Génétique de la résistance au charbon de la canne à sucre causé par Ustilago scitaminea syd. : caratérisation de la diversité génétique du pathogène, cartographie de QTL dans un croisement bi-parental et étude d'associations dans une population de cultivars modernes
Sugarcane smut, caused by Ustilago scitaminea Syd., is present in all sugarcane growing areas with the exception o f Papua New Guinea, Fiji and the eastern side of Australia. Breeding for smut resistance is efficient because this trait is fairly heritable but it requires complicated screenings. Moreover, the genetic control o f smut resistance is still unknown. With the objective to identify the mendelian factors involved in sugarcane resistance to smut, two strategies have been implemented (1) QTL mapping in a bi-parental progeny derived from a cross between a resistant cultivar 'R 570' and a highly susceptible clone 'MQ 76/53', evaluated in Reunion island for resistance to smut (2) Association study in a population of cultivars, evaluated in Burkina Faso for resistance to smut. First, the worldwide genetic structure of U. scitaminea was investigated. A total of 142 singleteliospore isolates from 15 countries worldwide were analysed using 17 polymorphic microsatellite loci. All isolates but one were homozygous for all loci, indicating that selfing is the highly preferential reproductive mode of U. scitaminea. In America and Africa, genetic diversity was found to be extremely low and all isolates belonged to a single inbred lineage. This inbred lineage was also found in some parts of the Asian continent where most U. scitaminea genetic diversity was detected. These observations support the hypothesis that the fungus originated in Asia. Thus, the bi-parental population and the population of cultivars used to study the genetic determinism of smut resistance have been evaluated towards isolates from the worldwide lineage. The genetic maps of the two parents o f the bi-parental progeny, 'R 570' and 'MQ 76/53', were constructed using a population o f 198 progeny. A total o f 1666 polymorphic markers were produced using 37 AFLP primer pairs combinations, 46 SSRs and 9 RFLP probes. Linkage analysis allowed the construction of 86 cosegregation groups for 'R 570' and 105 cosegregation groups for 'MQ 76/53' encompassing 424 and 536 single dose markers respectively. The cumulative length of 'R 570' map was 3144 cM. The cumulative length of 'MQ 76/53' map was 4329 cM. On 'MQ 76/53' map, a gene controlling the red colour of the stalks was identified at 6.5 cM of an AFLP marker and a new brown rust resistance gene was identified at 23.1 cM o f an AFLP marker. The structure of linkage disequilibrium in the population o f cultivars was investigated using 1626 AFLP markers, among which 408 have known positions on 'R 570' genetic map. Thus, it was possible to study the relationship between genetic distances and statistical associations between markers in the population of cultivars, calculated using the Fisher exact test. This analysis confirmed that linkage disequilibrium in sugarcane extends over distances o f tenth of centiMorgans but drops sharply for distances over 5 cM. This order of magnitude indicates that genome-wide association studies are achievable in sugarcane. Field trials and greenhouse trials using different inoculation methods were conducted in order to characterize the resistance o f the 198 progeny clones from the bi-parental population. The distribution of disease scores observed in all those trials were highly unbalanced toward the resistant parent indicating the segregation o f multiple dominant resistance factors. A QTL detection was performed using the 1666 available markers allowing the identification of a few genomic zones with small effects. Besides, the association study performed in the population of cultivars (constituted o f two subpopulation, one highly susceptible to smut and the other highly resistant to smut) revealed interesting haplotypes associated with resistance. Two QTLs have been detected through both approaches. The progress obtained toward a better understanding o f the genetic determinism of sugarcane resistance to smut are modest. The potential of association studies in sugarcane appeared interesting although much more markers would have to be used to make the most of it.