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NIASGBsnp: integration of single nucleotide polymorphism data of rice (Oryzasativa L.) genetic resources

Published online by Cambridge University Press:  21 March 2013

Masaru Takeya ,
Fukuhiro Yamasaki ,
Sachiko Hattori  and
Kaworu Ebana
Masaru Takeya*
Affiliation:
Genetic Resources Center, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki305-8602, Japan
Fukuhiro Yamasaki
Affiliation:
Genetic Resources Center, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki305-8602, Japan
Sachiko Hattori
Affiliation:
Genetic Resources Center, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki305-8602, Japan
Kaworu Ebana
Affiliation:
Genetic Resources Center, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki305-8602, Japan
*
* Corresponding author. E-mail: [email protected]
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Abstract

The NIASGBsnp system manages data on single nucleotide polymorphisms (SNPs) of rice (Oryzasativa L.) genetic resources in the National Institute of Agrobiological Science (NIAS) Genebank. NIASGBsnp currently holds data on 768 SNP markers for 301 rice accessions and plans to add the SNP data of active rice accessions in the NIAS Genebank. It can show differences between accessions by graphical genotyping. Passport, characteristics and evaluation data of accessions can be retrieved to allow phenotype to be associated with genotype. NIASGBsnp will support various research purposes such as genomic selection and plant pathology research.

Keywords

databasegenebanksgraphical genotypeOryzasativa LSNPWeb-based retrieval system
Type
Short Communication
Information
Plant Genetic Resources , Volume 11 , Issue 3 , December 2013 , pp. 221 - 224
Copyright
Copyright © NIAB 2013 

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References

Ebana, K, Yonemaru, J, Fukuoka, S, Iwata, H, Kanamori, H, Namiki, N, Nagasaki, H and Yano, M (2010) Genetic structure revealed by a whole-genome single-nucleotide polymorphism survey of diverse accessions of cultivated Asian rice (Oryza sativa L.). Breeding Science 60: 390–397.Google Scholar
International Rice Genome Sequencing Project (2005) The map-based sequence of the rice genome. Nature 436: 793–800.Google Scholar
Milne, I, Shaw, P, Stephen, G, Bayer, M, Cardle, L, Thomas, WTB, Flavell, AJ and Marshall, D (2010) Flapjack – graphical genotype visualization. Bioinformatics 26: 3133–3134.CrossRefGoogle ScholarPubMed
Okuno, K, Shirata, K, Niino, T and Kawase, M (2005) Plant genetic resources in Japan: platforms and destinations to conserve and utilize plant genetic diversity. Japan Agricultural Research Quarterly 39: 231–237.CrossRefGoogle Scholar
Takeya, M, Yamasaki, F, Uzuhashi, S, Aoki, T, Sawada, H, Nagai, T, Tomioka, K, Tomooka, N, Sato, T and Kawase, M (2011) NIASGBdb: NIAS Genebank databases for genetic resources and plant disease information. Nucleic Acids Research 39: D1108–D1113.CrossRefGoogle ScholarPubMed
Takeya, M, Yamasaki, F, Uzuhashi, S, Kumagai, M, Sawada, H, Nagai, T, Tomioka, K, Sato, T, Aoki, T and Kawase, M (2012) Development of a database of plant diseases in Japan and a system for making microorganism genetic resources and their DNA sequence data available to the research community. Japan Agricultural Research Quarterly 46: 193–198.Google Scholar