Identifying Quantitative Trait Loci Controlling Sugarcane Orange Rust Resistance via Genotyping by Sequencing

Orange rust of sugarcane has impacted the Florida sugarcane industry since its discovery in 2007. The use of resistant cultivars is the most efficient way to control the disease. Markers linked to the orange rust resistance genes can greatly facilitate the resistance line selection, and improve the efficiency of the breeding program. Development of genetic maps is the foundation for identification of markers linked to disease resistance genes. The objectives of this research are 1) to establish a high density genetic map in sugarcane and 2) to identify markers linked to sugarcane orange rust resistance genes. To establish the genetic map, we used a genotyping by sequencing (GBS) approach to genotype a bi-parental population from the cross between a resistant cultivar ‘CP95-1039’ and a susceptible cultivar ‘CP88-1762’. Phenotypic orange rust reactions of the segregating population were evaluated from 2010 to 2015. High quality single nucleotide polymorphisms (SNPs) were called through seven different SNP-calling pipelines. High-density sugarcane maps were constructed, which contained 1,702 and 1,713 markers for maternal and paternal maps, respectively. Four QTLs controlling orange rust resistance were identified, explaining phenotypic variation ranging from 14.8 to 26.4%. The high density genetic map and linked SNPs markers will greatly facilitate the sugarcane breeding program for disease resistant cultivar development.