Literature DB >> 16217601

The oryza map alignment project: the golden path to unlocking the genetic potential of wild rice species.

Rod A Wing1, Jetty S S Ammiraju, Meizhong Luo, Hyeran Kim, Yeisoo Yu, Dave Kudrna, Jose L Goicoechea, Wenming Wang, Will Nelson, Kiran Rao, Darshan Brar, Dave J Mackill, Bin Han, Cari Soderlund, Lincoln Stein, Phillip SanMiguel, Scott Jackson.   

Abstract

The wild species of the genus Oryza offer enormous potential to make a significant impact on agricultural productivity of the cultivated rice species Oryza sativa and Oryza glaberrima. To unlock the genetic potential of wild rice we have initiated a project entitled the 'Oryza Map Alignment Project' (OMAP) with the ultimate goal of constructing and aligning BAC/STC based physical maps of 11 wild and one cultivated rice species to the International Rice Genome Sequencing Project's finished reference genome--O. sativa ssp. japonica c. v. Nipponbare. The 11 wild rice species comprise nine different genome types and include six diploid genomes (AA, BB, CC, EE, FF and GG) and four tetrapliod genomes (BBCC, CCDD, HHKK and HHJJ) with broad geographical distribution and ecological adaptation. In this paper we describe our strategy to construct robust physical maps of all 12 rice species with an emphasis on the AA diploid O. nivara--thought to be the progenitor of modern cultivated rice.

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Year:  2005        PMID: 16217601     DOI: 10.1007/s11103-004-6237-x

Source DB:  PubMed          Journal:  Plant Mol Biol        ISSN: 0167-4412            Impact factor:   4.076


  28 in total

1.  Hd1, a major photoperiod sensitivity quantitative trait locus in rice, is closely related to the Arabidopsis flowering time gene CONSTANS.

Authors:  M Yano; Y Katayose; M Ashikari; U Yamanouchi; L Monna; T Fuse; T Baba; K Yamamoto; Y Umehara; Y Nagamura; T Sasaki
Journal:  Plant Cell       Date:  2000-12       Impact factor: 11.277

Review 2.  The genetic colinearity of rice and other cereals on the basis of genomic sequence analysis.

Authors:  Jeffrey L Bennetzen; Jianxin Ma
Journal:  Curr Opin Plant Biol       Date:  2003-04       Impact factor: 7.834

3.  Gramene: a resource for comparative grass genomics.

Authors:  Doreen Ware; Pankaj Jaiswal; Junjian Ni; Xiaokang Pan; Kuan Chang; Kenneth Clark; Leonid Teytelman; Steve Schmidt; Wei Zhao; Samuel Cartinhour; Susan McCouch; Lincoln Stein
Journal:  Nucleic Acids Res       Date:  2002-01-01       Impact factor: 16.971

4.  Rice transposable elements: a survey of 73,000 sequence-tagged-connectors.

Authors:  L Mao; T C Wood; Y Yu; M A Budiman; J Tomkins; S Woo; M Sasinowski; G Presting; D Frisch; S Goff; R A Dean; R A Wing
Journal:  Genome Res       Date:  2000-07       Impact factor: 9.043

5.  A draft sequence of the rice genome (Oryza sativa L. ssp. indica).

Authors:  Jun Yu; Songnian Hu; Jun Wang; Gane Ka-Shu Wong; Songgang Li; Bin Liu; Yajun Deng; Li Dai; Yan Zhou; Xiuqing Zhang; Mengliang Cao; Jing Liu; Jiandong Sun; Jiabin Tang; Yanjiong Chen; Xiaobing Huang; Wei Lin; Chen Ye; Wei Tong; Lijuan Cong; Jianing Geng; Yujun Han; Lin Li; Wei Li; Guangqiang Hu; Xiangang Huang; Wenjie Li; Jian Li; Zhanwei Liu; Long Li; Jianping Liu; Qiuhui Qi; Jinsong Liu; Li Li; Tao Li; Xuegang Wang; Hong Lu; Tingting Wu; Miao Zhu; Peixiang Ni; Hua Han; Wei Dong; Xiaoyu Ren; Xiaoli Feng; Peng Cui; Xianran Li; Hao Wang; Xin Xu; Wenxue Zhai; Zhao Xu; Jinsong Zhang; Sijie He; Jianguo Zhang; Jichen Xu; Kunlin Zhang; Xianwu Zheng; Jianhai Dong; Wanyong Zeng; Lin Tao; Jia Ye; Jun Tan; Xide Ren; Xuewei Chen; Jun He; Daofeng Liu; Wei Tian; Chaoguang Tian; Hongai Xia; Qiyu Bao; Gang Li; Hui Gao; Ting Cao; Juan Wang; Wenming Zhao; Ping Li; Wei Chen; Xudong Wang; Yong Zhang; Jianfei Hu; Jing Wang; Song Liu; Jian Yang; Guangyu Zhang; Yuqing Xiong; Zhijie Li; Long Mao; Chengshu Zhou; Zhen Zhu; Runsheng Chen; Bailin Hao; Weimou Zheng; Shouyi Chen; Wei Guo; Guojie Li; Siqi Liu; Ming Tao; Jian Wang; Lihuang Zhu; Longping Yuan; Huanming Yang
Journal:  Science       Date:  2002-04-05       Impact factor: 47.728

6.  A draft sequence of the rice genome (Oryza sativa L. ssp. japonica).

Authors:  Stephen A Goff; Darrell Ricke; Tien-Hung Lan; Gernot Presting; Ronglin Wang; Molly Dunn; Jane Glazebrook; Allen Sessions; Paul Oeller; Hemant Varma; David Hadley; Don Hutchison; Chris Martin; Fumiaki Katagiri; B Markus Lange; Todd Moughamer; Yu Xia; Paul Budworth; Jingping Zhong; Trini Miguel; Uta Paszkowski; Shiping Zhang; Michelle Colbert; Wei-lin Sun; Lili Chen; Bret Cooper; Sylvia Park; Todd Charles Wood; Long Mao; Peter Quail; Rod Wing; Ralph Dean; Yeisoo Yu; Andrey Zharkikh; Richard Shen; Sudhir Sahasrabudhe; Alun Thomas; Rob Cannings; Alexander Gutin; Dmitry Pruss; Julia Reid; Sean Tavtigian; Jeff Mitchell; Glenn Eldredge; Terri Scholl; Rose Mary Miller; Satish Bhatnagar; Nils Adey; Todd Rubano; Nadeem Tusneem; Rosann Robinson; Jane Feldhaus; Teresita Macalma; Arnold Oliphant; Steven Briggs
Journal:  Science       Date:  2002-04-05       Impact factor: 47.728

7.  Utility and distribution of conserved noncoding sequences in the grasses.

Authors:  Nicholas J Kaplinsky; David M Braun; Jon Penterman; Stephen A Goff; Michael Freeling
Journal:  Proc Natl Acad Sci U S A       Date:  2002-04-23       Impact factor: 11.205

8.  Rapid recent growth and divergence of rice nuclear genomes.

Authors:  Jianxin Ma; Jeffrey L Bennetzen
Journal:  Proc Natl Acad Sci U S A       Date:  2004-07-07       Impact factor: 11.205

9.  The genome sequence and structure of rice chromosome 1.

Authors:  Takuji Sasaki; Takashi Matsumoto; Kimiko Yamamoto; Katsumi Sakata; Tomoya Baba; Yuichi Katayose; Jianzhong Wu; Yoshihito Niimura; Zhukuan Cheng; Yoshiaki Nagamura; Baltazar A Antonio; Hiroyuki Kanamori; Satomi Hosokawa; Masatoshi Masukawa; Koji Arikawa; Yoshino Chiden; Mika Hayashi; Masako Okamoto; Tsuyu Ando; Hiroyoshi Aoki; Kohei Arita; Masao Hamada; Chizuko Harada; Saori Hijishita; Mikiko Honda; Yoko Ichikawa; Atsuko Idonuma; Masumi Iijima; Michiko Ikeda; Maiko Ikeno; Sachie Ito; Tomoko Ito; Yuichi Ito; Yukiyo Ito; Aki Iwabuchi; Kozue Kamiya; Wataru Karasawa; Satoshi Katagiri; Ari Kikuta; Noriko Kobayashi; Izumi Kono; Kayo Machita; Tomoko Maehara; Hiroshi Mizuno; Tatsumi Mizubayashi; Yoshiyuki Mukai; Hideki Nagasaki; Marina Nakashima; Yuko Nakama; Yumi Nakamichi; Mari Nakamura; Nobukazu Namiki; Manami Negishi; Isamu Ohta; Nozomi Ono; Shoko Saji; Kumiko Sakai; Michie Shibata; Takanori Shimokawa; Ayahiko Shomura; Jianyu Song; Yuka Takazaki; Kimihiro Terasawa; Kumiko Tsuji; Kazunori Waki; Harumi Yamagata; Hiroko Yamane; Shoji Yoshiki; Rie Yoshihara; Kazuko Yukawa; Huisun Zhong; Hisakazu Iwama; Toshinori Endo; Hidetaka Ito; Jang Ho Hahn; Ho-Il Kim; Moo-Young Eun; Masahiro Yano; Jiming Jiang; Takashi Gojobori
Journal:  Nature       Date:  2002-11-21       Impact factor: 49.962

10.  Comparative RFLP mapping of a wild rice, Oryza officinalis, and cultivated rice, O. sativa.

Authors:  K K Jena; G S Khush; G Kochert
Journal:  Genome       Date:  1994-06       Impact factor: 2.166

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  53 in total

1.  SyMAP: A system for discovering and viewing syntenic regions of FPC maps.

Authors:  Carol Soderlund; William Nelson; Austin Shoemaker; Andrew Paterson
Journal:  Genome Res       Date:  2006-09       Impact factor: 9.043

2.  Dynamic evolution of oryza genomes is revealed by comparative genomic analysis of a genus-wide vertical data set.

Authors:  Jetty S S Ammiraju; Fei Lu; Abhijit Sanyal; Yeisoo Yu; Xiang Song; Ning Jiang; Ana Clara Pontaroli; Teri Rambo; Jennifer Currie; Kristi Collura; Jayson Talag; Chuanzhu Fan; Jose Luis Goicoechea; Andrea Zuccolo; Jinfeng Chen; Jeffrey L Bennetzen; Mingsheng Chen; Scott Jackson; Rod A Wing
Journal:  Plant Cell       Date:  2008-12-19       Impact factor: 11.277

3.  Comparative sequence analysis of MONOCULM1-orthologous regions in 14 Oryza genomes.

Authors:  Fei Lu; Jetty S S Ammiraju; Abhijit Sanyal; Shengli Zhang; Rentao Song; Jinfeng Chen; Guisheng Li; Yi Sui; Xiang Song; Zhukuan Cheng; Antonio Costa de Oliveira; Jeffrey L Bennetzen; Scott A Jackson; Rod A Wing; Mingsheng Chen
Journal:  Proc Natl Acad Sci U S A       Date:  2009-01-22       Impact factor: 11.205

4.  The Oryza bacterial artificial chromosome library resource: construction and analysis of 12 deep-coverage large-insert BAC libraries that represent the 10 genome types of the genus Oryza.

Authors:  Jetty S S Ammiraju; Meizhong Luo; José L Goicoechea; Wenming Wang; Dave Kudrna; Christopher Mueller; Jayson Talag; HyeRan Kim; Nicholas B Sisneros; Barbara Blackmon; Eric Fang; Jeffery B Tomkins; Darshan Brar; David MacKill; Susan McCouch; Nori Kurata; Georgina Lambert; David W Galbraith; K Arumuganathan; Kiran Rao; Jason G Walling; Navdeep Gill; Yeisoo Yu; Phillip SanMiguel; Carol Soderlund; Scott Jackson; Rod A Wing
Journal:  Genome Res       Date:  2005-12-12       Impact factor: 9.043

5.  Genetic diversity and classification of Oryza sativa with emphasis on Chinese rice germplasm.

Authors:  C-H Wang; X-M Zheng; Q Xu; X-P Yuan; L Huang; H-F Zhou; X-H Wei; S Ge
Journal:  Heredity (Edinb)       Date:  2013-12-11       Impact factor: 3.821

6.  Sequence, annotation, and analysis of synteny between rice chromosome 3 and diverged grass species.

Authors:  C Robin Buell; Qiaoping Yuan; Shu Ouyang; Jia Liu; Wei Zhu; Aihui Wang; Rama Maiti; Brian Haas; Jennifer Wortman; Mihaela Pertea; Kristine M Jones; Mary Kim; Larry Overton; Tamara Tsitrin; Douglas Fadrosh; Jayati Bera; Bruce Weaver; Shaohua Jin; Shivani Johri; Matt Reardon; Kristen Webb; Jessica Hill; Kelly Moffat; Luke Tallon; Susan Van Aken; Matthew Lewis; Teresa Utterback; Tamara Feldblyum; Victoria Zismann; Stacey Iobst; Joseph Hsiao; Aymeric R de Vazeille; Steven L Salzberg; Owen White; Claire Fraser; Yeisoo Yu; HeyRan Kim; Teri Rambo; Jennifer Currie; Kristi Collura; Shelly Kernodle-Thompson; Fusheng Wei; Kudrna Kudrna; Jetty Siva S Ammiraju; Meizhong Luo; Jose Luis Goicoechea; Rod A Wing; David Henry; Ryan Oates; Michael Palmer; Gina Pries; Christopher Saski; Jessica Simmons; Carol Soderlund; William Nelson; Melissa de la Bastide; Lori Spiegel; Lidia Nascimento; Emily Huang; Raymond Preston; Theresa Zutavern; Lance Palmer; Andrew O'Shaughnessy; Sujit Dike; W Richard McCombie; Pat Minx; Holly Cordum; Richard Wilson; Weiwei Jin; Hye-Ran Lee; Jiming Jiang; Scott Jackson
Journal:  Genome Res       Date:  2005-08-18       Impact factor: 9.043

7.  Evolutionary analysis of the Sub1 gene cluster that confers submergence tolerance to domesticated rice.

Authors:  Takeshi Fukao; Tristan Harris; Julia Bailey-Serres
Journal:  Ann Bot       Date:  2008-09-29       Impact factor: 4.357

8.  Genomics for weed science.

Authors:  David Horvath
Journal:  Curr Genomics       Date:  2010-03       Impact factor: 2.236

9.  OryGenesDB 2008 update: database interoperability for functional genomics of rice.

Authors:  Gaëtan Droc; Christophe Périn; Sébastien Fromentin; Pierre Larmande
Journal:  Nucleic Acids Res       Date:  2008-11-26       Impact factor: 16.971

10.  A recent duplication revisited: phylogenetic analysis reveals an ancestral duplication highly-conserved throughout the Oryza genus and beyond.

Authors:  Julie Jacquemin; Michèle Laudié; Richard Cooke
Journal:  BMC Plant Biol       Date:  2009-12-10       Impact factor: 4.215

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