GeSNP prediction of SFPs in sorghum genes related to biofuel traits. The hybridization intensity between the perfect match and the mismatch oligonucleotides was averaged and scaled (GeSNP software output) and plotted against each sugarcane probe pair. Graphs are shown for four genes related to biofuel traits that have SFPs with t values of ≥7 and that were previously reported to be differentially expressed between grain sorghum BTx623 and sweet sorghum Rio (a). The SFP present in lysM identified a 13-bp indel, whereas the SFPs present in cellulose synthase 1 and dolichyl-disphospho-oligosaccharide identified an A/G and G/A SNP between BTx623 and Rio, respectively (b). In Rio, the third intron of the gene 4-coumarate coenzyme A ligase is mis-spliced and detected in the sugarcane probe pair #2 (c). Molecular markers for the genes lysM, cellulose synthase 1, and dolichyl-diphospho-oligosaccharide were generated based on allele-specific PCR (d). In the case of lysM, a primer spanning the 13-bp deletion in BTx623 was used to selectively amplify the allele from Rio. In the case of cellulose synthase 1 and dolichyl-diphospho-oligosaccharide, primer pairs specific for the SNP in question were generated by the WebSNAPER software and tested empirically.