SNP-Seek database of SNPs derived from 3000 rice genomes

By N. Alexandrov, S. Tai, Wensheng Wang, Locedie Mansueto, Kevin Palis, R. R. Fuentes, V. J. Ulat, D. Chebotarov, Gengyun Zhang, Zhikang Li and 3 more. Nucleic Acids Res., 2014

334 citations recorded by the source corpus.

We have identified about 20 million rice SNPs by aligning reads from the 3000 rice genomes project with the Nipponbare genome. The SNPs and allele information are organized into a SNP-Seek system (http://www.oryzasnp.org/iric-portal/), which consists of Oracle database having a total number of rows with SNP genotypes close to 60 billion (20 M SNPs × 3 K rice lines) and web interface for convenient querying. The database allows quick retrieving of SNP alleles for all varieties in a given genome region, finding different alleles from predefined varieties and querying basic passport and morphological phenotypic information about sequenced rice lines. 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.

Subfields: Genetics, Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/a34d2eb3779b7fb7e86789a182b19adbc3843ab5

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In Genetics

1. L. Guarino
2. Christine G. Elsik
3. Kenneth L. McNally
4. Inna Dubchak
5. Rod A. Wing
6. H. Dempewolf

In Molecular Biology

1. I. Holmes
2. Christine G. Elsik
3. Suzanna Lewis
4. Lincoln D. Stein
5. Inna Dubchak
6. Rod A. Wing
7. Paul D. Thomas
8. C. Mungall

In Plant Science

1. L. Guarino
2. Kenneth L. McNally
3. Inna Dubchak
4. Ramil Mauleon
5. H. Dempewolf

Citations in the corpus

• Past and Future Use of Wild Relatives in Crop Breeding (2017, background): “Abbreviations: CSSL, chromosome segment substitution line; CWR, crop wild relative; MAS, marker-assisted selection; QTL, quantitative trait locus; SNP, single-nucleotide polymorphism; WGS, wholegenome shotgun sequence.”
• JBrowse: a dynamic web platform for genome visualization and analysis (2016, methodology): “Sites that use JBrowse (or JBrowse-based tools) span plant genomics [19 – 25], animal genomics [12, 26 – 29], and disease-related databases [30 – 34].”
• Rice SNP-seek database update: new SNPs, indels, and queries (2016, methodology): “Since the first release of Rice SNP-Seek Database (7), we have undertaken considerable development to incorporate new analysis results, datasets, viewers and query interfaces for multiple reference genomes and assemblies.”