Genomic organization of sugarcane cultivars revealed by chromosome-specific oligonucleotide probes

International audienceSugarcane (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

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. and the wild species S. spontaneum L. Using genomic in situ hybridization, we revealed that between 15 and 27.5% of the genome of modern cultivars is derived from S. spontaneum, including 10-23% of entire chromosomes from this wild species and 8-13% chromosomes derived from interspecific recombination. We confirmed the occurrence of 2n + n transmission in crosses and first backcrosses between these two species and demonstrated that this also can occur in crosses between S. officinarum and modern cultivars. We analysed five S. officinarum clones with more than 80 chromosomes and demonstrated that they were derived from interspecific hybridization supporting the classical view that this species is characterized by 2n = 80. We also illustrated the complementarities between molecular cytogenetics and genetic mapping approaches for analysing complex genomes

Applications of advanced cytogenetic techniques in sugarcane

International audienceCytogenetic 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 specie

Saccharum spontaneum, a Novel Source of Resistance to Root-Lesion and Root-Knot Nematodes in Sugarcane

Root-lesion nematode (Pratylenchus zeae) and root-knot nematode (Meloidogyne javanica) are two important pathogens of sugarcane (Saccharum hybrid). No commercial cultivars are resistant to these nematodes in Australia. Twenty accession lines of S. spontaneum, a wild relative of sugarcane, were tested against these two nematode species. S. spontaneum lines were tested twice for resistance to root-lesion nematode and three times for root-knot nematode. Reproduction (final population/starting population) of root-lesion nematodes was significantly lower in 17 of the 20 S. spontaneum accession lines tested in two experiments compared with two commercial cultivars. Four S. spontaneum lines supported a significantly lower number of root-lesion nematodes per gram of root than that of two commercial sugarcane cultivars. Reproduction of root-knot nematodes was significantly lower in 16 S. spontaneum lines compared with two commercial cultivars. Fourteen of the S. spontaneum lines tested supported significantly fewer eggs per gram of root compared with two commercial cultivars. This study showed that S. spontaneum lines possessed resistance for root-lesion and root-knot nematodes. Targeted crossing with commercial hybrid parental lines should be conducted to introduce nematode resistance into sugarcane cultivars for the Australian sugar industry