangements in × allopolyploids identified by oligo-based painting.

Modern sugarcane cultivars ( spp., 2 = 100~120) are complex polyploids primarily derived from interspecific hybridization between and . Nobilization is the theory of utilizing wild germplasm in sugarcane breeding, and is the foundation for utilizing for stress resistance. However, the exact chromosomal transmission remains elusive due to a lack of chromosome-specific markers. Here, we applied chromosome-specific oligonucleotide (oligo)-based probes for identifying chromosomes 1-10 of the F hybrids between and . Then, -specific repetitive DNA probes were used to distinguish in these hybrids. This oligo- fluorescence hybridization (FISH) system proved to be an efficient tool for revealing individual chromosomal inheritance during nobilization. We discovered the complete doubling of derived chromosomes in most F hybrids. Notably, we also found defective -derived chromosome doubling in the F hybrid Yacheng75-4191, which exhibited 1.5n transmission for all nonhomologous chromosomes. Altogether, these results highlight the presence of variable chromosome transmission in nobilization between and , including 1.5n + n and 2n + n. These findings provide robust chromosome markers for in-depth studies into the molecular mechanism underlying chromosome doubling during the nobilization, as well as tracing chromosomal inheritance for sugarcane breeding.