The complex polyploid genome architecture of sugarcane.

Sugarcane, the world's most harvested crop by tonnage, has shaped global history, trade and geopolitics, and is currently responsible for 80% of sugar production worldwide. While traditional sugarcane breeding methods have effectively generated cultivars adapted to new environments and pathogens, sugar yield improvements have recently plateaued. The cessation of yield gains may be due to limited genetic diversity within breeding populations, long breeding cycles and the complexity of its genome, the latter preventing breeders from taking advantage of the recent explosion of whole-genome sequencing that has benefited many other crops.

Isolation and sequencing of a single copy of an introgressed chromosome from a complex genome for gene and SNP identification.

This manuscript describes the identification, isolation and sequencing of a single chromosome containing high value resistance genes from a complex polyploid where sequencing the whole genome is too costly. The large complex genomes of many crops constrain the use of new technologies for genome-assisted selection and genetic improvement. One method to simplify a genome is to break it into individual chromosomes by flow cytometry; however, in many crop species most chromosomes cannot be isolated individually.

GISH: Resolving Interspecific and Intergeneric Hybrids.

Genomic in situ hybridization (GISH) is an invaluable cytogenetic technique which enables the visualization of whole genomes in hybrids and polyploidy taxa. Total genomic DNA from one or two different species/genomes is used as a probe, labeled with a fluorochrome, and directly detected on mitotic chromosomes from root tip meristems. In sugarcane and sugarcane hybrids, we were able to characterize interspecific hybrids of two closely related species as well as intergeneric hybrids of two closely related genera.

Sugarcane genome architecture decrypted with chromosome-specific oligo probes.

Sugarcane (Saccharum spp.) is probably the crop with the most complex genome. Modern cultivars (2n = 100-120) are highly polyploids and aneuploids derived from interspecific hybridization between Saccharum officinarum (2n = 80) and Saccharum spontaneum (2n = 40-128).

Flow cytometric characterisation of the complex polyploid genome of Saccharum officinarum and modern sugarcane cultivars.

Sugarcane (Saccharum spp.) is a globally important crop for sugar and bioenergy production. Its highly polyploid, complex genome has hindered progress in understanding its molecular structure.

GISH: resolving interspecific and intergeneric hybrids.

Genomic in situ hybridization (GISH) is an invaluable cytogenetic technique which enables the visualization of whole genomes in hybrids and polyploidy taxa. Total genomic DNA from one or two different species/genome is used as a probe, labeled with a fluorochrome and directly detected on mitotic chromosomes from root-tip meristems. In sugarcane we were able to characterize interspecific hybrids of two closely related species as well as intergeneric hybrids of two closely related genera.

GISH characterization of Erianthus arundinaceus chromosomes in three generations of sugarcane intergeneric hybrids.

Within Erianthus, a genus close to Saccharum, the species E. arundinaceus has the potential to contribute valuable traits to sugarcane, including adaptation to biotic and abiotic stresses and ratooning ability. Sugarcane breeders have tried for a long time to use Erianthus species in their breeding programs but until recently were constrained by a lack of fertile Saccharum x Erianthus hybrids.

Molecular cytogenetic investigation of chromosome composition and transmission in sugarcane.

Modern sugarcane cultivars (Saccharum spp., 2n = 100-120) are complex polyploids derived from interspecific hybridization performed a century ago between the sugar-producing species S. officinarum L.