Details for: GSOR 310039, Oryza sativa L., C 5560


Summary Data
Taxonomy:
Oryza sativa L.
Top Name:
C 5560
Origin:
Collected – Thailand
Received by NPGS:
1969
Improvement Status:
Cultivated material
Form Received:
Seed
Life Form:
Annual
Life Cycle:
Annual
Availability
FormQuantityNoteInventoryCart
Seed3 gramGSOR 310039 A10FA3 SD
 
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KERNELS

Core Passport Data
Taxonomy:
Oryza sativa L.
Top Name:
C 5560
Origin:
Collected – Thailand
Received by NPGS:
1969
Improvement Status:
Cultivated material
Form Received:
Seed
Life Form:
Annual
Life Cycle:
Annual
Source History
Collected

Thailand
Coordinates: 15.0000, 100.0000 (Map it)
Georeference protocol: Center of country

Accession Group(s)
Group name: GSOR Core Collection
Note: 
To search for accessions in this group, click the following link. GSOR Core Collection

Group name: GSOR Mini Core
Note: 
To search for accessions in this group, click the following link. GSOR Mini Core

Accession Names and Identifiers
C 5560
Type: Institute identifier

IRRI-IRGC-7466
Type: Institute identifier
Group: SINGER-IRRI-RICE
Another genebank holding this accession
International Rice Research Institute

WC 4237
Type: Institute identifier
USDA, ARS

CI 9723
Type: Other or unclassified name

GPNO 21393
Type: Other or unclassified name
Group: GPNO
Stuttgart, AR number assigned 1984-1986.

Narrative
Core Accession from CIor 9723. The Core Collection containing about 10% of the whole NSGC Rice Collection was assembled by stratified random sampling method in 2002, evaluated comprehensively for 25 characteristics and proven to be highly representative of the whole collection. Information drawn from the Core Collection can effectively be used to assess the diversity of the whole collection with 88% certainty. A single plant was selected from each Core accession in 2006 and bulk seed from the single plant selection was produced in 2007 and deposited in the GSOR. DNA extracted from the selected plant was analyzed with one indel marker and 71 SSR (Single Sequence Repeat) markers that cover the entire rice genome about 30 cM apart. A Mini-Core Collection containing about 10% of the Core Collection was subsequently developed and genotyped through various means.The original narrative is: Upland.

Because the Core and Mini-Core were developed from single-plant selections from the NSGC accessions which may be phenotypically variable, there is the possibility that the GSOR seed sources are not exactly the same as the NSGC sources.

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
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Pathogens
Vouchers
Citations
  • Agrama, H. A, W. Yan, F. Lee, R. Fjellstrom, M.-H. Chen, M. Jia, & A. McClung. 2009. Genetic assessment of a Mini-Core subset developed from the USDA rice genebank. Crop Sci. (Madison) 49:1336-1346. DOI: 10.2135/cropsci2008.06.0551. Number of accessions cited: 1794
  • Agrama, H. A. & W. G. Yan. 2009. Association mapping of straighthead disorder induced by arsenic in Oryza sativa. Pl. Breed. (New York) 128:551-558. Number of accessions cited: 1794
  • Agrama, H. A. & W. G. Yan. 2009. Genetic diversity and relatedness of rice cultivars resistant to straighthead disorder. Pl. Breed. (New York) 129:304-312. Number of accessions cited: 1794
  • Agrama, H. A., W. G. Yan, M. Jia, R. Fjellstrom, & A. M. McClung. 2010. Genetic structure associated with diversity and geographic distribution in the USDA rice world collection. Nat. Sci. (Sci. Res. Press) 2:247-291. DOI: 10.4236/ns.2010.24036. Number of accessions cited: 1755
  • Agrama, H., A. M. McClung, & WenGui Yan. 2011. Using minimum DNA marker loci for accurate population classification in rice (Oryza sativa L.). Molec. Breed. 29:413-425. DOI: 10.1007/s11032-011-9558-x. Number of accessions cited: 1794
  • Barnaby, J. Y., T. D. Huggins, H. Lee, et al. 2020. Vis/NIR hyperspectral imaging distinguishes sub-population, production environment, and physicochemical grain properties in rice. Sci. Rep. 10:9284. DOI: 10.1038/s41598-020-65999-7. www.nature.com/srep/ Number of accessions cited: 417
  • Bryant, R. A. Proctor, M. Hawkridge, A. Jackson, K. Yeater, P. Counce, W. Yan, A. McClung, & R. Fjellstrom. 2011. Genetic variation and association mapping of silica concentration in rice hulls using a germplasm collection. Genetica 139:1383-1398. Number of accessions cited: 217
  • Hu, Biao-Lin et al. 2012. Analysis on genetic diversity of phenotypic traits in rice (Oryza sativa L.) core collection and its comprehensive assessment (in Chinese). Acta Agron. Sin. 38(5)829-839. Number of accessions cited: 1794
  • Huggins, T. D., M-H. Chen, R. G. Fjellstrom, A. K. Jackson, A. M. McClung, & J. D. Edwards. 2019. Association analysis of three diverse rice (Oryza sativa L.) germplasm collections for loci regulating grain quality traits. Pl. Genome 12(1)1-21. DOI: 10.3835/plantgenome2017.09.0085. Number of accessions cited: 173
  • Jia, Limeng et al. 2011. Searching for germplasm resistant to Sheath Blight from the USDA Rice Core Collection. Crop Sci. (Madison) 51:1507-1517. Number of accessions cited: 1794
  • Li, Kehu, J. Bao, H. Corke, & M. Sun. 2017. Genotypic diversity and environmental stability of starch physiochemical properties in the USDA rice mini-core collection. Food Chem. 221:1186-1196. DOI: 10.1016/j.foodchem.2016.11.040. Number of accessions cited: 217
  • Li, X. B., W. G. Yan, H. Agrama, B. L. Hu, L. M. Jia, M. Jia, A. Jackson, K. Moldenhauer, A. McClung, & D. X. Wu. 2010. Genotypic and phenotypic characterization of genetic differentiation and diversity in the USDA rice mini-core collection. Genetica 138:1221-1230. Number of accessions cited: 1755
  • Li, Xiaobai, Wengui Yan, H. Agrama, Limeng Jia, Xihong Shen, A. Jackson, K. Moldenhauer, K. Yeater, A. McClung, & Dianxing Wu. 2011. Mapping QTLs for improving grain yield using the USDA rice mini-core collection. Planta 234:347-361. DOI: 10.1007/s00425-011-1405-0. Number of accessions cited: 217
  • 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
  • Ren, J., Y. Yu, F. Gao, L. Zeng, X. Lu, X. Wu, W. Yan, & G. Ren. 2012. Analysis of genetic structure in the USDA rice mini-core collection using the SQUAMOSA promoter-binding-like gene family. Rice Genomics Genet. 3(1)1-7. Number of accessions cited: 217
  • Schlappi, M. R. et al. 2017. Assessment of five chilling tolerance traits and GWAS mapping in rice using the USDA Mini-Core Collection. Front. Plant Sci. 8:957. DOI: 10.3389/fpls.2017.00957. Number of accessions cited: 197
  • Wang, H. et al. 2016. The power of inbreeding: NGS based GWAS of rice reveals convergent evolution during rice domestication. Molec. Pl. DOI: 10.1016/j.molp.2016.04.018.. Number of accessions cited: 217
  • Wang, X., R. Fjellstrom, Y. Jia, W. G. Yan, M. H. Jia, B. E. Scheffler, D. Wu, Q. Shu, & A. McClung. 2009. Characterization of Pi-ta blast resistance gene in an international rice core collection. Pl. Breed. (New York) 129:491-501. DOI: 10.0000/j.1439-0523.2009.01706.x. Number of accessions cited: 1794
  • Yan, W. G., Y. Li, H. A. Agrama, D. Luo, F. Gao, X. Lu, & G. Ren. 2009. Association mapping of stigma and spikelet characteristics in rice (Oryza sativa L.). Molec. Breed. 24:277-292. DOI: 10.1007/s11032-009-9290-y. Number of accessions cited: 1794
  • Yan, W., H. Agrama, M. Jia, R. Fjellstrom, & A. McClung. 2010. Geographic description of genetic diversity and relationships in the USDA Rice World Collection. Crop Sci. (Madison) 50:2406-2417. Number of accessions cited: 1663
  • Yan, Wengui, J. N. Rutger, R. J. Bryant, H. E. Bockelman, R. G. Fjellstrom, Ming-Hsuan Chen, T. H. Tai, & A. M. McClung. 2007. Development and evaluation of a core subset of the USDA rice germplasm collection. Crop Sci. (Madison) 47:869-878. Number of accessions cited: 1793
  • Yan, WenGui. 2012. Genetic characterization of global rice germplasm for sustainable agriculture (book chapter). In: Aladjadjiyan, A., ed., Food production: approaches, challenges and tasks 243-270. DOI: 10.5772/1870. Note:
    • Intech – Open Access Company
    • http://www.intechopen.com/books/food-production-approaches-challenges-and-tasks
    Number of accessions cited: 1534
Pedigree

Observations

Phenotype Data

CategoryDescriptorDescriptionValueSample SizeStudyInventoryAvailability
CHEMICALAMYLOSEPercent amylose of milled rice.1 2010.CORE.EVALUATION Not Available
DISEASESheath BlightReaction to Sheath Blight (incited by Rhizoctonia solani)..61 SHEATHBLIGHTRESISTANT2011CROPSCI Not Available
DISEASEStraight HeadReaction to Straighthead, a physiological disease resulting in malformed panicles.8 - 100% MALFORMED PANICLES CORE.EVALUATION 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 1.134 2010.CORE.EVALUATION Not Available
MORPHOLOGYWIDTH OF KERNELWidth of kernel in millimeters for brown (dehulled) rice.2.9 2010.CORE.EVALUATION Not Available
MORPHOLOGYKERNEL LENGTH/WIDTH RATIOLength/Width ratio for brown (dehulled) rice2.5 2010.CORE.EVALUATION Not Available
MORPHOLOGYPlant Type - Culm AngleCulm Angle, rice direct-seeded in rows.1 - ERECT 2010.CORE.EVALUATION Not Available
MORPHOLOGYPanicle TypePanicle type classified according to their mode of branching, angle of primary branches, and spikelet density.5 - INTERMEDIATE 2010.CORE.EVALUATION Not Available
MORPHOLOGYHull ColorHull color (Lemma and Palea) when terminal spikelets are ripened2 - STRAW 2010.CORE.EVALUATION Not Available
MORPHOLOGYHull CoverPubescence of lemma or palea4 - SHORT HAIRS THROUGHOUT 2010.CORE.EVALUATION Not Available
MORPHOLOGYAwn TypeAmount and extent of awns.0 - ABSENT 2010.CORE.EVALUATION Not Available
MORPHOLOGYLodgingEstimated amount of plant lodging near maturity.1 - 0 - 10% LODGED 2010.CORE.EVALUATION Not Available
MORPHOLOGYBran ColorColor of seed coat (bran/pericarp) when fully mature and dry.1 - WHITE 2009.GERMPLASM.EVAL Not Available
MORPHOLOGYLength of KernelLength of kernel in millimeters for brown (dehulled) rice.7 2010.CORE.EVALUATION Not Available
OTHERMEMBER OF MINICORE A Mini-Core Collection containing about 10% of the Core Collection has been developed and fingerprinted with some 200 SSR markers.Y - Accession is part of the rice gentics stock collection minicore. 2010.CORE.EVALUATION Not Available
OTHERMINI-COREA flag to indicate the accession is part of the rice mini-core.Y - YES, THE ACCESSION IS PART OF THE RICE MINI-CORE SUBSET RICE.MINICORE Not Available
PHENOLOGYDays to FlowerDays from emergence to flowering. Actual values. See also related descriptor Days to Anthesis.103 2010.CORE.EVALUATION Not Available
PRODUCTION1000 Kernel Weight-BrownThousand kernel weight of brown rice, based on a count of 100 or more. Expressed in grams.25.96 2010.CORE.EVALUATION Not Available