Developing a Reference Genomic Map and Identifying the Markers Linked to Sugarcane Orange Rust Resistance Genes

Orange rust of sugarcane has impacted the Florida Sugarcane Industry since its discovery in 2007.  Developing genetic markers linked to orange rust resistance gene(s) would greatly benefit the efficiency of resistant sugarcane cultivar development. Despite the features of large genome size, polyploidy, and heterozygosity of sugarcane, we have established a high density genomic map with sugarcane SSRs and resistant (R) genes based on the complete sorghum genome.  This genomic map contains 1,151 SSR markers and 1,890 R gene models. We selected 391 SSR markers evenly distributed on the map to screen the resistant cultivar, CP95-1039, susceptible cultivar, CP88-1762, and a pool of resistant and susceptible progeny selected from a F1 segregating population derived from CP95-1039 x CP88-1762. Through this bulk segregation analysis, we identified nine SSR markers that are potentially linked to the orange rust resistance. These markers will be further validated through genotyping 130 individuals in the whole F1 segregating population and other resistant clones in the sugarcane breeding program.  The other markers near the validated linked markers will be identified based on the genomic map.