Cassava Online Archive: Genome-Wide Discovery and Information Resource Development of DNA Polymorphisms in Cassava

Cassava is an important crop that provides food security and income generation in many tropical countries and is known for its adaptability to various environmental conditions. Its genome draft sequence, including annotated protein-encoding genes, and over 80,000 transcribed sequences in GenBank are now publicly available, allowing for the development of cassava polymorphism information. Here, we describe the genome-wide discovery of cassava DNA polymorphism. Using the alignment of predicted transcribed sequences from cassava genome draft sequences and expressed sequence tags from GenBank, we discovered over 10,000 single nucleotide polymorphisms (SNPs) and short insertions and deletions (InDels). To facilitate the development of molecular markers, we designed their PCR primer pairs to amplify the genomic region around each DNA polymorphism. We found 62.7% of the discovered SNPs in protein-encoding regions. Disease-resistance genes were found to have a significantly higher ratio of nonsynonymous-to-synonymous SNPs. We identified 24 read-through (change a stop codon to a coding codon) SNPs and 38 premature stop (change a coding amino acid to a stop codon) SNPs and found that the 4 GO biological process terms were significantly over-represented in genes with read-through SNP compared to all cassava genes. All information on discovered DNA polymorphism was organized into the Cassava Online Archive. The web interface of the Cassava Online Archive contains SNP/InDels detail pages, which include the location, related gene model ID, and allele per variety or library for each discovered SNP. The database is publicly available at http://cassava.psc.riken.jp/.