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SNP-Seek database of SNPs derived from 3000 rice genomes.

Alexandrov N, Tai S, Wang W, Mansueto L, Palis K, Fuentes RR, Ulat VJ, Chebotarov D, Zhang G, Li Z, Mauleon R, Hamilton RS, McNally KL - Nucleic Acids Res. (2014)

Bottom Line: We have identified about 20 million rice SNPs by aligning reads from the 3000 rice genomes project with the Nipponbare genome.SNPs can be visualized together with the gene structures in JBrowse genome browser.Evolutionary relationships between rice varieties can be explored using phylogenetic trees or multidimensional scaling plots.

View Article: PubMed Central - PubMed

Affiliation: T.T.Chang Genetic Resources Center, IRRI, Los Baños, Laguna 4031, Philippines n.alexandrov@irri.org.

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Related in: MedlinePlus

Jbrowse view of the SNP genotypes within the sd-1 gene (each variety is one row). Red blocks indicate polymorphism of the variety against Nipponbare. Shared SNP blocks are seen as vertical columns in red. The blue rectangle box in the bottom contains varieties that do not have these blocks.
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Figure 5: Jbrowse view of the SNP genotypes within the sd-1 gene (each variety is one row). Red blocks indicate polymorphism of the variety against Nipponbare. Shared SNP blocks are seen as vertical columns in red. The blue rectangle box in the bottom contains varieties that do not have these blocks.

Mentions: We used Rice SNP-Seek database to quickly examine the diversity of the entire panel at a particular region of interest. We chose the sd-1 gene as test case due to its scientific importance in rice breeding. This semi-dwarf locus, causing a semi-dwarf stature of rice, was discovered by three different research groups to be a spontaneous mutation of GA 20-oxidase (formally named sd-1 gene), originating from the Taiwanese indica variety Deo-woo-gen. Its incorporation into IR8 and other varieties by rice breeding programs spurred the First Green Revolution in rice production in the late 1960s (15). Sd-1 is annotated in the Nipponbare genome by Michigan State University's Rice Genome Annotation Project as LOC_Os01g66100, on chromosome 1 from position 38 382 382 to 38 385 504 base pairs. On the home page of SNP-Seek, the <Genotype> module was opened and the coordinates of sd-1 were used to define the region to retrieve all SNPs, with <All Varieties> checked to select from all the varieties. Clicking on <Search> button resulted in the identification of 80 SNP positions (Supplementary Figure S1). An overall view of the SNP positions in the polymorphic panel shows at least eight distinct SNP blocks (Figure 5). In this particular panel group of mostly temperate japonica, two distinct SNP blocks can be seen as shared (Figure 5). Variety information can be obtained by typing the name of the varieties you see on the genome browser into the <Variety name> field of the Variety module. This use case is one of the examples detailed in the <Help> module.


SNP-Seek database of SNPs derived from 3000 rice genomes.

Alexandrov N, Tai S, Wang W, Mansueto L, Palis K, Fuentes RR, Ulat VJ, Chebotarov D, Zhang G, Li Z, Mauleon R, Hamilton RS, McNally KL - Nucleic Acids Res. (2014)

Jbrowse view of the SNP genotypes within the sd-1 gene (each variety is one row). Red blocks indicate polymorphism of the variety against Nipponbare. Shared SNP blocks are seen as vertical columns in red. The blue rectangle box in the bottom contains varieties that do not have these blocks.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4383887&req=5

Figure 5: Jbrowse view of the SNP genotypes within the sd-1 gene (each variety is one row). Red blocks indicate polymorphism of the variety against Nipponbare. Shared SNP blocks are seen as vertical columns in red. The blue rectangle box in the bottom contains varieties that do not have these blocks.
Mentions: We used Rice SNP-Seek database to quickly examine the diversity of the entire panel at a particular region of interest. We chose the sd-1 gene as test case due to its scientific importance in rice breeding. This semi-dwarf locus, causing a semi-dwarf stature of rice, was discovered by three different research groups to be a spontaneous mutation of GA 20-oxidase (formally named sd-1 gene), originating from the Taiwanese indica variety Deo-woo-gen. Its incorporation into IR8 and other varieties by rice breeding programs spurred the First Green Revolution in rice production in the late 1960s (15). Sd-1 is annotated in the Nipponbare genome by Michigan State University's Rice Genome Annotation Project as LOC_Os01g66100, on chromosome 1 from position 38 382 382 to 38 385 504 base pairs. On the home page of SNP-Seek, the <Genotype> module was opened and the coordinates of sd-1 were used to define the region to retrieve all SNPs, with <All Varieties> checked to select from all the varieties. Clicking on <Search> button resulted in the identification of 80 SNP positions (Supplementary Figure S1). An overall view of the SNP positions in the polymorphic panel shows at least eight distinct SNP blocks (Figure 5). In this particular panel group of mostly temperate japonica, two distinct SNP blocks can be seen as shared (Figure 5). Variety information can be obtained by typing the name of the varieties you see on the genome browser into the <Variety name> field of the Variety module. This use case is one of the examples detailed in the <Help> module.

Bottom Line: We have identified about 20 million rice SNPs by aligning reads from the 3000 rice genomes project with the Nipponbare genome.SNPs can be visualized together with the gene structures in JBrowse genome browser.Evolutionary relationships between rice varieties can be explored using phylogenetic trees or multidimensional scaling plots.

View Article: PubMed Central - PubMed

Affiliation: T.T.Chang Genetic Resources Center, IRRI, Los Baños, Laguna 4031, Philippines n.alexandrov@irri.org.

Show MeSH
Related in: MedlinePlus