Genome-Wide discovery and information resource development of DNA polymorphisms in Cassava
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...
| Main Authors: | , , , , , , |
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| Format: | Journal Article |
| Language: | Inglés |
| Published: |
Public Library of Science
2013
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| Online Access: | https://hdl.handle.net/10568/51520 |
| _version_ | 1855532426445455360 |
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| author | Sakurai, T. Mochida, Keiichi Yoshida, T Akiyama, K. Ishitani, Manabu Seki, M. Shinozaki, Kazuo |
| author_browse | Akiyama, K. Ishitani, Manabu Mochida, Keiichi Sakurai, T. Seki, M. Shinozaki, Kazuo Yoshida, T |
| author_facet | Sakurai, T. Mochida, Keiichi Yoshida, T Akiyama, K. Ishitani, Manabu Seki, M. Shinozaki, Kazuo |
| author_sort | Sakurai, T. |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | 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/. |
| format | Journal Article |
| id | CGSpace51520 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2013 |
| publishDateRange | 2013 |
| publishDateSort | 2013 |
| publisher | Public Library of Science |
| publisherStr | Public Library of Science |
| record_format | dspace |
| spelling | CGSpace515202025-03-11T12:14:31Z Genome-Wide discovery and information resource development of DNA polymorphisms in Cassava Sakurai, T. Mochida, Keiichi Yoshida, T Akiyama, K. Ishitani, Manabu Seki, M. Shinozaki, Kazuo 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/. 2013 2014-11-12T13:42:26Z 2014-11-12T13:42:26Z Journal Article https://hdl.handle.net/10568/51520 en Open Access Public Library of Science Sakurai, Tetsuya, Mochida, Keiichi, Yoshida, Takuhiro, Akiyama, Kenji, Ishitani, Manabu, Seki, Motoaki, Shinozaki, Kazuo. 2013. Genome-Wide discovery and information resource development of DNA polymorphisms in Cassava. PLoS One. 8(9): e74056. |
| spellingShingle | Sakurai, T. Mochida, Keiichi Yoshida, T Akiyama, K. Ishitani, Manabu Seki, M. Shinozaki, Kazuo Genome-Wide discovery and information resource development of DNA polymorphisms in Cassava |
| title | Genome-Wide discovery and information resource development of DNA polymorphisms in Cassava |
| title_full | Genome-Wide discovery and information resource development of DNA polymorphisms in Cassava |
| title_fullStr | Genome-Wide discovery and information resource development of DNA polymorphisms in Cassava |
| title_full_unstemmed | Genome-Wide discovery and information resource development of DNA polymorphisms in Cassava |
| title_short | Genome-Wide discovery and information resource development of DNA polymorphisms in Cassava |
| title_sort | genome wide discovery and information resource development of dna polymorphisms in cassava |
| url | https://hdl.handle.net/10568/51520 |
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