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...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Tetsuya Sakurai, Keiichi Mochida, Takuhiro Yoshida, Kenji Akiyama, Manabu Ishitani, Motoaki Seki, Kazuo Shinozaki
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2013
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/b02a6a931bf448139bae0d2541b181ac
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:b02a6a931bf448139bae0d2541b181ac
record_format	dspace
spelling	oai:doaj.org-article:b02a6a931bf448139bae0d2541b181ac2021-11-18T08:55:45ZGenome-wide discovery and information resource development of DNA polymorphisms in cassava.1932-620310.1371/journal.pone.0074056https://doaj.org/article/b02a6a931bf448139bae0d2541b181ac2013-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/24040164/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203Cassava (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/.Tetsuya SakuraiKeiichi MochidaTakuhiro YoshidaKenji AkiyamaManabu IshitaniMotoaki SekiKazuo ShinozakiPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 8, Iss 9, p e74056 (2013)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Tetsuya Sakurai Keiichi Mochida Takuhiro Yoshida Kenji Akiyama Manabu Ishitani Motoaki Seki Kazuo Shinozaki Genome-wide discovery and information resource development of DNA polymorphisms in cassava.
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	article
author	Tetsuya Sakurai Keiichi Mochida Takuhiro Yoshida Kenji Akiyama Manabu Ishitani Motoaki Seki Kazuo Shinozaki
author_facet	Tetsuya Sakurai Keiichi Mochida Takuhiro Yoshida Kenji Akiyama Manabu Ishitani Motoaki Seki Kazuo Shinozaki
author_sort	Tetsuya Sakurai
title	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_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_sort	genome-wide discovery and information resource development of dna polymorphisms in cassava.
publisher	Public Library of Science (PLoS)
publishDate	2013
url	https://doaj.org/article/b02a6a931bf448139bae0d2541b181ac
work_keys_str_mv	AT tetsuyasakurai genomewidediscoveryandinformationresourcedevelopmentofdnapolymorphismsincassava AT keiichimochida genomewidediscoveryandinformationresourcedevelopmentofdnapolymorphismsincassava AT takuhiroyoshida genomewidediscoveryandinformationresourcedevelopmentofdnapolymorphismsincassava AT kenjiakiyama genomewidediscoveryandinformationresourcedevelopmentofdnapolymorphismsincassava AT manabuishitani genomewidediscoveryandinformationresourcedevelopmentofdnapolymorphismsincassava AT motoakiseki genomewidediscoveryandinformationresourcedevelopmentofdnapolymorphismsincassava AT kazuoshinozaki genomewidediscoveryandinformationresourcedevelopmentofdnapolymorphismsincassava
_version_	1718421161312780288

Genome-wide discovery and information resource development of DNA polymorphisms in cassava.

Ejemplares similares