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Sugarcane (Saccharum spp.) is probably the crop with the most complex genome. Modern cultivars (2n=100-120) are derived from interspecific hybridization between the noble cane S. officinarum (2n=80) and the wild cane S. spontaneum (2n=40-128). We investigated the genome organization of important sugarcane cultivars and their parental species using chromosome-specific probes combined with genomic in situ hybridization (GISH). This allowed the genomic and genetic characterisation of Australian sugarcane cultivars and one of the major contributing parental clones, Mandalay. The S. spontaneum clone Mandalay follows the classical organization of S. spontaneum clones with x=8 with a major discrepancy related to an extra six chromosomes compared to the previously reported 2n=96 for Mandalay's clone. Our previous results reported the rearrangements between the S. officinarum (x=10) and S. spontaneum (x=8) chromosomes, with a most likely scenario of a two-step process leading to x= 9 and then x=8, where each step involved three chromosomes that were rearranged into two. Further polyploidization led to the wide geographical dispersion of S. spontaneum clones with x= 8. 111 modern cultivars, 13-20% of the S. spontaneum: contribution originated from cytotypes with x=8. Modern cultivars have mainly 12 copies of each of the first four basic chromosomes and a more variable number for those basic chromosomes whose structure differs between the two parental species. These new insights and cytogenetic tools substantially improve our understanding of the extreme complexity of modern sugarcane cultivar genomes and could lead to guiding breeding strategies developing new, improved varieties for the Australian industry.

Introgression of Erianthus arundinaceus into the SRA sugarcane-breeding program has been a goal for researchers for many years. The Erianthus genome was finally accessible to sugarcane breeders with the identification in 2005 of the first Saccharum/Erianthus fertile hybrids, developed in China. Today, Saccharum/Erianthus BC3 and BC4 clones are available in Australia, and Erianthus-sugarcane hybrids have been characterised by cytogenetics and investigated for their potential resistance against pachymetra root rot, sugarcane smut and nematodes. Some clones have shown potential as new sources of resistance for incorporation into the SRA breeding program. These hybrids were created from Erianthus clones indigenous to China and their reaction to the above diseases is unknown in Australian conditions. In Meringa we also have access to many Erianthus clones of Indonesian origin. Some of these Erianthus clones have previously shown immunity to pachymetra root rot. In the late 1990s, these Indonesian Erianthus clones were used in crossing but no fertile hybrids were ever produced due to an incompatibility between the Saccharum and the Erianthus genomes. We revisited this untapped source of resistance by utilising the fertile Erianthus hybrids derived from China to cross with the Indonesian Erianthus of known resistance to pachymetra root rot. Here we report on the early stage results of introgressing Indonesian Erianthus into the SRA breeding program.

Cytogenetics applied to sugarcane has brought our fundamental understanding of the sugarcane genome to a new level. In the mid-nineties, Genomic in situ Hybridisation (GISH) was first applied to sugarcane to determine the specific composition of the modern cultivar R570. GISH revealed the chromosomal composition of R570 was 80% Saccharum officinarum, 10% S. spontaneum and 10% of recombined chromosomes. The Australian counterpart Q165, revealed a slightly different species composition as 75%, 15% and 10%, respectively. Both R570 and Q165 genetic maps have portrayed a partial coverage of linkage groups (LG) despite the large number of molecular markers invested in the maps. It also shows that S. spontaneum chromosomes seem to have a better vertical coverage than S. officinarum chromosomes as the S. spontaneum genome is more polymorphic. To gain a better understanding of the genome composition in terms of LG number per homology group (HG) and species attribution of the LG, we applied BAC-FISH to sugarcane. Bacterial Artificial Chromosomes (BAC) consist of large chromosome segments (around 100kb). BAC from the Sorghum or Saccharum genomes were used as anchorage points on the sugarcane cultivars to identify homologous/homeologous chromosomes for each HG. We will present some examples of results of BAC-FISH applied to several cultivars for at least 4 different HG. The determination and comparison of the number of chromosomes per HG to the number of LG from the genetic maps will determine the saturation level of the genetic maps. This will help us to obtain critical knowledge of the horizontal chromosome distribution for a particular cultivar and compare its structure to another cultivar. Eventually we will have a better understanding of the distribution of the chromosomes during crossing and this will help breeders to make more informed and targeted choices in their selection programs. (Texte intégral)

The progress that has been achieved in understanding sugarcane (Saccharum spp.) genome structure over the last 15 years, thanks to the development of molecular cytogenetics is reviewed here. The basic chromosome numbers of the species S. spontaneum, S. officinarum and S. robustum have been determined using fluorescent in situ hybridization (FISH) with rDNA probes. Genomic in situ hybridization allowed the differentiation of chromosomes from S. officinarum and S. spontaneum, the two species involved in the origin of modern sugarcane cultivars, assessment of the proportion of chromosomes of these species in the genome of the modem cultivars and assessment of the extent of interspecific chromosome recombination. GISH has also been used to clarify the origin of the related taxa S. barberi and S. sinense. These techniques also proved to be very useful in monitoring introgression from the related genera.

International audience; Cytogenetic techniques, GISH (Genomic In Situ Hybridisation) and FISH (Fluorescence In Situ Hybridisation), are essential tools to characterize the chromosome composition and the mode of chromosome transmission in complex polyploid interspecific hybrids such as sugarcane. Four examples will be presented. i) Erianthus arundinaceus, a related genus to Saccharum is considered as having a great potential as a germplasm source for better ratoonability, vigour, tolerance to environmental stresses, and disease resistance in sugarcane. Fertile clones from intergeneric crosses between Saccharum officinarum and E. arundinaceus and two backcross generations have been generated in China. GISH was used to characterise this material and revealed n+n transmission in the I1 and the second back-cross (I3) and 2n+n transmission in the first back-cross (I2). No recombination events were observed between Saccharum and E. arundinaceus chromosomes in either I2 or I3 clones. ii) We analysed a few atypical S. officinarum clones with more than 80 chromosomes and demonstrated that they were derived from interspecific hybridization supporting classical cytogeneticist view that this species is characterized by 2n=80. iii) We conducted GISH analysis of two progeny, from a cross between S. officinarum and a cultivar (Q165,) used to generate genetic maps and revealed the occurrence of 2n+n transmission. iv) the basic number in S. officinarum and S. spontaneum is different with x=10 and x=8 respectively. We are currently mapping on the chromosomes, BAC clones anchored to the R570 genetic map, to investigate the structural difference between the chromosomes of these two species