Sugarcane genome architecture revealed by chromosome-specific probes, implication for chromosome nomenclature

Sugarcane (Saccharum spp. hybrids) is probably the crop with the most complex genome. Modern cultivars (2n = 100–120) are highly polyploid and aneuploid, derived from interspecific hybridization between S. officinarum (2n = 80) and S. spontaneum (2n = 40–128). Based on the R570 genome sequence assembly, chromosome-specific oligo probes were designed and used in cytogenetic analysis to improve our understanding of the origin of the sugarcane genome and its architecture. The results validated a basic chromosome number of x = 10 for S. officinarum and x = 8 in most S. spontaneum. In S. spontaneum, a few accessions from North India with x = 10 and x = 9 were also identified. From a basic chromosome of x = 10, rearrangements occurred in two steps leading to x = 9 and then x = 8. Each step involved three chromosomes that were rearranged into two. Further polyploidization led to the wide geographical distribution of clones with x = 8. The S. spontaneum contribution to modern cultivars seems to originate from cytotypes with x = 8 and varies in proportion among cultivars. Modern cultivars have mainly 12 copies for each of the 10 basic chromosomes with variation between 10 and 13 copies. A few of these copies correspond to entire S. spontaneum chromosomes or interspecific recombinant chromosomes. In addition, a few inter-chromosome translocations were found. This difference in the basic chromosome number for the two species involved in cultivars led us to propose a nomenclature of the chromosomes that optimize the correspondence between the two species. This study substantially improved our understanding of the extreme complexity of the genomes of modern sugarcane cultivars.