The major contribution of resistance to orange rust and yellow leaf in modern sugarcane hybrids comes from Saccharum spontaneum as evidenced by genome-wide association studies

Jean-Yves Hoarau^1,2,3, Jordan Dijoux^1,2,3, Thomas Dumont¹, Laurent Barau¹, Olivier Garsmeur^2,3, Simon Rio^2,3 and Angélique D’Hont^2,3

¹eRcane, 29 rue D’Emmerez de Charmoy, 97 494, Sainte-Clotilde, Réunion Island; jean-yves.hoarau@ercane.re

²CIRAD, UR AGAP Institute, F-34398 Montpellier, France

³UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France

Resistance to most sugarcane diseases in modern interspecific hybrids (Saccharum spp.) is often intuitively attributed to resistance alleles that may have been derived from the wild species S. spontaneum. This intuitive breeders’ opinion stems from the fact that, for many diseases, the noble species S. officinarum is often relatively susceptible, while the wild species shows good levels of resistance, and is therefore thought to be the main species that have provided improved resistance. Genomic analysis using dense SNP polymorphism mapped on a reference sugarcane genome allows the investigation of this widely held view. Genome-wide association studies (GWAS) were conducted to dissect the genetic basis of resistance to orange rust (caused by Puccinia kuehnii) and yellow leaf (caused by Sugarcane yellow leaf virus) and to detect Quantitative Trait Loci (QTL) of resistance for both diseases. GWAS experiments were conducted on two large panels of modern interspecific clones (n=526 and 673) using a large number of SNPs (>180,000) distributed across the sugarcane genome. The experiments revealed four major-effect resistance QTLs for yellow leaf and five major-effect resistance QTLs for orange rust. The comparative frequency of all these resistance QTL alleles in 10 S. officinarum and in 9 S. spontaneum accessions clearly support a S. spontaneum origin for most resistance alleles. Taken together, these small sets of major-effect resistance alleles are sufficient to predict the resistance levels of the surveyed clones with an interesting accuracy (0.50 for yellow leaf and 0.60 for orange rust). These novel QTL results pave the way for effective marker-assisted breeding approaches in the view of improving genetic resistance to these two important sugarcane diseases.