Details for: GSOR 301159, Oryza sativa L., Vary Vato 462


Summary Data
Taxonomy:
Oryza sativa L.
Top Name:
Vary Vato 462
Origin:
Developed – Madagascar
Received by NPGS:
28 Jul 2007
Improvement Status:
Genetic material
Form Received:
Seed
Life Form:
Annual
Life Cycle:
Annual
Availability
FormQuantityNoteInventoryCart
Seed20 countGSOR 301159 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.
  
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PANICLE

Core Passport Data
Taxonomy:
Oryza sativa L.
Top Name:
Vary Vato 462
Origin:
Developed – Madagascar
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
Vary Vato 462
Type: Local name

NSFTV# 168
Type: Developer identifier

GSOR 301159
Type: Site identifier
Group: NSF
RICE DIVERSITY PANEL 1 (RPD1)

IRGC 117926
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
Deposit Form
Click here to go to the Rice Diversity website for additional information
Click here to be directed to the GSOR website to download Excel file of phenotypic and SSR marker data.
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
  • Chen, M.-H., C. J. Bergman, A. M. McClung, J. D. Everette, & R. E. Tabien. 2017. Resistant starch: variation among high amylose rice varieties and its relationship with apparent amylose content, pasting properties and cooking methods. Food Chem. 234:180-189. Number of accessions cited: 39
  • 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
  • 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
  • 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.23 NSF.PROJECT.OBS Not Available
CHEMICALAlkali/Spreading ValueAlkali/Spreading value6.4 NSF.PROJECT.OBS Not Available
CHEMICALProteinProtein content of the kernel, expressed as percent dry weight basis of brown rice.9 NSF.PROJECT.OBS Not Available
DISEASERice BlastReaction to Rice Blast (incited by Pyricularia oryzae). Standard blast rating scale.2.0 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 2.8 - 150 - 159 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 1.159 NSF.PROJECT.OBS Not Available
MORPHOLOGYPlant Type - Culm AngleCulm Angle, rice direct-seeded in rows.5 - OPEN NSF.PROJECT.OBS Not Available
MORPHOLOGYHull ColorHull color (Lemma and Palea) when terminal spikelets are ripened6 - MOTTTLED, SPECKLED, OR PIEBALD 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.6.4 NSF.PROJECT.OBS Not Available
MORPHOLOGYWidth of KernelWidth of kernel in millimeters for brown (dehulled) rice.2.6 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.5 - 100 - 109 DAYS NSF.PROJECT.OBS Not Available
PHENOLOGYDays to FlowerDays from emergence to flowering. Actual values. See also related descriptor Days to Anthesis.101 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.30.6 NSF.PROJECT.OBS Not Available
Genotype Data
Poly TypeMarkerValueEvaluationStudy TypeInventory
MICROSATELLITERM5105 105RICEDIVERSITY2011CROPSCIGDIVERSITYGSOR 301159 0.002 LV
MICROSATELLITERM001109 109RICEDIVERSITY2011CROPSCIGDIVERSITYGSOR 301159 0.002 LV
MICROSATELLITERM484294 294RICEDIVERSITY2011CROPSCIGDIVERSITYGSOR 301159 0.002 LV
MICROSATELLITERM171345 345RICEDIVERSITY2011CROPSCIGDIVERSITYGSOR 301159 0.002 LV
MICROSATELLITERM55missingRICEDIVERSITY2011CROPSCIGDIVERSITYGSOR 301159 0.002 LV
MICROSATELLITERM162209 209RICEDIVERSITY2011CROPSCIGDIVERSITYGSOR 301159 0.002 LV
MICROSATELLITERM27199 99RICEDIVERSITY2011CROPSCIGDIVERSITYGSOR 301159 0.002 LV
MICROSATELLITERM41372 72RICEDIVERSITY2011CROPSCIGDIVERSITYGSOR 301159 0.002 LV
MICROSATELLITERM447missingRICEDIVERSITY2011CROPSCIGDIVERSITYGSOR 301159 0.002 LV
MICROSATELLITERM44109 109RICEDIVERSITY2011CROPSCIGDIVERSITYGSOR 301159 0.002 LV
MICROSATELLITERM536235 235RICEDIVERSITY2011CROPSCIGDIVERSITYGSOR 301159 0.002 LV
MICROSATELLITERM133228 228RICEDIVERSITY2011CROPSCIGDIVERSITYGSOR 301159 0.002 LV
MICROSATELLITERM307172 172RICEDIVERSITY2011CROPSCIGDIVERSITYGSOR 301159 0.002 LV
MICROSATELLITERM22194 194RICEDIVERSITY2011CROPSCIGDIVERSITYGSOR 301159 0.002 LV
MICROSATELLITERM237194 194RICEDIVERSITY2011CROPSCIGDIVERSITYGSOR 301159 0.002 LV
MICROSATELLITERM495157 157RICEDIVERSITY2011CROPSCIGDIVERSITYGSOR 301159 0.002 LV
MICROSATELLITERM125123 123RICEDIVERSITY2011CROPSCIGDIVERSITYGSOR 301159 0.002 LV
MICROSATELLITERM178120 120RICEDIVERSITY2011CROPSCIGDIVERSITYGSOR 301159 0.002 LV
MICROSATELLITERM316197 197RICEDIVERSITY2011CROPSCIGDIVERSITYGSOR 301159 0.002 LV
MICROSATELLITERM154181 181RICEDIVERSITY2011CROPSCIGDIVERSITYGSOR 301159 0.002 LV
MICROSATELLITERM277118 118RICEDIVERSITY2011CROPSCIGDIVERSITYGSOR 301159 0.002 LV
MICROSATELLITERM215146 146RICEDIVERSITY2011CROPSCIGDIVERSITYGSOR 301159 0.002 LV
MICROSATELLITERM152141 141RICEDIVERSITY2011CROPSCIGDIVERSITYGSOR 301159 0.002 LV
MICROSATELLITERM011missingRICEDIVERSITY2011CROPSCIGDIVERSITYGSOR 301159 0.002 LV
MICROSATELLITERM408119 119RICEDIVERSITY2011CROPSCIGDIVERSITYGSOR 301159 0.002 LV
MICROSATELLITERM284142 142RICEDIVERSITY2011CROPSCIGDIVERSITYGSOR 301159 0.002 LV
MICROSATELLITERM338181 181RICEDIVERSITY2011CROPSCIGDIVERSITYGSOR 301159 0.002 LV
MICROSATELLITERM124267 267RICEDIVERSITY2011CROPSCIGDIVERSITYGSOR 301159 0.002 LV
MICROSATELLITERM161164 164RICEDIVERSITY2011CROPSCIGDIVERSITYGSOR 301159 0.002 LV
MICROSATELLITERM454271 271RICEDIVERSITY2011CROPSCIGDIVERSITYGSOR 301159 0.002 LV
MICROSATELLITERM507255 255RICEDIVERSITY2011CROPSCIGDIVERSITYGSOR 301159 0.002 LV
MICROSATELLITERM208164 164RICEDIVERSITY2011CROPSCIGDIVERSITYGSOR 301159 0.002 LV
MICROSATELLITERM431251 251RICEDIVERSITY2011CROPSCIGDIVERSITYGSOR 301159 0.002 LV
MICROSATELLITERM118missingRICEDIVERSITY2011CROPSCIGDIVERSITYGSOR 301159 0.002 LV
MICROSATELLITERM28797 97RICEDIVERSITY2011CROPSCIGDIVERSITYGSOR 301159 0.002 LV
MICROSATELLITERM452204 204RICEDIVERSITY2011CROPSCIGDIVERSITYGSOR 301159 0.002 LV