Oryza sativa Germplasm "Tokyo Shino Mochi"

Accession Name	Tokyo Shino Mochi
Institute(s) Holding Accession	NSGC
Accession Number	GSOR301202
Synonym(s)
Germplasm Type	Breeding/research material
Genus	Oryza
Species	sativa
Subspecies
Subtaxa
Taxonomy Cross-Reference	GR_tax:013681

Experiments (4)

Title	Design	Polymorphism Type	PI(s)	Comments	Data
'1536 chip' - 1311 SNPs x 395 rice accessions (Zhao et. al, PLoS, 2010; ricediversity.org). MSU6 coordinates	Genotyping of 395 O. sativa accessions with 1536 SNPs	N/A	Zhao K et. al.; ricediversity.org	Reference: Zhao K et. al., PLoS One, May 2010 vol 5, issue 5	Show Allele Data
'1536 chip' - 1311 SNPs x 395 rice accessions (Zhao et. al, PLoS, 2010; ricediversity.org). MSU7 coordinates	Genotyping of 395 O. sativa accessions with 1536 SNPs	N/A	Zhao K et. al.; ricediversity.org	Reference: Zhao K et. al., PLoS One, May 2010 vol 5, issue 5. LiftOver from MSU6->MSU7, 3/2012	Show Allele Data
RiceDiversity 44K SNP assay, 34 trait GWAS study, Nat Comm Sept 2011. MSU6 coordinates	A genome-wide association study based on genotyping 44,100 SNP variants across 413 diverse accessions of O. sativa collected from 82 countries that were systematically phenotyped for 34 traits.	N/A	Susan McCouch	Reference: Zhao-K, et al Nat Comm 2011 [Gramene Lit ID 54925]; Project website: Rice Diversity	Show Allele Data
RiceDiversity 44K SNP assay, 34 trait GWAS study, Nat Comm Sept 2011. MSU7 coordinates	A Rice Diversity Panel consists of 413 Asian rice representing all the major rice growing regions of the world were evaluated in the field.	N/A	Susan McCouch	Reference: Zhao-K, et al Nat Comm 2011 [Gramene Lit ID 54925]; Project website: Rice Diversity. LiftOver from MSU6->MSU7, 3/2012, RiceDiversity Project.	Show Allele Data

Related Stocks (2)

Stock Source	Seed Lot ID	Comments
NSGC	nsftv211
McCouch Lab	RA6523	RiceDiversity NSFTV

Traits (36)

Trait id	value	exp id
19037	2010-05-01	18
19038	2010-05-01	18
21466	0.063333333	47
21888	9.7	47
22310	present	47
22732	6	47
23154	2.05	47
23576	6.059091667	47
23998	3.497950207	47
24420	2.9556	47
24842	7.221308333	47
25264	23.79167	47
25686	1.083333333	47
26108	107	47
26530	66	47
26952	70.08	47
27374	not dark	47
27796	Light	47
28218	present	47
28640	4.601831285	47
29062	7.5	47
29484	23.79166667	47
29906	20.36666667	47
30328	3.083437854	47
30750	Not light	47
31172	3.666666667	47
31594	101.1666667	47
32016	8.923466667	47
32438	2.475	47
32860	4.508108473	47
33282	3.969046799	47
33704	2.609975426	47
34126	3.604725	47
34548	6.665	47
34970	2.187922185	47
35392	6.958333334	47

Traits UOM (32)

Trait Name	Trait Protocol	LINK TO TRAIT VALUES
seed length with hull
amylose content
brown rice protein	Protein content in brown rice (dehulled grain with pericarp) as described in 54926
awn presence	Presence or absence of awns, frequency and length of awns along a panicle was evaluated
blast disease
brown rice ratio	Ratio of unpolished rice grain length to grain width was measured
brown rice length	Length of the dehulled, unpolished rice grain was measured
grain surface area	Surface area of the dehulled, unpolished rice grain was calculated.
grain width	Width of the dehulled, unpolished rice grain was measured
grain volume	Volume of the unpolished rice grain (dehulled) was measured
flag leaf length	Length of the flag leaf measured from leaf base to leaf tip
flag leaf lamina width	Width of the flag leaf measured at the widest portion of the leaf lamina
flowering time
hull color	Color of the hull was visually examinedexamined
leaf lamina pubescence	Presence or absence of hairs on the leaf blade surface was evaluated
floret number per inflorescence	Number of flowers (florets) on the primary panicle was counted
primary branch number	Number of primary branches along the panicle was counted
spikelet fertility	Percent of spikelets that filled and produced seeds determined as the ratio of seeds per panicle/spikelets per panicle
Panicle length	Panicle length was measured as the average number of centimeters from the panicle neck to the panicle tip, excluding awns.
Panicle number	Panicles per plant was calculated as the average number of panicles per plant at harvest.
pericarp color	Ten seeds per plant were dehulled and then visually inspected; PATO:0000322, PATO:0000323; ECO:0000002; GAZ:00004426
culm angle	Average angle of the plant culm with respect to the ground surface at maturity was measured
Plant height	Plant height was measured in centimeters from the soil surface to the tip of the tallest panicle, excluding the awns.
seed length	Length of the seed with hull was measured
seed length to width ratio	Ratio of seed length to seed width was measured
seed number	Number of seeds per panicle (inflorescence), determined by counting the number of filled spikelets along the main panicle
surface area of grain with hull	Surface area of the seed with hul was measured
volume of grain with hull	Volume of the seed with hull was measured
seed width	Width of the seed with hull was measured
straighthead	Rated visually based on floret sterility and panicle emergence on a scale from 1 (normal panicle emergence and less than 20% sterility) to 9 (stubby plants with no panicle emergence)
unfilled grain number
alkali digestion	Rice grains were treated with 1.7% KOH and scored for the extent of digestion of the starch based on its level of intactness.