Development of Functional Markers for Resistance to Smut and Identification of Genes Differentially Expressed in Response to Brown Rust in Sugarcane

Smut, caused by Sporisorium scitamineum and brown rust, caused by Puccinia melanocephala, are two of the most important diseases that affect sugarcane production in Louisiana and worldwide. Smut continues to cause losses in the breeding program in Louisiana. Therefore, a QTL analysis was conducted to identify molecular markers associated with resistance in F1 progeny (162) of a biparental cross between susceptible cultivar L 99-233 and resistant HoCP 96-540. Using 1,574 single-dose SNP markers, a total of 253 linkage groups (LG) were obtained with a genome coverage of 24,580.15 cM. Six QTLs were localized on five LGs. The highest % PVE was 9.17%, which confirms that smut resistance is a quantitative trait controlled by multiple small-effect QTLs. However, four of 12 SNP markers, heterozygous for the alternate allele and flanking the six loci, explained more than 10% of variance for resistance. The markers need further validation in another sugarcane population before being used in resistance screening in the breeding program. Genes related to cell-wall modification, protein degradation by ubiquitination, signal perception and protection from oxidative environment by glycosylation were some of the genes found to be linked to genomic regions associated with smut resistance. A differential gene expression analysis, using RNA-seq technology, was conducted to evaluate mechanisms of quantitative resistance to brown rust. Resistance expression was compared in three resistant cultivars, with (L 01-299) and without (L 99-233, L 11-172) the Bru1 resistance gene, and three susceptible cultivars. An active response to infection by the pathogen for incompatible and compatible reactions was indicated by the higher numbers of up-regulated genes. Genes uniquely detected across all resistant cultivars, such as chalcone synthase, E3 ubiquitin ligase, and those involved in cell wall modification, suggest an important role in defense against the pathogen. Chitinase, glycosyltransferase, and genes involved in biosynthesis of antimicrobial- metabolites were activated uniquely and could provide quantitative resistance in L 99-233. In contrast, for resistant cultivar L 01-299, signal perception of the pathogen, PR protein, ethylene, lignin, phytoalexins and anthocyanins biosynthesis were genes uniquely expressed. A breeding effort to combine the different quantitative resistance mechanisms possessed by these two cultivars, possibly through identification of molecular markers associated with resistance in L 99-233, could lead to the development of cultivars with very effective and durable resistance to brown rust