Phenotype-genotype association for the identification of resistance to stem borers (Diatraea spp., Lepidoptera: Crambidae) in sugarcane.

Sugarcane (Saccharum spp.) is a major crop for sugar production, but its productivity is affected by stem borers (Diatraea spp.). These insects cause significant losses by damaging the stem and disrupting the transport of photosynthates and nutrients. Although biological control has been effective in Colombia, the identification of genetic resources for the resistance would provide complementary long-term crop protection. This study aimed to identify markers associated with the resistance to insects. For this purpose, a population of 348 genotypes was evaluated by infesting 30 stalks per genotype with four 9-day-old larvae. The proportion of bored internodes, insect survival, and the Damage Survival Index were recorded for each stem. Genotypic data was obtained using GBS, RADseq, and WGS. A total of six marker-model associations, which includes 4 unique markers, were significantly associated with DS Index, but only 2 were effectively validated. Candidate genes were searched within a 353.1 kb window surrounding the validated markers, revealing 48 genes involved in signaling pathways, receptor-mediated recognition, metabolic responses, direct defense mechanisms, and structural modifications. The DS Index variable integrates plant damage and insect performance, providing a robust metric to study resistance. These results provide a foundation for the identification of genetic resources for Diatraea spp., with key components including receptor-like kinases involved in herbivore recognition, calcium-dependent signaling cascades, and regulatory elements that finely balance immune activation through both positive and negative mechanisms. The validated SNPs, together with the functional annotation of nearby genes, represent an innovative approach to incorporate molecular tools into sugarcane breeding such as genomic selection, genome editing and/or genetic transformation.