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Annual Report: CIRAD 2006

Sugarcane smut: genetic diversity of the fungus and genetics of resistance

Smut is found in every zone in which sugarcane is grown, except for Papua New Guinea, which strangely enough is where the ancestral domesticated species Saccharum officinarum originated. Recent studies have provided a clearer picture of the genetic diversity of the fungus and the genetic determinism of sugarcane resistance.

Sugarcane smut takes the form of a whip-like smutty growth at the tip of infected canes © J.-C. Girard/CIRAD

Sugarcane smut is a disease caused by the fungus Ustilago scitaminea, whose genetic diversity is very limited outside Asia. Control of the disease could centre on breeding resistant varieties, but the genetic determinism of that resistance is not known. A new strategy was recently adopted in the hope of identifying the chromosome regions involved. It is based on a study of the associations between markers and resistance, and the results so far are very promising.

A single lineage is behind the disease outside Asia

Sugarcane smut takes the form of a whip-like smutty growth (a smut whip) at the tip of infected canes, which may release large numbers of spores. The specific structure of the genetic diversity of the fungus has now been studied on a global scale, using microsatellite markers. It transpires that the major share of the diversity is found in certain populations from Asia. The genetic diversity of populations from the Americas and Africa, on the other hand, is extremely limited, and all the non-Asian strains studied proved to originate from the same genotype. These results suggest that gene flow between continents is rare, since a single lineage, which originated in Asia, has spread worldwide, probably through the accidental transfer of infected cuttings. Outside Asia, using resistant varieties should thus be a sustainable, effective way of controlling the disease. In Asia, given the variability of the pathogen, it would be a good move to characterize the available resistance sources more clearly, particularly those in the wild species S. spontaneum.

Identifying the associations between markers and resistance

Modern sugarcane varieties stem from a few interspecific hybridizations of S. officinarum and S. spontaneum at the start of the 20th century, in India and Indonesia, the results of which have since been intercrossed a limited number of times to give the varieties we know now. There has thus been a marked founder effect likely to lead to linkage disequilibrium (LD). This LD, which is a measure of the nonrandom association of alleles to distinct loci, is more or less marked in cultivated plants depending on the history of their domestication and their reproductive regime. In sugarcane, a marked LD was confirmed by monitoring the behaviour of AFLP (Amplified Fragment Length Polymorphism) markers whose position on reference genetic maps was known: significant associations between markers could be detected at distances of anything up to 20 cM and more, although the mean degree of LD fell considerably if the distance between markers was more than 5 cM. The structure of the LD means that it may be possible to locate worthwhile genes by analysing the associations between markers and characters across the genome.

It was on the basis of this observation that the genetic determinism of smut resistance was explored, within a cultivar population comprising two subpopulations, one highly resistant and the other highly susceptible to smut. A study of the associations between the presence or absence of markers and resistance revealed chromosome regions linked to resistance. Some of them correspond to QTLs (Quantitative Trait Loci) detected during a genetic mapping study conducted on a controlled cross between a resistant cultivar (R 570) and a susceptible clone (MQ 76-53).

Studies of associations are looking particularly promising for sugarcane. They complement the studies conducted using QTLs, which are complex in this highly polyploid plant.

Contacts

Louis-Marie Raboin, e-maail ; Laurent Costet
UMR: Plant Communities and Biological Invaders in Tropical Environments (PVBMT)

Jean Carlier
UMR: Biology and Genetics of Plant-Pathogen Interactions for Integrated Protection (BGPI)

Jérôme Pauquet ; Angélique D’Hont
UMR: Polymorphisms of Interest in Agriculture (PIA)

Partners

  • Centre d’étude, de recherche et de formation (CERF, Réunion)
  • Centro de Investigación de la Caña de Azúcar de Colombia (CENICANA, Colombia)
  • Compagnie sucrière sénégalaise (Senegal)
  • Cooperativa de Produtores de Cana-de-Açúcar, Açúcar e Álcool do Estado de São Paulo (COPERSUCAR, Brazil)
  • Hawaii agriculture Research Center (United States)
  • GPM Sugar Group (Indonesia)
  • Japan International Research Center for Agricultural Sciences (JIRCAS, Japan)
  • Mauritius Sugar Industry Research Institute (MSIRI, Mauricius)
  • Mitr Phol Sugarcane Research Center (Thailand)
  • Philippine Sugar Research Institute Foundation (Philippines)
  • Société nationale sucrière (SOSUCO, Burkina Faso)
  • South African Sugar Research Institute (SASRI, South Africa)
  • Texas Agricultural Experiment Station (United States)
  • Uttar Pradesh Council of Sugarcane Research (India)

For further information

  • Raboin L.M., 2005. Génétique de la résistance au charbon de la canne à sucre causé par Ustilago scitaminea Syd. : caractérisation de la diversité génétique du pathogène, cartographie de QTL dans un croisement biparental et étude d'associations dans une population de cultivars modernes. Thèse de doctorat, AgroM, Montpellier, 119 p.
  • Raboin L.M., Oliveira K.M., Le Cunff L., Telismart H., Roques D., Butterfield M., Hoarau J.Y., D’Hont A., 2006. Genetic mapping in sugarcane, a high polyploid, using bi-parental progeny: identification of a gene controlling stalk colour and a new rust resistance gene. Theoretical and Applied Genetics, 112 : 1382-1391.
  • Raboin L.M., Selvi A., Miranda Oliveira K., Paulet F., Calatayud C., Zapater M.F., Brottier P., Luzaran R., Garsmeur O., Carlier J., D’Hont A., 2007. Evidence for the dispersal of a unique lineage from Asia to America and Africa in the sugarcane fungal pathogen Ustilago scitaminea. Fungal Genetics and Biology, 44 : 64-76. (doi:10.1016/j.fgb.2006.07.004)