publication . Article . Other literature type . 2016

Ricebase: a breeding and genetics platform for rice, integrating individual molecular markers, pedigrees and whole-genome-based data

J. D. Edwards; A. M. Baldo; L. A. Mueller;
Open Access English
  • Published: 01 Aug 2016 Journal: Database: The Journal of Biological Databases and Curation, volume 2,016 (eissn: 1758-0463, Copyright policy)
  • Publisher: Oxford University Press
Abstract
Ricebase (http://ricebase.org) is an integrative genomic database for rice (Oryza sativa) with an emphasis on combining datasets in a way that maintains the key links between past and current genetic studies. Ricebase includes DNA sequence data, gene annotations, nucleotide variation data and molecular marker fragment size data. Rice research has benefited from early adoption and extensive use of simple sequence repeat (SSR) markers; however, the majority of rice SSR markers were developed prior to the latest rice pseudomolecule assembly. Interpretation of new research using SNPs in the context of literature citing SSRs requires a common coordinate system. A new...
Subjects
Medical Subject Headings: food and beverages
free text keywords: Original Article, Molecular marker, chemistry.chemical_compound, chemistry, Amplicon, Biology, Genome, Genetic marker, Molecular Sequence Annotation, Bioinformatics, Gene Annotation, DNA sequencing, Genome browser, Genetics
23 references, page 1 of 2

1 Arumuganathan K.Earle E. (1991) Nuclear DNA content of some important plant species. Plant Mol. Biol. Rep., 9, 208–218. [OpenAIRE]

2 Khush G.S. (2005) What it will take to feed 5.0 billion rice consumers in 2030. Plant Mol. Biol., 59, 1–6.16217597 [PubMed]

3 FAO. (2009) Increasing Crop Production Sustainably. The Perspective of Biological Processes. Food and Agriculture Organization of the United Nations, Rome.

4\Goff S.A.Ricke D.Lan T.H., (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science, 296, 92–100.11935018 [OpenAIRE] [PubMed]

5 Yu J.Hu S.Wang J., (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science, 296, 79–92.11935017 [OpenAIRE] [PubMed]

6 International Rice Genome Sequencing Project (2005) The map-based sequence of the rice genome. Nature, 436, 793–800.16100779 [PubMed]

7 Kawahara Y.de la Bastide M.Hamilton J.P., (2013) Improvement of the Oryza sativa nipponbare reference genome using next generation sequence and optical map data. Rice, 6, 4.24280374 [OpenAIRE] [PubMed]

8 McCouch S.R.Wright M.H.Tung C., (2016) Open access resources for genome-wide association mapping in rice. Nat. Commun, 7, 10532.26842267 [OpenAIRE] [PubMed]

9 Zhao K.Tung C.Eizenga G.C., (2011) Genome-wide association mapping reveals a rich genetic architecture of complex traits in Oryza sativa. Nat. Commun., 2, 467.21915109 [OpenAIRE] [PubMed]

10 Alexandrov N.Tai S.Wang W., (2015) SNP-seek database of SNPs derived from 3000 rice genomes. Nucleic Acids Res., 43, D1023–D1027.25429973 [OpenAIRE] [PubMed]

11 Duitama J.Silva A.Sanabria Y., (2015) Whole genome sequencing of elite rice cultivars as a comprehensive information resource for marker assisted selection. PloS One, 10, e0124617.25923345 [OpenAIRE] [PubMed]

12 Temnykh S.DeClerck G.Lukashova A., (2001) Computational and experimental analysis of microsatellites in rice (Oryza sativ a L.): frequency, length variation, transposon associations, and genetic marker potential. Genome Res., 11, 1441–1452.11483586 [OpenAIRE] [PubMed]

13 McCouch S.R.Teytelman L.Xu Y., (2002) Development and mapping of 2240 new SSR markers for rice (Oryza sativa L.). DNA Res, 9, 199–207.12597276 [OpenAIRE] [PubMed]

14 Bligh H.Till R.Jones C. (1995) A microsatellite sequence closely linked to the waxy gene of Oryza sativa. Euphytica, 86, 83–85.

15 Altschul S.F.Gish W.Miller W., (1990) Basic local alignment search tool. J. Mol. Biol., 215, 403–410.2231712 [OpenAIRE] [PubMed]

23 references, page 1 of 2
Abstract
Ricebase (http://ricebase.org) is an integrative genomic database for rice (Oryza sativa) with an emphasis on combining datasets in a way that maintains the key links between past and current genetic studies. Ricebase includes DNA sequence data, gene annotations, nucleotide variation data and molecular marker fragment size data. Rice research has benefited from early adoption and extensive use of simple sequence repeat (SSR) markers; however, the majority of rice SSR markers were developed prior to the latest rice pseudomolecule assembly. Interpretation of new research using SNPs in the context of literature citing SSRs requires a common coordinate system. A new...
Subjects
Medical Subject Headings: food and beverages
free text keywords: Original Article, Molecular marker, chemistry.chemical_compound, chemistry, Amplicon, Biology, Genome, Genetic marker, Molecular Sequence Annotation, Bioinformatics, Gene Annotation, DNA sequencing, Genome browser, Genetics
23 references, page 1 of 2

1 Arumuganathan K.Earle E. (1991) Nuclear DNA content of some important plant species. Plant Mol. Biol. Rep., 9, 208–218. [OpenAIRE]

2 Khush G.S. (2005) What it will take to feed 5.0 billion rice consumers in 2030. Plant Mol. Biol., 59, 1–6.16217597 [PubMed]

3 FAO. (2009) Increasing Crop Production Sustainably. The Perspective of Biological Processes. Food and Agriculture Organization of the United Nations, Rome.

4\Goff S.A.Ricke D.Lan T.H., (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science, 296, 92–100.11935018 [OpenAIRE] [PubMed]

5 Yu J.Hu S.Wang J., (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science, 296, 79–92.11935017 [OpenAIRE] [PubMed]

6 International Rice Genome Sequencing Project (2005) The map-based sequence of the rice genome. Nature, 436, 793–800.16100779 [PubMed]

7 Kawahara Y.de la Bastide M.Hamilton J.P., (2013) Improvement of the Oryza sativa nipponbare reference genome using next generation sequence and optical map data. Rice, 6, 4.24280374 [OpenAIRE] [PubMed]

8 McCouch S.R.Wright M.H.Tung C., (2016) Open access resources for genome-wide association mapping in rice. Nat. Commun, 7, 10532.26842267 [OpenAIRE] [PubMed]

9 Zhao K.Tung C.Eizenga G.C., (2011) Genome-wide association mapping reveals a rich genetic architecture of complex traits in Oryza sativa. Nat. Commun., 2, 467.21915109 [OpenAIRE] [PubMed]

10 Alexandrov N.Tai S.Wang W., (2015) SNP-seek database of SNPs derived from 3000 rice genomes. Nucleic Acids Res., 43, D1023–D1027.25429973 [OpenAIRE] [PubMed]

11 Duitama J.Silva A.Sanabria Y., (2015) Whole genome sequencing of elite rice cultivars as a comprehensive information resource for marker assisted selection. PloS One, 10, e0124617.25923345 [OpenAIRE] [PubMed]

12 Temnykh S.DeClerck G.Lukashova A., (2001) Computational and experimental analysis of microsatellites in rice (Oryza sativ a L.): frequency, length variation, transposon associations, and genetic marker potential. Genome Res., 11, 1441–1452.11483586 [OpenAIRE] [PubMed]

13 McCouch S.R.Teytelman L.Xu Y., (2002) Development and mapping of 2240 new SSR markers for rice (Oryza sativa L.). DNA Res, 9, 199–207.12597276 [OpenAIRE] [PubMed]

14 Bligh H.Till R.Jones C. (1995) A microsatellite sequence closely linked to the waxy gene of Oryza sativa. Euphytica, 86, 83–85.

15 Altschul S.F.Gish W.Miller W., (1990) Basic local alignment search tool. J. Mol. Biol., 215, 403–410.2231712 [OpenAIRE] [PubMed]

23 references, page 1 of 2
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publication . Article . Other literature type . 2016

Ricebase: a breeding and genetics platform for rice, integrating individual molecular markers, pedigrees and whole-genome-based data

J. D. Edwards; A. M. Baldo; L. A. Mueller;