EA Rincón1, JC Rincón2, JC Ángel1, JH Trujillo1, JJ Riascos1, FA Salazar1 and FF Garcés1
1Colombian Sugarcane Research Center (Cenicaña), Cali, Colombia; earincon@cenicana.org, jjriascos@cenicana.org
2National University of Colombia, Palmira, Colombia
Orange rust, caused by Puccinia kuehnii,is a significant disease affecting sugarcane production in many countries worldwide. Variation in disease susceptibility among commercial varieties highlights the need for genetic resistance as a primary strategy for disease control. This study aimed to identify host genome regions associated with resistance to orange rust using a genotype-phenotype association approach (GWAS). A total of 220 diverse individuals, referred to as the discovery population, were evaluated under controlled conditions for their resistance to orange rust by assessing reaction levels, disease severity, and damage indices. Utilizing the GWASPoly R package for polyploids, we associated disease phenotypic data with 297,327 single nucleotide polymorphisms (SNPs) derived from whole genome sequencing of the discovery population. Validation of significantly associated SNPs was performed using a separate population of 178 individuals (validation population) that was also genotyped through whole genome sequencing. A total of 23 SNPs were identified as significantly associated with resistance or susceptibility to orange rust across five genetic models (additive, simplex dominant, duplex dominant, diploidized, and recessive). These SNPs explained phenotypic variation (R²) ranging from 1.4% to 10.2%, consistent with previously reported values for orange rust resistance in sugarcane. Additionally, we identified 42 candidate genes with defense functions located within 500 kbp of the marker positions, using the genome of the variety CC 01-1940 as the reference. Of the 23 associated SNPs, 13 were validated with significant associations (P < 0.05). These 13 validated SNPs represent a valuable resource for the early identification of sugarcane genotypes resistant to orange rust.