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Background  In recent years, sugarcane has attracted increasing attention as an energy crop. Wild resources are widely used to improve the narrow genetic base of sugarcane. However, the infertility of F 1  hybrids between  Saccharum officinarum  ( S. officinarum ) and  Erianthus arundinaceus  ( E. arundinaceus ) has hindered sugarcane breeding efforts. To discover the cause of this infertility, we studied the hybridization process from a cytological perspective.    Results  We examined the meiotic process of pollen mother cells (PMCs) in three F 1  hybrids between  S. officinarum  and  E. arundinaceus . Cytological analysis showed that the male parents, Hainan 92–77 and Hainan 92–105, had normal meiosis. However, the meiosis process in F 1  hybrids showed various abnormal phenomena, including lagging chromosomes, micronuclei, uneven segregation, chromosome bridges, and inability to form cell plates. Genomic in situ hybridization (GISH) showed unequal chromatin distribution during cell division. Interestingly, 96.70% of lagging chromosomes were from  E. arundinaceus . Furthermore, fluorescence in situ hybridization (FISH) was performed using 45S rDNA and 5S rDNA as probes. Either 45S rDNA or 5S rDNA sites were lost during abnormal meiosis, and results of unequal chromosomal separation were also clearly observed in tetrads.    Conclusions  Using cytogenetic analysis, a large number of meiotic abnormalities were observed in F 1 . GISH further confirmed that 96.70% of the lagging chromosomes were from  E. arundinaceus . Chromosome loss was found by further investigation of repeat sequences. Our findings provide insight into sugarcane chromosome inheritance to aid innovation and utilization in sugarcane germplasm resources.    Supplementary Information  The online version contains supplementary material available at 10.1186/s12870-021-02911-z.

Chromosome behavior during meiosis in pollen mother cells from Saccharum officinarum × Erianthus arundinaceus F1 hybrids