Predominant Sugarcane Cultivars in the Northwestern Colombian Amazon Exhibit High Susceptibility to Orange Rust (Puccinia kuehnii)

Sugarcane (Saccharum spp.) is crucial for sweetener production but is highly susceptible to diseases such as orange rust, caused by Puccinia kuehnii. In the northwestern Colombian Amazon, sugarcane is increasingly cultivated, mainly for panela production, a traditional sweetener. However, the introduction of sugarcane has occurred without systematic planning, resulting in limited knowledge about cultivars’ characteristics and disease susceptibility. This study aimed to characterize sugarcane cultivars in the region and assess the occurrence and field-level impact of orange rust, while also confirming the identity of the pathogen using molecular and morphological analysis. We identified five sugarcane cultivars, with only CP 57-603 having an official designation, while the others were known by local names: Regional Without Fuzz, Hairy Purple, and two unnamed genotypes (Cultivar-1 and -2). CP 57-603 and Regional Without Fuzz were the most commonly cultivated (by 49.2% and 74.5% of farms, respectively), while Cultivar-1 (11.8%), Cultivar-2 (7.8%), and Hairy Purple (1.96%) were less frequent. Orange rust was detected in 72% of farms with CP 57-603, 66% with Regional Without Fuzz, and 50% with Cultivar-1, but was absent in farms growing Cultivar-2 and Hairy Purple. Molecular analysis of the ITS1/2 region revealed a single haplotype within the P. kuehnii population, indicating low diversity at this locus in the region. Phylogenetic analysis grouped our ITS1/2 haplotype within a clade alongside isolates from the Americas. Morphological characterization of the pathogen showed no significant trait variation among samples. These findings confirm the presence of P. kuehnii in the region and highlight the urgent need for cultivar diversification and improved disease management to safeguard sugarcane production.