Intergeneric chromosome-specific painting reveals differential chromosomal transmission from Tripidium arundinaceum in sugarcane progeny

Sugarcane has recently attracted increased attention for its potential as a source of sugar and bioethanol, and increasing its yields is essential to ensure the sugar security and bioenergy production. Intergeneric hybridization is a highly efficient method to produce new genetic variants of crop plants, particularly those species with high ploidy such as sugarcane (Saccharum spp.). Tripidium arundinaceum exhibits many desirable agronomic traits, and has been widely studied to produce hybrid with improved stress tolerance and other characteristics in sugarcane breeding. However, the genetic relationship between T. arundinaceum and Saccharum species, and the individual T. arundinaceum chromosomal composition in sugarcane hybrids are still elusive. Here we used whole-genome single-nucleotide polymorphisms (SNPs) to ascertain the phylogenetic relationships between these species and found that T. arundinaceum was more closely related to Saccharum than Sorghum, in contrast to the previous narrow genetic analyses utilizing chloroplast DNA. Additionally, oligonucleotide (oligo)-based chromosome-specific painting derived from Saccharum officinarum was found to be able to distinctly identify the chromosomes of T. arundinaceum. We developed the oligo- genomic in situ hybridization (GISH) system, for the first time, to unveil the novel chromosome translocations and the individual chromosomal transmission of T. arundinaceum in sugarcane progeny. Notably, we discovered the chromosomal transmission of T. arundinaceum exhibited several inheritances, including n, 2n, and over 2n in BC1 progenies. Such inheritances may be resulted from the first division restitution (FDR), FDR + nondisjunction of a chromosome with sister chromatids in the second meiosis division/second division restitution (FDR + NSC/SDR) model during meiosis. These results will be of substantial benefit in further selection of T. arundinaceum chromosome for sugarcane genetic improvement.