Functional SNP in Sugarcane through Transcriptome Analyses

Sugarcane is one of the most important source of income, employment and energy in Brazil. As a result of their genetic complexity, sugarcane breeding programs require long time to obtain a new cultivar. Thus, functional markers can be used to accelerate the process and select important agronomic traits. The aim of this work was develop the transcriptome of mapping population parents (IACSP95-3018 and IACSP93-3046) in order to develop functional SNPs. Were sequenced 420 million paired-end short reads (2x72bp) using the platform Illumina GAIIx. To correlate sugarcane parental unigenes with known metabolic pathways, we used the KAAS server to assign sequences with KEGG orthology (KO) terms. We select two important pathways: Carbon Fixation in Photosynthetic (C4 photosynthetic pathway) and the Starch and Sucrose Metabolism. To identify putative SNPs we use BWA aligner and in-house script to identify the unique and shared SNPs between the parental genotype. In C4 photosynthetic pathway we found 32 unigenes associated with 21 KO terms. In these unigenes were identified 587 putative SNPs, where about 43% are share between the parents and 162 (IACSP95-3018) and 170 (IACSP93-3046) are unique. In the Starch and Sucrose pathway, 20 unigenes were found association with 10 KO terms, that presents 798 SNPs in total with around 36% share between the parents and 264 (IACSP95-3018) and 244 (IACSP93-3046) unique. All of these putative SNPs presents an important source data and would also be priority candidates for development of functional specific makers.