Oligo-FISH-Based Analysis of the Mechanisms Underlying Chromosome Number Variation in Saccharum spontaneum

Interspecific hybridization serves as a crucial strategy for innovating sugarcane germplasms. Currently, nearly all modern sugarcane varieties that incorporate genetic material are derived from Saccharum spontaneum. The number of chromosomes in S. spontaneum ranges from 40 to 128, contributing significantly to the diversity of its genetic resources. However, the genetic mechanisms driving chromosome number variation in S. spontaneum remain to be fully elucidated. Here, oligonucleotide fluorescence in situ hybridization (Oligo-FISH) was conducted to identify individual chromosomes and explore chromosome transmission during the intraspecific hybridization of S. spontaneum. The results indicate that from the progenies generated from S. spontaneum Yunnan2017-22 (2n = 8x = 64) and Yunnan82-1 (2n = 8x = 64) emerged two distinct karyotypes, 2n = 12x = 96 (A1) and 2n = 8x = 64 (A2, A33-1, A18). This implies that the chromosome inheritances were 2n + n and n + n in the progenies. However, self-pollinated samples of A1 (2n = 12x = 96) produced normal offspring C1 (2n = 94) and C2 (2n = 96). The 2n + n inheritance pattern did not continue. In another cross, the progenies derived from S. spontaneum Yunnan2017-41 (2n = 8x = 64) and Yunnan8 (2n = 10x = 80) carried a karyotype of 2n = 9x = 72, with n + n inheritance mode. These findings highlight the existence of two chromosome inheritance modes, 2n + n and n + n, in the context of the intraspecific hybridization of S. spontaneum. Additionally, hybridization between different ploidy S. spontaneum was also accompanied by chromosomal translocations (A1, A2, A18, A18) and loss (A2, A33-1, AA-4, and C2) that further resulted in the complexity of the S. spontaneum genome. Together, these findings highlight diverse chromosome inheritance in S. spontaneum hybridization, and provide a theoretical foundation for the further utilization of S. spontaneum germplasm in sugarcane breeding.