Rice SNP-seek database update: new SNPs, indels, and queries

Mansueto, Locedie; Fuentes, Roven Rommel; Borja, Frances Nikki; Detras, Jeffery; Abriol-Santos, Juan Miguel; Chebotarov, Dmytro; Sanciangco, Millicent; Palis, Kevin; Copetti, Dario; Poliakov, Alexandre; Dubchak, Inna; Solovyev, Victor; Wing, Rod A.; Hamilton, Ruaraidh Sackville; Mauleon, Ramil; McNally, Kenneth L.; Alexandrov, Nickolai

doi:10.1093/nar/gkw1135

Rice SNP-seek database update: new SNPs, indels, and queries

Journal Article · Tue Nov 29 00:00:00 EST 2016 · Nucleic Acids Research

DOI:https://doi.org/10.1093/nar/gkw1135· OSTI ID:1625549

Mansueto, Locedie ^[1]; Fuentes, Roven Rommel ^[2]; Borja, Frances Nikki ^[2]; Detras, Jeffery ^[2]; Abriol-Santos, Juan Miguel ^[2]; Chebotarov, Dmytro ^[2]; Sanciangco, Millicent ^[2]; Palis, Kevin ^[3]; Copetti, Dario ^[4]; Poliakov, Alexandre ^[5]; Dubchak, Inna ^[5]; Solovyev, Victor ^[6]; Wing, Rod A. ^[7]; Hamilton, Ruaraidh Sackville ^[2]; Mauleon, Ramil ^[2]; McNally, Kenneth L. ^[2]; Alexandrov, Nickolai ^[2]

International Rice Research Inst., Los Banos (Philippines); DOE/OSTI
International Rice Research Inst., Los Banos (Philippines)
International Rice Research Inst., Los Banos (Philippines); Boyce Thompson Institute for Plant Research, Ithaca, NY (United States)
Univ. of Arizona, Tucson, AZ (United States). School of Plant Sciences. Arizona Genomics Inst.
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
Softberry, Inc., Mount Kisco, NY (United States)
International Rice Research Inst., Los Banos (Philippines); Univ. of Arizona, Tucson, AZ (United States). School of Plant Sciences. Arizona Genomics Inst.

We describe updates to the Rice SNP-Seek Database since its first release. We ran a new SNP-calling pipeline followed by filtering that resulted in complete, base, filtered and core SNP datasets. Besides the Nipponbare reference genome, the pipeline was run on genome assemblies of IR 64, 93-11, DJ 123 and Kasalath. New genotype query and display features are added for reference assemblies, SNP datasets and indels. JBrowse now displays BAM, VCF and other annotation tracks, the additional genome assemblies and an embedded VISTA genome comparison viewer. Middleware is redesigned for improved performance by using a hybrid of HDF5 and RDMS for genotype storage. Query modules for genotypes, varieties and genes are improved to handle various constraints. An integrated list manager allows the user to pass query parameters for further analysis. The SNP Annotator adds traits, ontology terms, effects and interactions to markers in a list. Webservice calls were implemented to access most data. These features enable seamless querying of SNPSeek across various biological entities, a step toward semi-automated gene-trait association discovery. URL: http://snp-seek.irri.org.

View Accepted Manuscript (DOE)

Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1625549

Journal Information:: Nucleic Acids Research, Journal Name: Nucleic Acids Research Journal Issue: D1 Vol. 45; ISSN 0305-1048

Publisher:: Oxford University PressCopyright Statement

Country of Publication:: United States

Language:: English

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A large-scale whole-genome sequencing analysis reveals highly specific genome editing by both Cas9 and Cpf1 (Cas12a) nucleases in rice Tang, Xu; Liu, Guanqing; Zhou, Jianping Genome Biology, Vol. 19, Issue 1 https://doi.org/10.1186/s13059-018-1458-5	journal	July 2018
Natural variations in the promoter of OsSWEET13 and OsSWEET14 expand the range of resistance against Xanthomonas oryzae pv. oryzae Zaka, Abha; Grande, Genelou; Coronejo, Thea PLOS ONE, Vol. 13, Issue 9 https://doi.org/10.1371/journal.pone.0203711	journal	September 2018
Genetic Mapping of Quantitative Trait Loci for Grain Yield under Drought in Rice under Controlled Greenhouse Conditions Solis, Julio; Gutierrez, Andres; Mangu, Venkata Frontiers in Chemistry, Vol. 5 https://doi.org/10.3389/fchem.2017.00129	journal	January 2018
Association Study Reveals Genetic Loci Responsible for Arsenic, Cadmium and Lead Accumulation in Rice Grain in Contaminated Farmlands Liu, Xiuyan; Chen, Sunlu; Chen, Mingxue Frontiers in Plant Science, Vol. 10 https://doi.org/10.3389/fpls.2019.00061	journal	February 2019
Sequence Dynamics of Pre-mRNA G-Quadruplexes in Plants Kopec, Piotr M.; Karlowski, Wojciech M. Frontiers in Plant Science, Vol. 10 https://doi.org/10.3389/fpls.2019.00812	journal	June 2019
HKT1;5 Transporter Gene Expression and Association of Amino Acid Substitutions With Salt Tolerance Across Rice Genotypes Shohan, Mohammad Umer Sharif; Sinha, Souvik; Nabila, Fahmida Habib Frontiers in Plant Science, Vol. 10 https://doi.org/10.3389/fpls.2019.01420	journal	November 2019
Identification of Superior Alleles for Seedling Stage Salt Tolerance in the USDA Rice Mini-Core Collection Rohila, Jai S.; Edwards, Jeremy D.; Tran, Gioi D. Plants, Vol. 8, Issue 11 https://doi.org/10.3390/plants8110472	journal	November 2019
Allelic diversity of flowering-time regulatory gene Hd3a in rice Zoysa, Malsha De; Nanayakkara, Dhanesha; Herath, Venura Taylor & Francis https://doi.org/10.6084/m9.figshare.10072574.v1	text	January 2019