Title |
Design |
Polymorphism Type |
Allele Scoring Protocol |
PI(s) |
Comments |
Data |
Genetic structure and diversity in Oryza sativa L. |
234 rice accessions from wide geographical regions of the world genotyped at 169 nuclear and 2 chloroplast loci to elucidate diversity within subspecies Oryza sativa indica and japonica |
N/A
|
|
McCouch-S-R, Tai-T-H |
Prediction of population structure was model-based (STRUCTURE) and based on data from 169 genomic SSRs. Reference: Garris et al., 2005. |
Show Allele Data
|
Genome-wide patterns of nucleotide polymorphism in domesticated rice |
SNP Assay |
N/A
|
|
Caicedo-A-L |
Reference: Caicedo et al., 2007. Pervasive positive selection shapes genome-wide patterns of nucleotide polymorphism in domesticated Asian rice (Oryza sativa). Data for the STS paper was generated based up on TIGRv3 pseudomolecules. The data in this system is based upon version 4. |
Show Allele Data
|
Selection under domestication: Evidence for a sweep in the rice Waxy genomic region |
SNP assay. Sequence analysis across 500-kb region centered on Waxy |
N/A
|
|
Olsen-K-M |
Reference: Olsen et al.,2006. |
Show Allele Data
|
Population Structure and Breeding Patterns of 145 U.S. Rice Cultivars Based on SSR Marker Analysis |
115 U.S rice cultivars and 30 ancestral rice accessions introduced from Asia were genotyped by means of 169 genomic SSR markers. |
N/A
|
|
McCouch-S-R, Tai-T-H |
Population structure was inferred using genetic-distance method with 169 SSR markers. Reference: Lu et al., 2005. |
Show Allele Data
|
B-Gross/J-Yulin SNP Pi-ta study in AA Oryza; 143 accessions x 632 SNP |
Genotyping of 143 germplasm accessions with 632 SNPs |
N/A
|
|
Yulin Jia, USDA-ARS DBNRRC |
Reference: Lee-S et. al, Genetics, vol 183, 2009. GR_ID:54910 |
Show Allele Data
|
Global dissemination of a single mutation conferring white pericarp in rice |
Genotyping of 440 geographically and genetically diverse rice cultivars using the rice indel RID 12 primers |
N/A
|
|
Sweeney/McCouch |
Reference: Sweeney et. al. PLoS Genetics, 2007; Genotyping analysis revealed a single 14-bp deletion in the Rc gene is responsible for white pericarp in 97.9% of rice |
Show Allele Data
|