Uncovering Alternate Splicing Events and Premature Stop Codons Associated with Early Sucrose Accumulation in Sugarcane Using BSR-seq

Identification of the source of genetic variation in the large and complex genome of sugarcane has been comparatively less explored through next-generation sequencing tools. In this study, RNA-seq libraries of two extreme bulks from a segregating full-sib population and its parents were used to identify highly significant, alternate splicing (AS) events and premature stop codons (PMC) associated with early sucrose accumulation. An important differential AS event was identified within the β-subunit of pyrophosphate-fructose 6-phosphate 1-phosphotransferase (PFP) which plays a key role in carbon partitioning in sugarcane. Premature stop codons that could result in truncated proteins were also detected in genes coding for aquaporin, aldolase, cytochrome C-oxidase, ribophorin and plant plasma membrane intrinsic proteins. A major proportion of these AS events and premature stop codons was validated for their differential enrichment in an independent set of sugarcane varieties having high and low sucrose content. The results provide useful insights into the role of putative AS events and premature stop codons which could be useful as candidate markers in marker-assisted breeding for developing high sugar varieties in sugarcane.