We have created two tools to make it convenient for researchers to use the large rice SNP dataset:  the Oryza SNP Browser and the Oryza SNP Search Pages. The Oryza SNP Browser provides a graphical view of putatively identified SNPs relative either to the TIGR version 5 pseudomolecules and gene models or to the IRGSP version 4 pseudomolecules and RAP version 1 gene models.  The browser also shows the genomic regions used for SNP discovery from each cultivar.  The glyphs for each of these regions are color-coded to indicate the quality of the sequence that was obtained by the Perlegen technology and the glyphs link to text files of sequence FASTA files.  Additionally, the browser contains glyphs that represent the long range PCR products that were amplified for hybridization to the Perlegen arrays. 

. The Oryza SNP Search Pages allow researchers to make targeted queries to the Oryza SNP Database.  Users can search for SNPs by chromosome coordinates within a single cultivar or between two or more cultivars.  Cultivar searches return SNP identifiers as well as reference and cultivar-specific SNP base calls.  Alternatively, with SNP identifiers, researchers can discover base calls for each cultivar or find the gene-model-based classifications for each SNP such as intronic, exonic, 5’-UTR, 3’-UTR, etc.  SNP identifiers can also be used to obtain the 1,000 bp of reference sequence surrounding the SNP.  Given a list of gene identifiers (TIGR or RAP), a user may also query for any SNPs that lie within those genes. All search pages have links to the Oryza SNP Browser.  Output generated from any of the Oryza SNP Search Pages can be copied as tab-delimited text for transfer to files or spreadsheets which can be uploaded into local databases designed by the user to ask specific research questions.  Researchers can obtain search results relative to either IRGSP or TIGR pseudomolecules and relative to either RAP or TIGR gene models. 

 Although there are many questions that may be answered using this type of data, here we provide two examples of how to utilize the rice SNP search tools. 

Example 1:

Analyze QTL Regions using the Pairwise Cultivar SNP Search For many QTL mapping studies, the narrowing of QTL regions is limited in part by the lack of knowledge of polymorphic sites between parental lines. The rice SNP dataset alleviates this problem by providing chromosome coordinate-based SNP searches between any two cultivars included in the rice SNP discovery project. In addition, this search provides TIGR locus IDs or RAP gene identifiers with gene annotations for each putative SNP identified in a gene model. If one searches for SNPs in genes between cultivars IR64 and Azucena, on chromosome 1 between coordinates 5.0 - 6.0Mb on the TIGR pseudomolecules, then this type of output is displayed:  

This particular query identifies 136 putative genic SNPs and an additional 97 intergenic SNPs. Using TIGR or RAP gene identifiers, polymorphic loci may then be correlated to gene expression data acquired from microarrays and/or EST databases.  Putative polymorphic sites can be genotyped using a variety of SNP detection methods, and to facilitate this process, we provide 1,000 bp of FASTA sequence surrounding each SNP site. 

Example 2:

Obtain genome-wide SNP data using the Multiple Cultivar SNP Search Genome wide SNP data is valuable for studying genomic diversity, inferring gene evolution and identifying haplotype regions. A genome wide SNP dataset is complemented by phenotypic data that is accumulating for the 20 rice cultivars. All SNPs identified throughout the genome for 20 cultivars can be acquired using the chromosome information from the TIGR Rice Genome Annotation website http://www.tigr.org/tdb/e2k1/osa1/pseudomolecules/info.shtml#info_table and the Multiple Cultivar SNP Search. If one asks for all SNPs for all 20 rice cultivars on TIGR chromosome 10, then this type of data is returned:

Where "..." denotes other varietal genotypes omitted for brevity. If SNPs with any undetermined base calls (N’s) are excluded from this query, then 1,214 putative SNP sites are identified for chromosome 10.