Details for: GSOR 301409, Oryza sativa L., Jefferson


Summary Data
Taxonomy:
Oryza sativa L.
Top Name:
Jefferson
Origin:
Developed – United States
Received by NPGS:
28 Jul 2007
Improvement Status:
Genetic material
Form Received:
Seed
Life Form:
Annual
Life Cycle:
Annual
Availability
FormQuantityNoteInventoryCart
Seed20 countGSOR 301409 A11FA3 SD
Please send an email to gsor@ars-grin.gov to order the entire Rice Diversity Panel 1. Note that a few accessions are restricted and not available for distribution through the GSOR. Also in 2013, the Oryza SNP Set was included into the RDP1, increasing the accession count to 419.
  
Images (1 total. Click on image for more.)

PANICLE

Core Passport Data
Taxonomy:
Oryza sativa L.
Top Name:
Jefferson
Origin:
Developed – United States
Received by NPGS:
28 Jul 2007
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
Jefferson
Type: Local name

NSFTV# 628
Type: Developer identifier

GSOR 301409
Type: Site identifier
Group: NSF
RICE DIVERSITY PANEL 1 (RPD1)

IRGC 126385
Type: Other or unclassified name

Narrative
To represent the range of genetic diversity found in cultivated Asian rice, 409 Oryza sativa accessions were selected from around the world. They cover the full geographic and ecological range of rice- from Indonesian paddy terraces, to the harsh upland soils of northern Thailand; from rapidly rising Chinese riverbeds to African mangrove environments. The 409 O. sativa accessions represent all five sub-populations of rice: indica, aus, tropical japonica, temperate japonica and Group V (sometimes called aromatic or basmati) varieties. The diverse set of rice accessions also includes a wide range of important economic phenotypes, including varieties known to be resistant to diseases and insects or tolerant to flooding, drought, high salt concentrations, low mineral nutrition. There are also varieties with varying cooking qualities, such as different grain colors, lengths, textures, and fragrance. The accessions were chosen to build upon several previous studies, including a subset of the varieties used by Garris et al. (2005) to evaluate sub-population structure in O. sativa. Approximately 200 of our accessions overlap with the 3,000 analyzed for diversity within the internationally-funded Generation Challenge Program (GCP) and 159 overlap with the USDA-ARS rice core collection. This Rice Diversity Panel was fingerprinted with 36 simple sequence repeat (SSR) markers and evaluated for 18 agro-morphological traits. The rice diversity panel with the accompanying genetic and phenotypic information provides a valuable foundation for association mapping, understanding the basis of both genotypic and phenotypic differences within and between subpopulations, and rice improvement programs.
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
Deposit Form
Click here to be directed to the GSOR website to download Excel file of phenotypic and SSR marker data.
Deposit Form
Click here to go to the Rice Diversity website for additional information
Actions
Pathogens
Vouchers
Citations
  • Ali, M. L., A. M. McClung, M. H. Jia, J. A. Kimball, S. R. McCouch, & G. C. Eizenga. 2011. A rice diversity panel evaluated for genetic and agro-morphological diversity between subpopulations and its geographic distribution. Crop Sci. (Madison) 51:2021-2035. DOI: 10.2135/cropsci2010.11.0641. Number of accessions cited: 410
  • 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: 168
  • 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
  • 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: 29
  • Pinson, S. R. M., L. Tarpley, W. Yan, K. Yeater, B. Lahner, E. Yakubova, X.-Y. Huang, M. Zhang, M. L. Guerinot, & D. E. Salt. 2015. World-wide genetic diversity for mineral element concentrations in rice grain. Crop Sci. (Madison) 55:1-18. DOI: 10.2135/cropsci2013.10.0656. Note: Key Words: Biofortification, Ionomics, Rice, Oryza sativa L., Genetic Diversity Number of accessions cited: 1763
  • 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
  • Zhao, K. et al. 2010. Genomic diversity and introgression in O. sativa reveal the impact of domestication and breeding on the rice genome. PLoS One 5(5):e10780. DOI: 10.1371/journal.pone.0010780. Number of accessions cited: 410
  • Zhao, Keyan, C.-W. Tung, G. C. Eizenga, M. H. Wright, Md. L. Ali, A. H. Price, G. J. Norton, M. R. Islam, A. Reynolds, J. Mezey, A. M. McClung, C. D. Bustamate, & S. R. McCouch. 2011. Genome-wide association mapping reveals a rich genetic architecture of complex traits in Oryza sativa. Nat. Commun. 2:467. DOI: 10.1038/ncomms1467. Number of accessions cited: 410
  • 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

Observations

Phenotype Data

CategoryDescriptorDescriptionValueSample SizeStudyInventoryAvailability
CHEMICALAmylosePercent amylose of milled rice.26 NSF.PROJECT.OBS Not Available
CHEMICALAlkali/Spreading ValueAlkali/Spreading value6.2 NSF.PROJECT.OBS Not Available
CHEMICALProteinProtein content of the kernel, expressed as percent dry weight basis of brown rice.8.7 NSF.PROJECT.OBS Not Available
DISEASERice BlastReaction to Rice Blast (incited by Pyricularia oryzae). Standard blast rating scale.1.0 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 2.1 - 80 - 89 CENTIMETERS NSF.PROJECT.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 1.82 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.0 - ABSENT 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.7.4 NSF.PROJECT.OBS Not Available
MORPHOLOGYWidth of KernelWidth of kernel in millimeters for brown (dehulled) rice.2.4 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 FlowerDays from emergence to flowering. Actual values. See also related descriptor Days to Anthesis.83 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.25.14 NSF.PROJECT.OBS Not Available
Genotype Data
Poly TypeMarkerValueEvaluationStudy TypeInventory
MICROSATELLITERM5126 126RICEDIVERSITY2011CROPSCIGDIVERSITYGSOR 301409 0.002 LV
MICROSATELLITERM00184 84RICEDIVERSITY2011CROPSCIGDIVERSITYGSOR 301409 0.002 LV
MICROSATELLITERM484292 292RICEDIVERSITY2011CROPSCIGDIVERSITYGSOR 301409 0.002 LV
MICROSATELLITERM171345 345RICEDIVERSITY2011CROPSCIGDIVERSITYGSOR 301409 0.002 LV
MICROSATELLITERM55missingRICEDIVERSITY2011CROPSCIGDIVERSITYGSOR 301409 0.002 LV
MICROSATELLITERM162239 239RICEDIVERSITY2011CROPSCIGDIVERSITYGSOR 301409 0.002 LV
MICROSATELLITERM27186 86RICEDIVERSITY2011CROPSCIGDIVERSITYGSOR 301409 0.002 LV
MICROSATELLITERM41377 77RICEDIVERSITY2011CROPSCIGDIVERSITYGSOR 301409 0.002 LV
MICROSATELLITERM447110 110RICEDIVERSITY2011CROPSCIGDIVERSITYGSOR 301409 0.002 LV
MICROSATELLITERM4492 92RICEDIVERSITY2011CROPSCIGDIVERSITYGSOR 301409 0.002 LV
MICROSATELLITERM536226 226RICEDIVERSITY2011CROPSCIGDIVERSITYGSOR 301409 0.002 LV
MICROSATELLITERM133230 230RICEDIVERSITY2011CROPSCIGDIVERSITYGSOR 301409 0.002 LV
MICROSATELLITERM307127 127RICEDIVERSITY2011CROPSCIGDIVERSITYGSOR 301409 0.002 LV
MICROSATELLITERM22192 192RICEDIVERSITY2011CROPSCIGDIVERSITYGSOR 301409 0.002 LV
MICROSATELLITERM237192 192RICEDIVERSITY2011CROPSCIGDIVERSITYGSOR 301409 0.002 LV
MICROSATELLITERM495160 160RICEDIVERSITY2011CROPSCIGDIVERSITYGSOR 301409 0.002 LV
MICROSATELLITERM125126 126RICEDIVERSITY2011CROPSCIGDIVERSITYGSOR 301409 0.002 LV
MICROSATELLITERM178114 114RICEDIVERSITY2011CROPSCIGDIVERSITYGSOR 301409 0.002 LV
MICROSATELLITERM316214 214RICEDIVERSITY2011CROPSCIGDIVERSITYGSOR 301409 0.002 LV
MICROSATELLITERM154183 183RICEDIVERSITY2011CROPSCIGDIVERSITYGSOR 301409 0.002 LV
MICROSATELLITERM277113 113RICEDIVERSITY2011CROPSCIGDIVERSITYGSOR 301409 0.002 LV
MICROSATELLITERM215154 154RICEDIVERSITY2011CROPSCIGDIVERSITYGSOR 301409 0.002 LV
MICROSATELLITERM152144 144RICEDIVERSITY2011CROPSCIGDIVERSITYGSOR 301409 0.002 LV
MICROSATELLITERM011129 129RICEDIVERSITY2011CROPSCIGDIVERSITYGSOR 301409 0.002 LV
MICROSATELLITERM408127 127RICEDIVERSITY2011CROPSCIGDIVERSITYGSOR 301409 0.002 LV
MICROSATELLITERM284144 144RICEDIVERSITY2011CROPSCIGDIVERSITYGSOR 301409 0.002 LV
MICROSATELLITERM338181 181RICEDIVERSITY2011CROPSCIGDIVERSITYGSOR 301409 0.002 LV
MICROSATELLITERM124271 271RICEDIVERSITY2011CROPSCIGDIVERSITYGSOR 301409 0.002 LV
MICROSATELLITERM161180 180RICEDIVERSITY2011CROPSCIGDIVERSITYGSOR 301409 0.002 LV
MICROSATELLITERM454missingRICEDIVERSITY2011CROPSCIGDIVERSITYGSOR 301409 0.002 LV
MICROSATELLITERM507259 259RICEDIVERSITY2011CROPSCIGDIVERSITYGSOR 301409 0.002 LV
MICROSATELLITERM208164 164RICEDIVERSITY2011CROPSCIGDIVERSITYGSOR 301409 0.002 LV
MICROSATELLITERM431253 253RICEDIVERSITY2011CROPSCIGDIVERSITYGSOR 301409 0.002 LV
MICROSATELLITERM118161 161RICEDIVERSITY2011CROPSCIGDIVERSITYGSOR 301409 0.002 LV
MICROSATELLITERM287101 101RICEDIVERSITY2011CROPSCIGDIVERSITYGSOR 301409 0.002 LV
MICROSATELLITERM452207 207RICEDIVERSITY2011CROPSCIGDIVERSITYGSOR 301409 0.002 LV