SNP Mining in Sugarcane through Next-Generation RNA Sequencing

Sugarcane is a complex polyploidy crop specie, economically important because it is the main source of both sugar and alcohol production. In sugarcane breeding programs, 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 SNP markers that will saturate the genetic map of the population in study. Were sequenced 420 million paired-end short reads (2x72bp) using the platform Illumina GAIIx. De novo assembly was performed with data set using the Trinity assembler. Were obtained 60,166 contigs (IACSP95-3018) and 56,620 contigs (IACSP93-3046). To SNP discovery, the reads of each parent were mapped with transcriptome assembled using the CLC Workbench platform, considering minimum coverage 20 and quality score 30. The aligned sequences enabled the detection of 400,000 putative single nucleotide polymorphism (SNP) between the parents. The density observed was one SNP per 130 bp. The data generated in this work increase the probability to development functional SNPs, associated important agronomic traits to sugarcane breeding programs.