Oryza sativa Germplasm "Azucena"

Accession Name	Azucena
Institute(s) Holding Accession	NSGC
Accession Number	GSOR301165
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	nsftv174
McCouch Lab	RA6592	RiceDiversity NSFTV

Traits (36)

Trait	Value	Experiment
seed length with hull	2010-05-01	'1536 chip' - 1311 SNPs x 395 rice accessions (Zhao et. al, PLoS, 2010; ricediversity.org). MSU6 coordinates
amylose content	2010-05-01	'1536 chip' - 1311 SNPs x 395 rice accessions (Zhao et. al, PLoS, 2010; ricediversity.org). MSU6 coordinates
amylose content	22.84	RiceDiversity 44K SNP assay, 34 trait GWAS study, Nat Comm Sept 2011. MSU6 coordinates
brown rice protein	9	RiceDiversity 44K SNP assay, 34 trait GWAS study, Nat Comm Sept 2011. MSU6 coordinates
awn presence	absent	RiceDiversity 44K SNP assay, 34 trait GWAS study, Nat Comm Sept 2011. MSU6 coordinates
blast disease	2	RiceDiversity 44K SNP assay, 34 trait GWAS study, Nat Comm Sept 2011. MSU6 coordinates
brown rice ratio	3.111	RiceDiversity 44K SNP assay, 34 trait GWAS study, Nat Comm Sept 2011. MSU6 coordinates
brown rice length	7.429525	RiceDiversity 44K SNP assay, 34 trait GWAS study, Nat Comm Sept 2011. MSU6 coordinates
grain surface area	3.49105916	RiceDiversity 44K SNP assay, 34 trait GWAS study, Nat Comm Sept 2011. MSU6 coordinates
grain width	2.388266667	RiceDiversity 44K SNP assay, 34 trait GWAS study, Nat Comm Sept 2011. MSU6 coordinates
grain volume	5.782291667	RiceDiversity 44K SNP assay, 34 trait GWAS study, Nat Comm Sept 2011. MSU6 coordinates
flag leaf length	39.53333	RiceDiversity 44K SNP assay, 34 trait GWAS study, Nat Comm Sept 2011. MSU6 coordinates
flag leaf lamina width	1.544444444	RiceDiversity 44K SNP assay, 34 trait GWAS study, Nat Comm Sept 2011. MSU6 coordinates
flowering time	118	RiceDiversity 44K SNP assay, 34 trait GWAS study, Nat Comm Sept 2011. MSU6 coordinates
flowering time	78	RiceDiversity 44K SNP assay, 34 trait GWAS study, Nat Comm Sept 2011. MSU6 coordinates
flowering time	101.08	RiceDiversity 44K SNP assay, 34 trait GWAS study, Nat Comm Sept 2011. MSU6 coordinates
hull color	not dark	RiceDiversity 44K SNP assay, 34 trait GWAS study, Nat Comm Sept 2011. MSU6 coordinates
hull color	not light	RiceDiversity 44K SNP assay, 34 trait GWAS study, Nat Comm Sept 2011. MSU6 coordinates
leaf lamina pubescence	present	RiceDiversity 44K SNP assay, 34 trait GWAS study, Nat Comm Sept 2011. MSU6 coordinates
floret number per inflorescence	5.277385531	RiceDiversity 44K SNP assay, 34 trait GWAS study, Nat Comm Sept 2011. MSU6 coordinates
primary branch number	14.42857143	RiceDiversity 44K SNP assay, 34 trait GWAS study, Nat Comm Sept 2011. MSU6 coordinates
spikelet fertility	39.53333333	RiceDiversity 44K SNP assay, 34 trait GWAS study, Nat Comm Sept 2011. MSU6 coordinates
Panicle length	31.24285714	RiceDiversity 44K SNP assay, 34 trait GWAS study, Nat Comm Sept 2011. MSU6 coordinates
Panicle number	2.47793798	RiceDiversity 44K SNP assay, 34 trait GWAS study, Nat Comm Sept 2011. MSU6 coordinates
pericarp color	Not light	RiceDiversity 44K SNP assay, 34 trait GWAS study, Nat Comm Sept 2011. MSU6 coordinates
culm angle	2	RiceDiversity 44K SNP assay, 34 trait GWAS study, Nat Comm Sept 2011. MSU6 coordinates
Plant height	151.6666667	RiceDiversity 44K SNP assay, 34 trait GWAS study, Nat Comm Sept 2011. MSU6 coordinates
seed length	9.854327273	RiceDiversity 44K SNP assay, 34 trait GWAS study, Nat Comm Sept 2011. MSU6 coordinates
seed length to width ratio	3.458	RiceDiversity 44K SNP assay, 34 trait GWAS study, Nat Comm Sept 2011. MSU6 coordinates
seed number	5.088477781	RiceDiversity 44K SNP assay, 34 trait GWAS study, Nat Comm Sept 2011. MSU6 coordinates
surface area of grain with hull	3.898137778	RiceDiversity 44K SNP assay, 34 trait GWAS study, Nat Comm Sept 2011. MSU6 coordinates
volume of grain with hull	2.321397926	RiceDiversity 44K SNP assay, 34 trait GWAS study, Nat Comm Sept 2011. MSU6 coordinates
seed width	2.849645455	RiceDiversity 44K SNP assay, 34 trait GWAS study, Nat Comm Sept 2011. MSU6 coordinates
straighthead	8.833333334	RiceDiversity 44K SNP assay, 34 trait GWAS study, Nat Comm Sept 2011. MSU6 coordinates
unfilled grain number	3.517921656	RiceDiversity 44K SNP assay, 34 trait GWAS study, Nat Comm Sept 2011. MSU6 coordinates
alkali digestion	6.25	RiceDiversity 44K SNP assay, 34 trait GWAS study, Nat Comm Sept 2011. MSU6 coordinates

Traits UOM (32)

Trait Name	Trait Protocol	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.