title: SNP-Seek database of SNPs derived from 3000 rice genomes.
abstract: 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.
authors.affiliation: T.T.Chang Genetic Resources Center, IRRI, Los Baños, Laguna 4031, Philippines n.alexandrov@irri.org.
authors.forename: Nickolai
authors.initials: N
authors.lastname: Alexandrov
authors.affiliation: BGI, Shenzhen 518083, China.
authors.forename: Shuaishuai
authors.initials: S
authors.lastname: Tai
authors.affiliation: Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, 100081.
authors.forename: Wensheng
authors.initials: W
authors.lastname: Wang
authors.affiliation: T.T.Chang Genetic Resources Center, IRRI, Los Baños, Laguna 4031, Philippines.
authors.forename: Locedie
authors.initials: L
authors.lastname: Mansueto
authors.affiliation: T.T.Chang Genetic Resources Center, IRRI, Los Baños, Laguna 4031, Philippines.
authors.forename: Kevin
authors.initials: K
authors.lastname: Palis
authors.affiliation: T.T.Chang Genetic Resources Center, IRRI, Los Baños, Laguna 4031, Philippines.
authors.forename: Roven Rommel
authors.initials: RR
authors.lastname: Fuentes
authors.affiliation: T.T.Chang Genetic Resources Center, IRRI, Los Baños, Laguna 4031, Philippines.
authors.forename: Victor Jun
authors.initials: VJ
authors.lastname: Ulat
authors.affiliation: T.T.Chang Genetic Resources Center, IRRI, Los Baños, Laguna 4031, Philippines.
authors.forename: Dmytro
authors.initials: D
authors.lastname: Chebotarov
authors.affiliation: BGI, Shenzhen 518083, China zhanggengyun@genomics.cn.
authors.forename: Gengyun
authors.initials: G
authors.lastname: Zhang
authors.affiliation: Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, 100081 lizhikang@caas.cn.
authors.forename: Zhikang
authors.initials: Z
authors.lastname: Li
authors.affiliation: T.T.Chang Genetic Resources Center, IRRI, Los Baños, Laguna 4031, Philippines.
authors.forename: Ramil
authors.initials: R
authors.lastname: Mauleon
authors.affiliation: T.T.Chang Genetic Resources Center, IRRI, Los Baños, Laguna 4031, Philippines.
authors.forename: Ruaraidh Sackville
authors.initials: RS
authors.lastname: Hamilton
authors.affiliation: T.T.Chang Genetic Resources Center, IRRI, Los Baños, Laguna 4031, Philippines.
authors.forename: Kenneth L
authors.initials: KL
authors.lastname: McNally
mesh_terms: D030561:Databases, Nucleic Acid; D018745:Genome, Plant; D012275:Oryza / Q000033:anatomy & histology / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide