Genetic dissection of a modern sugarcane cultivar (Saccharum spp.). I. Genome mapping with AFLP markers

Sugarcane cultivars are polyploid, aneuploid clones derived from interspeci fic hybridization between Saccharum officinarum and S. spontaneum. Their ge nome has recently started to be unravelled as a result of the development o f molecular markers. We constructed an AFLP genetic map based on a selfing population of a specific cultivar. R570. Using 37 AFLP primer pairs. we det ected 1,185 polymorphic markers of which 939 were simplex (segregated 3:1); these were used to construct the map. Of those 939. 887 were distributed o n 120 cosegregation groups (CGs) based on linkages in coupling, while 52 re mained unlinked. The cumulative length of all the groups was 5.849 cM. whic h is probably around one-third of the total genome length. Comparison with reference S. officinarum clones enabled us to assign I I and 79 CGs to S. s pontaneum and S. officinarum. respectively, whereas I I CGs were probably d erived from recombination between chromosomes of the two ancestral species. The patchy size of the groups, which ranges from I to 232 cM, illustrates the difficulty to access large portions of chromosomes, particularly those inherited from S. officinarum. Repulsion phase linkages suggested a high pr eferential pairing for 13 CG pairs. Out of the 120 CGs. 34 could be assigne d to one of the 10 homo(eo)logy groups already defined in a previous RFLP m ap owing to the use of a small common marker set. The genome coverage was s ignificantly increased in the map reported here. Implications for quantitat ive trait loci (QTL) research and marker-assisted breeding perspectives are discussed.