title: Genome-wide discovery and information resource development of DNA polymorphisms in cassava.
abstract: Cassava (Manihot esculenta Crantz) 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 draft genome sequence and many expressed sequence tags are now publicly available, allowing the development of cassava polymorphism information. Here, we describe the genome-wide discovery of cassava DNA polymorphisms. Using the alignment of predicted transcribed sequences from the cassava draft genome sequence and ESTs from GenBank, we discovered 10,546 single-nucleotide polymorphisms and 647 insertions and deletions. To facilitate molecular marker development for cassava, we designed 9,316 PCR primer pairs to amplify the genomic region around each DNA polymorphism. Of the discovered SNPs, 62.7% occurred in protein-coding regions. Disease-resistance genes were found to have a significantly higher ratio of nonsynonymous-to-synonymous substitutions. We identified 24 read-through (changes of a stop codon to a coding codon) and 38 premature stop (changes of a coding codon to a stop codon) single-nucleotide polymorphisms, and found that the 5 gene ontology terms in biological process were significantly different in genes with read-through single-nucleotide polymorphisms compared with all cassava genes. All data on the discovered DNA polymorphisms were organized into the Cassava Online Archive database, which is available at http://cassava.psc.riken.jp/.
authors.affiliation: RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, Kanagawa, Japan.
authors.forename: Tetsuya
authors.initials: T
authors.lastname: Sakurai
authors.forename: Keiichi
authors.initials: K
authors.lastname: Mochida
authors.forename: Takuhiro
authors.initials: T
authors.lastname: Yoshida
authors.forename: Kenji
authors.initials: K
authors.lastname: Akiyama
authors.forename: Manabu
authors.initials: M
authors.lastname: Ishitani
authors.forename: Motoaki
authors.initials: M
authors.lastname: Seki
authors.forename: Kazuo
authors.initials: K
authors.lastname: Shinozaki
mesh_terms: D030541:Databases, Genetic; D018745:Genome, Plant; D055106:Genome-Wide Association Study; D054643:INDEL Mutation; D002365:Manihot / Q000235:genetics* / Q000378:metabolism; D058977:Molecular Sequence Annotation; D009862:Online Systems; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism; D011110:Polymorphism, Genetic; D020641:Polymorphism, Single Nucleotide; D015203:Reproducibility of Results
chemical_list: D010940:Plant Proteins
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