Doctor of Philosophy (PhD)


Plant, Environmental Management and Soil Sciences

Document Type



Leaf scald, caused by Xanthomonas albilineans, is a major sugarcane disease worldwide. The disease is managed primarily with resistant cultivars obtained through classical breeding; however, the erratic symptom expression hinders the reliability and reproducibility of the selection process. The development of molecular markers associated with incompatible/compatible reaction can overcome this limitation. Suppression subtractive hybridization (SSH) and quantitative trait locus (QTL) mapping were the strategies used to find leaf scald resistance-associated genes and molecular markers in sugarcane. SSH results showed that genes involved in signal perception and transduction, and DNA binding, were highly expressed in the resistant clone LCP 85-384 compared to the susceptible clone HoCP 89-846. Also, a higher proportion of overexpressed genes were located in the chloroplast in the resistant clone. Early accumulation and maintenance of high mRNA concentration was hypothesized as the determining factor for leaf scald resistance. A linkage map was constructed using 89 F1 progeny of a cross between the cultivars LCP 85-384 (resistant) and L 99-226 (susceptible) using simple sequence repeat (SSR), leaf scald responsive genes-derived SSR and single nucleotide polymorphic (SNP) markers. Single marker analysis showed that the markers c3-579 (LOD = 3.7189; phenotypic variance explained (PVE = 17.56%), 1x71593 (LOD = 3.0453; PVE = 14.65%) and c1-586b (LOD = 3.013; PVE = 14.48%) were associated with leaf scald resistance. Interval mapping identified 15 QTLs associated with disease resistance that explained 2.5 to 18.6% of the phenotypic variance. Comparative genomic analysis with Sorghum bicolor identified genes previously associated with resistance or tolerance to biotic and abiotic stresses within and flanking the QTLs. The present study resulted in a strong platform for future functional validation of the genes to ascertain their role in leaf scald resistance and marker validation in larger and diverse populations toward development of allele-specific markers for their use in breeding resistant sugarcane varieties.



Document Availability at the Time of Submission

Release the entire work immediately for access worldwide.

Committee Chair

Baisakh, Niranjan