Details for: GSOR 312005, Oryza sativa L., 'Nipponbare'


Summary Data
Taxonomy:
Oryza sativa L.
Cultivar:
'Nipponbare'
Origin:
Donated – Japan
Received by NPGS:
30 Apr 2010
Improvement Status:
Genetic material
Form Received:
Seed
Life Form:
Annual
Life Cycle:
Annual
Availability
FormQuantityNoteInventoryCart
Seed20 countGSOR 312005 A10FA3 SD
 
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PANICLE

Core Passport Data
Taxonomy:
Oryza sativa L.
Cultivar:
'Nipponbare'
Origin:
Donated – Japan
Received by NPGS:
30 Apr 2010
Improvement Status:
Genetic material
Form Received:
Seed
Life Form:
Annual
Life Cycle:
Annual
Source History
Accession Group(s)
Group name: GSOR Rice Diversity Panel 1
Note: 
To search for accessions in this group, click the following link. GSOR Rice Diversity Panel 1

Accession Names and Identifiers
'Nipponbare'
Type: Cultivar name

NSFTV# 639
Type: Developer identifier

GSOR 312005
Type: Site identifier
Group: ORYZASNP

IRGC 117274
Type: Other or unclassified name

Narrative
A consortium of NRI funded researchers at Colorado State University, The Institute for Genomic Research, the International Rice Research Institute, Perlegen Sciences, and the Max Planck Institute collaborated on the OryzaSNP Project that involved genome-wide single nucleotide polymorphism (SNP) discovery across a unique fraction of the rice genome. This partnership has identified SNPs from across the whole genome of 20 rice cultivars. SNPs are a marker of genetic variation between individuals of species that allow scientists to identify regions of genetic variation that may be linked. Examples of traits that might be linked include plant development, yield, disease resistance, drought tolerance, and nutritional value. Rice is the world's top food crop and principal source of nourishment for nearly half the world's population. By identifying and comparing differences in DNA sequences, the new knowledge will accelerate development of hardier, more productive types of rice, particularly for people in the poorest but fastest growing nations. The consortium released all the SNP data at a public workshop held during the 5th International Symposium of Rice Functional Genomics, October 15-17, 2007, in Tsukuba, Japan. The research team facilitated discussions with participants on how to use the many SNPs generated to forward rice genomics, genetics and breeding.
Oryza sativa L.
Genus:
Oryza
Section:
Oryza
Subsection:
Oryza
Family:
Poaceae (alt. Gramineae)
Subfamily:
Oryzoideae
Tribe:
Oryzeae
Subtribe:
Oryzinae
Nomen number:

26077
Place of publication:

Sp. pl. 1:333. 1753
Comment:
some seed lots of domesticated rice may contain contaminants of a noxious weed hybrid-form that are not distinguishable by seed visualization, which is responsible for the rice-growing state's noxious-weed seed regulations indicated below
Verified:
05/11/1992 by ARS Systematic Botanists.
Other conspecific taxa
Autonyms (not in current use), synonyms and invalid designations
Autonym(s)
Oryza sativa L. f. sativa
Oryza sativa L. subsp. sativa
Oryza sativa L. var. sativa

Heterotypic Synonym(s)
Common names
LanguageNameAlternate namenoteseqCitation
EnglishAsian rice  1Hanelt, P., ed. 2001. Mansfeld's encyclopedia of agricultural and horticultural crops. Volumes 1-6
Englishlowland rice  1Hanelt, P., ed. 2001. Mansfeld's encyclopedia of agricultural and horticultural crops. Volumes 1-6
Englishrice  1Wiersema, J. H. & B. León. 1999. World economic plants: a standard reference CRC Press, Boca Raton, FL.
Englishupland rice  1Hanelt, P., ed. 2001. Mansfeld's encyclopedia of agricultural and horticultural crops. Volumes 1-6
Arabicrozz  2Boulos, L. 1999-. Flora of Egypt
Frenchriz  2Rehm, S. 1994. Multilingual dictionary of agronomic plants
GermanReis  2Rehm, S. 1994. Multilingual dictionary of agronomic plants
Indiachavel  2Rehm, S. 1994. Multilingual dictionary of agronomic plants
Italianriso  2Hanelt, P., ed. 2001. Mansfeld's encyclopedia of agricultural and horticultural crops. Volumes 1-6
Japanese Rōmajiine  2Batra, L. R. 1995. Names of Japanese plants sorted by their Japanese names in Romanized Katakana and scientific nomenclature
Portuguesearroz  2Rehm, S. 1994. Multilingual dictionary of agronomic plants
Spanisharroz  2Rehm, S. 1994. Multilingual dictionary of agronomic plants
Swedishris  2Aldén, B., S. Ryman, & M. Hjertson. 2012. Svensk Kulturväxtdatabas, SKUD (Swedish Cultivated and Utility Plants Database; online resource)
Transcribed Chinesedao  2Wu Zheng-yi & P. H. Raven et al., eds. 1994-. Flora of China (English edition).
Annotations
Other Links
Click here to be directed to the GSOR website to download Excel file of phenotypic and SSR marker data.
Click here to go to the Rice Diversity website for additional information
Deposit Form
Deposit Form
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Pathogens
Vouchers
Citations
  • Dimpka, S. O. N., Z. Lahari, R. Shrestha, A. Douglas, G. Gheysen, & A. H. Price. 2015. A genome-wide association study of a global rice panel reveals resistance in Oryza sativa to root-knot nematodes. J. Exp. Bot. 67(4):1191-1200. DOI: 10.1093/jxb/erv470. Number of accessions cited: 419
  • Eizenga, G. C., M. L. Ali, R. J. Bryant, K. M. Yeater, A. M. McClung, & S. R. McCouch. 2014. Registration of the rice diversity panel 1 for genome-wide association studies. J. Pl. Registr. 8(1):109. Number of accessions cited: 423
  • Eizenga, Georgia C., Anna M. McClung, & Trevis D. Huggins. 2021. Registration of two Oryza sativa tropical japonica germplasm lines selected for panicle architecture and grain size traits. J. Pl. Registr. 2021:1-10. DOI: 10.1002/plr.20145. Number of accessions cited: 419
  • McCouch, S. R. et al. 2016. Open access resources for genome-wide association mapping in rice. Nat. Commun. 7:10532. DOI: 10.1038/NCOMMS10532. Number of accessions cited: 1720
  • McNally, K. L., K. L. Childs, R. Bohnert, R. M. Davidson, K. Zhao, V. J. Ulat, G. Zeller, R. M. Clark, D. R. Hoen, T. E. Bureau, R. Stokowski, D. G. Ballinger, K. A. Frazer, D. R. Cox, B. Padhukasahasram, C. D. Bustamante, D. Weigel, D. J. Mackill, R. M. Bruskiewich, G. Ratsch, C. R. Buell, H. Leung, & J. E. Leach. 2009. Genomewide SNP variation reveals relationships among landraces and modern varieties of rice. Proc. Natl. Acad. Sci. U.S.A. 106:12273-12278. DOI: 10.1073/pnas.0900992106. Number of accessions cited: 20
  • McNally, K. L., R. Bruskiewich, D. Mackill, C. R. Buell, J. E. Leach, & H. Leung. 2006. Sequencing multiple and diverse rice varieties. Connecting whole-genome variation with phenotypes. Pl. Physiol. (Lancaster) 141:26-31. DOI: 10.1104/pp.106.077313. Number of accessions cited: 11
  • McNally, K., R. Bruskiewich, D. Mackill, D. Weigel, K. Frazer, K. Childs, R. Buell, J. Leach, & H. Leung. 2007. The OryzaSNP Project - SNP discovery in diverse rice. Molec. Pl. Breed. 5(2)246-247. Number of accessions cited: 20
  • Norton, G. J. et al. 2014. Genome wide association mapping of grain Arsenic, Copper, Molybdenum and Zinc in rice (Oryza sativa L.) grown at four international field sites. PLoS One 9(2):e89685. DOI: 10.1371/journal.pone.0089685. Number of accessions cited: 390
  • Shakiba, E., J. D. Edwards, F. Jodari, S. E. Duke, A. M. Baldo, P. Korniliev, S. R. McCouch, & G. C. Eizenga. 2017. Genetic architecture of cold tolerance in rice (Oryza sativa) determined through high resolution genome-wide analysis. PLoS One 12(3):e0172133. DOI: 10.1371/journal.pone.0172133. Number of accessions cited: 419
  • Shimoyama, Naoki, M. Johnson, A. Beaumont, & M. Schlappi. 2020. Multiple cold tolerance trait phenotyping reveals shared quantitative trait loci in Oryza sativa. Rice 2020:13:57. DOI: 10.1186/s12284-020-00414-3. Number of accessions cited: 419
  • Wang, D., J. Liu, C. Li, H. Kang, Y. Wang, X. Tan, M. Liu, Y. Deng, Z. Wang, Y. Liu, D. Zhang, Y. Xiao, & G.-L. Wang. 2016. Genome-wide association mapping of cold tolerance genes at the seedling stage in rice. Rice 9:61. DOI: 10.1186/s12284-016-0133-2. Number of accessions cited: 419
  • Zhu, D., H. Kang, Z. Li, M. Liu, X. Zhu, Y. Wang, D. Wang, Z. Wang, W. Liu, & G.-L. Wang. 2016. A genome-wide association study of field resistance to Magnaporthe oryzae in rice. Rice 9:44. DOI: 10.1186/s12284-016-0116-3. Number of accessions cited: 419
Pedigree
Intellectual Property Rights
IRRI Disclaimer. Issued: 26 Oct 1994.

Observations

Phenotype Data

CategoryDescriptorDescriptionValueSample SizeStudyInventoryAvailability
CHEMICALAmylosePercent amylose of milled rice.19 NSF.PROJECT.OBS Not Available
CHEMICALAlkali/Spreading ValueAlkali/Spreading value7 NSF.PROJECT.OBS Not Available
CHEMICALProteinProtein content of the kernel, expressed as percent dry weight basis of brown rice.7.3 NSF.PROJECT.OBS Not Available
DISEASERice BlastReaction to Rice Blast (incited by Pyricularia oryzae). Standard blast rating scale.4.0 NSF.PROJECT.OBS Not Available
GROWTHPlant Height 1Plant height measured from the soil surface to the tip of extended panicles. Coded values. See also related descriptor Plant Height 2.2 - 90 - 99 CENTIMETERS NSF.PROJECT.OBS Not Available
GROWTHPlant Height 1Plant height measured from the soil surface to the tip of extended panicles. Coded values. See also related descriptor Plant Height 2.2 - 90 - 99 CENTIMETERS 2010.GSOR.FIELD.OBS Not Available
GROWTHPlant Height 2Plant height measured in centimeters from the soil surface to the middle of extended panicles. Actual values. See also related descriptor Plant Height 1.95 NSF.PROJECT.OBS Not Available
MORPHOLOGYPlant Type - Culm AngleCulm Angle, rice direct-seeded in rows.3 - INTERMEDIATE NSF.PROJECT.OBS Not Available
MORPHOLOGYHull ColorHull color (Lemma and Palea) when terminal spikelets are ripened2 - STRAW NSF.PROJECT.OBS Not Available
MORPHOLOGYAwn TypeAmount and extent of awns.1 - SHORT AND PARTLY AWNED NSF.PROJECT.OBS Not Available
MORPHOLOGYBran ColorColor of seed coat (bran/pericarp) when fully mature and dry.2 - LIGHT BROWN NSF.PROJECT.OBS Not Available
MORPHOLOGYLength of KernelLength of kernel in millimeters for brown (dehulled) rice.5.2 NSF.PROJECT.OBS Not Available
MORPHOLOGYWidth of KernelWidth of kernel in millimeters for brown (dehulled) rice.3 NSF.PROJECT.OBS Not Available
PHENOLOGYDays to AnthesisNumber of days from effective seeding date until 50% of main tillers show panicles at least partly emerged from boot. Coded values. See also related descriptor Days to Flower.3 - 80 - 89 DAYS NSF.PROJECT.OBS Not Available
PHENOLOGYDays to AnthesisNumber of days from effective seeding date until 50% of main tillers show panicles at least partly emerged from boot. Coded values. See also related descriptor Days to Flower.6 - 110 - 119 DAYS 2010.GSOR.FIELD.OBS Not Available
PHENOLOGYDays to FlowerDays from emergence to flowering. Actual values. See also related descriptor Days to Anthesis.81 NSF.PROJECT.OBS Not Available
PRODUCTION1000 Kernel Weight-RoughThousand kernel weight of rough rice, based on a count of 100 or more. Expressed in grams.26.05 NSF.PROJECT.OBS Not Available