SNP-Seek database of SNPs derived from 3000 rice genomes

被引：256
作者：
Alexandrov, Nickolai [1 ]
Tai, Shuaishuai [2 ]
Wang, Wensheng [3 ]
Mansueto, Locedie [1 ]
Palis, Kevin [1 ]
Fuentes, Roven Rommel [1 ]
Ulat, Victor Jun [1 ]
Chebotarov, Dmytro [1 ]
Zhang, Gengyun [2 ]
Li, Zhikang [3 ]
Mauleon, Ramil [1 ]
Hamilton, Ruaraidh Sackville [1 ]
McNally, Kenneth L. [1 ]
机构：
[1] IRRI, TT Chang Genet Resources Ctr, Los Banos 4031, Laguna, Philippines
[2] BGI, Shenzhen 518083, Peoples R China
[3] Chinese Acad Agr Sci, Natl Key Facil Crop Gene Resources & Genet Improv, Inst Crop Sci, Beijing 100081, Peoples R China
来源：
NUCLEIC ACIDS RESEARCH | 2015年 / 43卷 / D1期
关键词：
FRAMEWORK;
D O I：
10.1093/nar/gku1039
中图分类号：
Q5 [生物化学]; Q7 [分子生物学];
学科分类号：
071010 ; 081704 ;
摘要：
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 x 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.
引用
收藏
页码：D1023 / D1027
页数：5
相关论文
共 14 条
  • [1] Disease resistance in rice and the role of molecular breeding in protecting rice crops against diseases
    Fahad, Shah
    Nie, Lixiao
    Khan, Faheem Ahmed
    Chen, Yutiao
    Hussain, Saddam
    Wu, Chao
    Xiong, Dongliang
    Jing, Wang
    Saud, Shah
    Khan, Farhan Anwar
    Li, Yong
    Wu, Wei
    Khan, Fahad
    Hassan, Shah
    Manan, Abdul
    Jan, Amanullah
    Huang, Jianliang
    [J]. BIOTECHNOLOGY LETTERS, 2014, 36 (07) : 1407 - 1420
  • [2] Dissecting yield-associated loci in super hybrid rice by resequencing recombinant inbred lines and improving parental genome sequences
    Gao, Zhen-Yu
    Zhao, Shan-Cen
    He, Wei-Ming
    Guo, Long-Biao
    Peng, You-Lin
    Wang, Jin-Jin
    Guo, Xiao-Sen
    Zhang, Xue-Mei
    Rao, Yu-Chun
    Zhang, Chi
    Dong, Guo-Jun
    Zheng, Feng-Ya
    Lu, Chang-Xin
    Hu, Jiang
    Zhou, Qing
    Liu, Hui-Juan
    Wu, Hai-Yang
    Xu, Jie
    Ni, Pei-Xiang
    Zeng, Da-Li
    Liu, Deng-Hui
    Tian, Peng
    Gong, Li-Hui
    Ye, Chen
    Zhang, Guang-Heng
    Wang, Jian
    Tian, Fu-Kuan
    Xue, Da-Wei
    Liao, Yi
    Zhu, Li
    Chen, Ming-Sheng
    Li, Jia-Yang
    Cheng, Shi-Hua
    Zhang, Geng-Yun
    Wang, Jun
    Qian, Qian
    [J]. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2013, 110 (35) : 14492 - 14497
  • [3] The genes of the Green Revolution
    Hedden, P
    [J]. TRENDS IN GENETICS, 2003, 19 (01) : 5 - 9
  • [4] Genetic Engineering and Breeding of Drought-Resistant Crops
    Hu, Honghong
    Xiong, Lizhong
    [J]. ANNUAL REVIEW OF PLANT BIOLOGY, VOL 65, 2014, 65 : 715 - 741
  • [5] Conservation of rice genetic resources: the role of the International Rice Genebank at IRRI
    Jackson, MT
    [J]. PLANT MOLECULAR BIOLOGY, 1997, 35 (1-2) : 61 - 67
  • [6] Fast and accurate short read alignment with Burrows-Wheeler transform
    Li, Heng
    Durbin, Richard
    [J]. BIOINFORMATICS, 2009, 25 (14) : 1754 - 1760
  • [7] The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data
    McKenna, Aaron
    Hanna, Matthew
    Banks, Eric
    Sivachenko, Andrey
    Cibulskis, Kristian
    Kernytsky, Andrew
    Garimella, Kiran
    Altshuler, David
    Gabriel, Stacey
    Daly, Mark
    DePristo, Mark A.
    [J]. GENOME RESEARCH, 2010, 20 (09) : 1297 - 1303
  • [8] A Chado case study: an ontology-based modular schema for representing genome-associated biological information
    Mungall, Christopher J.
    Emmert, David B.
    [J]. BIOINFORMATICS, 2007, 23 (13) : I337 - I346
  • [9] BioJava']Java: an open-source framework for bioinformatics in 2012
    Prlic, Andreas
    Yates, Andrew
    Bliven, Spencer E.
    Rose, Peter W.
    Jacobsen, Julius
    Troshin, Peter V.
    Chapman, Mark
    Gao, Jianjiong
    Koh, Chuan Hock
    Foisy, Sylvain
    Holland, Richard
    Rimsa, Gediminas
    Heuer, Michael L.
    Brandstaetter-Mueller, H.
    Bourne, Philip E.
    Willis, Scooter
    [J]. BIOINFORMATICS, 2012, 28 (20) : 2693 - 2695
  • [10] Yield Trends Are Insufficient to Double Global Crop Production by 2050
    Ray, Deepak K.
    Mueller, Nathaniel D.
    West, Paul C.
    Foley, Jonathan A.
    [J]. PLOS ONE, 2013, 8 (06):
12