Analysis of Allelic Variation of Sugarcane Drought-Induced Genes

Sugarcane is a C4 grass used for food and bioenergy production derived from interspecific hybridization from Saccharum officinarum and Saccharum spontaneum. Despite its importance, biotechnology for sugarcane is less advanced compared to other important crops, mainly due to the complexity of its genome. Modern sugarcane varieties have a highly polyploid genome, comprising 10 to 12 copies of the complete set of chromosomes, and different levels of aneuploidy. Here, we carried out an analysis of four drought-induced genes to search for allelic variations using a cloning and sequencing approach plus the analysis of 21 Gb of genomic sequence (21x coverage of the monoploid genome) produced by long-read sequencing technology by the ongoing Sugarcane Genome Sequencing Initiative. Both transcribed and promoter regions of each gene were analyzed. Putative alleles were identified for all analyzed genes and phylogenetic analysis showed separated groups of alleles, which may suggests that one group may be originated from S. officinarum and the other group from S. spontaneum. Sequence identity among putative alleles is higher in transcribed regions (including in introns) than in promoter regions, indicating that promoters are less conserved among alleles. This is an important step to characterize sugarcane genome and its variations and these results will be important to study allelic ancestry, identify differentially expressed alleles and their relation to traits of interest.