Identifying markers for resistance to sugarcane orange rust (Puccinia kuehnii) via selective genotyping and capture sequencing

Sugarcane orange rust, caused by the fungus Puccinia kuehnii, is a serious disease of sugarcane. The most effective strategy to combat the disease is to develop resistant cultivars. Phenotypic screening for resistance is laborious, and breeders would benefit from molecular markers linked to the trait. The objective of this research was to identify, via association mapping, markers linked to resistance to orange rust. From the germplasm collection at Canal Point, Florida, 724 genotypes were screened for orange rust resistance via artificial inoculation of field-grown plants. A total of 38 susceptible and 37 resistant genotypes that were at or near the extremes of the population distribution were chosen for genotyping. Genotyping was accomplished via capture sequencing using 32,555 sugarcane probes anchored to the sorghum genome. Several methods were used to account for population structure and/or kinship. The most appropriate methods (determined by the genomic inflation factor) were mixed models and EIGENSTRAT. A total of 38 unique SNPs identified by these methods were then validated on 560 members of the population, using high resolution melting of PCR amplicons. Ten of these markers were statistically significant for the quantitative measure of rust severity, of which nine were also significant for the qualitative measure of 'status' (resistant/susceptible). The maximum amount of variation explained by any single marker was approximately 11%. This research has provided markers which can be deployed to help select superior parents for orange rust resistance, and also provided valuable insight for future research towards genetic control of orange rust in sugarcane.