Genome-wide linkage disequilibrium analysis and association study for smut resistance in the highly polyploid genome of sugarcane

Linkage disequilibrium (LD) in crops, established by domestication and early breeding, can be a valuable basis for mapping the genome. We undertook an assessment of LD in sugarcane (Saccharum spp), characterized by one of the most complex crop genomes, with its high ploidy level (greater or equal to 8) and chromosome number (greater than 100) as well as its interspecific origin. Using AFLP markers, we surveyed 1537 polymorphisms among 72 modern sugarcane cultivars. We exploited information from available genetic maps in order to determine a relevant statistical threshold that discriminates marker associations due to linkage from other associations. LD is very common among closely linked markers and steadily decreases within a 0-30 cM window. LD, within a sample of cultivars, appears as efficient as linkage analysis within a controlled progeny in terms of assigning markers to cosegregation groups. The 72 cultivars were evaluated for smut resistance. Several markers were found in association with smut resistance of which some had already been highlighted in an QTL analysis. Saturating the genome coverage remains a challenge, but applying LD-based mapping within breeding programs will considerably speed up the localisation of genes controlling important traits by making use of phenotypic information produced in the course of selection. (Texte integral)