Molecular characterization of brown spot disease resistance in sugarcane using candidate gene and RGA markers

Abstract

Brown spot disease caused by Cercospora longipes has recently emerged as a serious threat to sugarcane cultivation, leading to reduced yield, and sugar recovery. The present study aimed to identify brown spot–resistant sugarcane genotypes using a combination of field screening and molecular marker analysis. A total of 24 sugarcane genotypes were evaluated under natural disease conditions at the Central Sugarcane Research Station, Padegaon, during 2024–25. Field screening revealed wide variation in disease incidence, ranging from 1% (resistant) to 25–35% (moderately susceptible). Four genotypes (CoM 86032, Co 09004, CoM 22005, and CoM 22013) showed significant resistant at filed, while CoM 0265 and PDN 13007 were identified as moderately susceptible. Molecular characterization was carried out using two candidate gene primers (ZmCCoAOMT2 and ZmRLK) along with RGA, SRAP, ISSR-RGA, and SRAP-RGA markers. The ZmCCoAOMT2 primer amplified a resistance-associated 200 bp allele consistently present in all resistant genotypes but absent in susceptible ones, indicating a strong association with brown spot resistance. High polymorphism (71–100%) was observed among RGA and SRAP markers, with PIC values ranging from 0.26 to 0.37. Cluster analysis grouped genotypes according to their disease reactions, validating marker efficiency. Overall, the study highlights the usefulness of identified markers and resistant genotypes for marker-assisted breeding of brown spot–resistant sugarcane varieties.