A Genetic Linkage Map of Louisiana Sugarcane (Saccharum spp. hybrids) Using AFLP and SSR Markers.

Modern sugarcane cultivars (Saccharum spp. hybrids) are polyploid and aneuploid inter-specific hybrids.  They are believed to originate from the initial hybridizations between S. officinarum (x = 10) and S. spontaneum (x = 8), where S. officinarum is normally the recurrent parent.  From repeated backcrossing, the chromosome number in these hybrids ranges from 2n = 100 to 130 with > 85% of their nuclear genomes contributed by S. officinarum.  A genetic linkage map is being developed using 300 genetically verified selfed progeny of a commercial cultivar LCP 85-384.  LCP 85-384 has been chosen because it is a self-fertile and high-yielding cultivar that in 2004 occupied more than 91% of the Louisiana sugarcane land.  The mapping population has been characterized for stalk diameter, height, number, and weight; sugar and fiber content; response to RSD, leaf scald, smut, and mosaic diseases; and response to the sugarcane borer in plant cane and ratoon crops in replicated field plots.  Amplified Fragment Length Polymorphism (AFLP) and Simple Sequence Repeat (SSR) markers were used to fingerprint the population.  To date, 64 AFLP (951 bands) and 19 SSR (64 bands) marker profiles produced a total of 1015 polymorphic bands.  All the polymorphic bands were tested for single- (3:1), double- (15:1) and triple- (63:1) dose segregating ratios using Chi-square tests and a total of 866 markers fit these ratios.  A preliminary linkage map was constructed by JoinMap^® 3.0 using LOD scores > 7, a threshold recombination value of 0.4 and the Kosambi mapping function.  Of these 866 markers, 618 markers were placed onto 138 co-segregation linkage groups with a genome span of 3709 cM and an average of approximately 6 cM between any two linked markers.  The preliminary genetic linkage map will be used to facilitate the QTL analysis and ultimately the development of trait-specific DNA markers.