Identification of GBS-Generated Bi-Allelic SNPs Associated with Leaf Scald Resistance in Sugarcane

Leaf scald, caused by Xanthomonas albilineans, is a major sugarcane disease worldwide. Erratic symptom expression hinders the reliability and reproducibility of the selection for breeding resistant varieties. Molecular markers associated with incompatible/compatible reaction can overcome this limitation. Transcriptome analysis showed that genes involved in signaling and transcription regulation were highly expressed in the resistant clone LCP 85-384 compared to the susceptible clone HoCP 89-846, with a higher proportion of overexpressed genes located in the chloroplast in the resistant clone. Early accumulation and maintenance of high mRNA content seemed important for leaf scald resistance. Linkage mapping by selective genotyping of 89 F₁ progeny of LCP 85-384 (resistant) x L 99-226 (susceptible) assigned 1,146 single dose markers to 205 linkage groups (LGs) with the genome coverage of 19,230 cM, of which 95 LGs were assigned to LCP 85-384 (2,793 cM), and109 LGs were assigned to L 99-226 (4,121 cM). Single marker analysis showed that the markers c3-579 (phenotypic variance explained (PVE) = 17.56%), 1x71593 (PVE = 14.65%) and c1-586b (PVE = 14.48%) were associated with leaf scald resistance. Interval mapping identified 11 QTLs with more than 5% PVE. 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 provided 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 for their use in breeding leaf scald resistant sugarcane varieties.