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  1. Content type: Article

    In rice-consuming countries, specific varieties are recognized as premium, “gold standard” varieties, while others are recognized as being superior but second best, despite being identical using the current su...

    Authors: Elaine T. Champagne, Karen L. Bett-Garber, Melissa A. Fitzgerald, Casey C. Grimm, Jeanne Lea, Ken’ichi Ohtsubo, Supanee Jongdee, Lihong Xie, Priscila Zaczuk Bassinello, Adoracion Resurreccion, Rauf Ahmad, Fatemah Habibi and Russell Reinke

    Citation: Rice 2010 3:9057

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  2. Content type: Article

    We present an overview of a research platform that provides essential germplasm, genotypic and phenotypic data and analytical tools for dissecting phenotype–genotype associations in rice. These resources inclu...

    Authors: Chih-Wei Tung, Keyan Zhao, Mark H. Wright, M. Liakat Ali, Janelle Jung, Jennifer Kimball, Wricha Tyagi, Michael J. Thomson, Kenneth McNally, Hei Leung, Hyunjung Kim, Sang-Nag Ahn, Andy Reynolds, Brian Scheffler, Georgia Eizenga, Anna McClung…

    Citation: Rice 2010 3:9056

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  3. Content type: Article

    Repetitive sequences, primarily transposable elements form an indispensable part of eukaryotic genomes. However, little is known about how these sequences originate, evolve and function in context of a genome....

    Authors: Navdeep Gill, Phillip SanMiguel, Braham Deep Singh Dhillon, Brian Abernathy, HyeRan Kim, Lincoln Stein, Doreen Ware, Rod Wing and Scott A. Jackson

    Citation: Rice 2010 3:9054

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  4. Content type: Article

    The main objectives of the “Oryza Map Alignment Project” (OMAP) are to characterize the rice genome from a comparative standpoint by establishing a genus-wide and genome-scale comparative framework from represent...

    Authors: Jose Luis Goicoechea, Jetty Siva S. Ammiraju, Pradeep Reddy Marri, Mingsheng Chen, Scott Jackson, Yeisoo Yu, Steve Rounsley and Rod A. Wing

    Citation: Rice 2010 3:9052

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  5. Content type: Article

    This study characterized Pokkali-derived quantitative trait loci (QTLs) for seedling stage salinity tolerance in preparation for use in marker-assisted breeding. An analysis of 100 SSR markers on 140 IR29/Pokk...

    Authors: Michael J. Thomson, Marjorie de Ocampo, James Egdane, M. Akhlasur Rahman, Andres Godwin Sajise, Dante L. Adorada, Ellen Tumimbang-Raiz, Eduardo Blumwald, Zeba I. Seraj, Rakesh K. Singh, Glenn B. Gregorio and Abdelbagi M. Ismail

    Citation: Rice 2010 3:9053

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  6. Content type: Article

    Rice landraces tolerant of up to 2 weeks of complete submergence were collected from farmers’ fields in the 1950s. Success in fine mapping of SUBMERGENCE 1 (SUB1), a robust quantitative trait locus from the subme...

    Authors: Julia Bailey-Serres, Takeshi Fukao, Pamela Ronald, Abdelbagi Ismail, Sigrid Heuer and David Mackill

    Citation: Rice 2010 3:9048

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  7. Content type: Article

    One of the major challenges in genetics has been to identify the nucleotide polymorphisms responsible for phenotypic variation. Through intensive analysis, several major quantitative trait loci (QTLs) for agro...

    Authors: Shuichi Fukuoka, Kaworu Ebana, Toshio Yamamoto and Masahiro Yano

    Citation: Rice 2010 3:9044

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  8. Content type: Article

    Iron (Fe) is an important micronutrient for living organisms. Fe deficiency severely impairs plant growth and is a widespread human dietary problem, with particularly high numbers of affected children and fema...

    Authors: Khurram Bashir, Yasuhiro Ishimaru and Naoko K. Nishizawa

    Citation: Rice 2010 3:9042

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  9. Content type: Article

    In plants, polyglutamylated folate forms account for a significant proportion of the total folate pool. Polyglutamylated folate forms are produced by the enzyme folylpolyglutamate synthetase (FPGS). The FPGS e...

    Authors: Nampeung Anukul, Riza Abilgos Ramos, Payam Mehrshahi, Anahi Santoyo Castelazo, Helen Parker, Anne Diévart, Nadège Lanau, Delphine Mieulet, Gregory Tucker, Emmanuel Guiderdoni, David A. Barrett and Malcolm J. Bennett

    Citation: Rice 2010 3:9040

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  10. Content type: Article

    Over the past two decades, genetic dissection of complex phenotypes of economic and biological interest has revealed the chromosomal locations of many quantitative trait loci (QTLs) in rice and their contribut...

    Authors: Jun-ichi Yonemaru, Toshio Yamamoto, Shuichi Fukuoka, Yusaku Uga, Kiyosumi Hori and Masahiro Yano

    Citation: Rice 2010 3:9041

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  11. Content type: Article

    Germin-like protein (GLP) markers were associated with quantitative trait loci (QTL) for resistance to the rice blast pathogen, Magnaporthe oryzae in multiple rice (Oryza sativa) mapping populations. Twelve paral...

    Authors: Rebecca M. Davidson, Patricia M. Manosalva, Jacob Snelling, Myron Bruce, Hei Leung and Jan E. Leach

    Citation: Rice 2010 3:9038

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  12. Content type: Article

    WRKY transcription factors regulate diverse plant processes including responses to biotic stresses. Our previous studies indicate that OsWRKY62, an OsWRKY IIa subfamily member, functions as a negative regulato...

    Authors: Ying Peng, Laura E. Bartley, Patrick Canlas and Pamela C. Ronald

    Citation: Rice 2010 3:9039

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  13. Content type: Article

    Carbon isotope discrimination (∆13C) is considered as an index of leaf-level water use efficiency, an important objective for plant breeders seeking to conserve water resources. We report in rice a genetic analys...

    Authors: Dominique This, Jonathan Comstock, Brigitte Courtois, Yunbi Xu, Nourollah Ahmadi, Wendy M. Vonhof, Christine Fleet, Tim Setter and Susan McCouch

    Citation: Rice 2010 3:9036

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  14. Content type: Article

    The beet armyworm (Spodoptera exigua) and the rice water weevil (Lissorhoptrus oryzophilus) are two important insect pests in rice production. To identify insect-responsive genes in rice, we performed a deep tran...

    Authors: R. C. Venu, M. Sheshu Madhav, M. V. Sreerekha, Kan Nobuta, Yuan Zhang, Peter Carswell, Michael J. Boehm, Blake C. Meyers, Kenneth L. Korth and Guo-Liang Wang

    Citation: Rice 2010 3:9037

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  15. Content type: Article

    Diseases caused by fungal and bacterial pathogens like Magnaporthe oryzae and Xanthomonas oryzae pv. oryzae are responsible for considerable yield loss. Up to now, in rice, the modification of the expression of m...

    Authors: Amandine Delteil, Jie Zhang, Philippe Lessard and Jean-Benoit Morel

    Citation: Rice 2010 3:9035

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  16. Content type: Article

    A secreted cellulase of Xanthomonas oryzae pv. oryzae induces innate immune responses in rice including a hypersensitive response (HR) like reaction. Microarray analysis was conducted using RNA isolated 12 h foll...

    Authors: Gopaljee Jha, Hitendra Kumar Patel, Madhumita Dasgupta, Ramesh Palaparthi and Ramesh V. Sonti

    Citation: Rice 2009 3:9033

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  17. Content type: Article

    Transcriptional profiling has identified genes associated with adaptive responses to phosphorus (P) deficiency; however, distinguishing stress response from tolerance has been difficult. We report gene express...

    Authors: Juan Pariasca-Tanaka, Kouji Satoh, Terry Rose, Ramil Mauleon and Matthias Wissuwa

    Citation: Rice 2009 2:9032

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  18. Content type: Article

    In humans, iron (Fe) and zinc (Zn) deficiencies result in major worldwide health problems. Transgenic technologies to produce Fe- and Zn-biofortified rice varieties offer a promising potential solution. Nicoti...

    Authors: Hiroshi Masuda, Kanako Usuda, Takanori Kobayashi, Yasuhiro Ishimaru, Yusuke Kakei, Michiko Takahashi, Kyoko Higuchi, Hiromi Nakanishi, Satoshi Mori and Naoko K. Nishizawa

    Citation: Rice 2009 2:9031

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  19. Content type: Article

    During the last 10 years, a large number of quantitative trait loci (QTLs) controlling rice root morphological parameters have been detected in several mapping populations by teams interested in improving drou...

    Authors: Brigitte Courtois, Nourollah Ahmadi, Farkhanda Khowaja, Adam H. Price, Jean-François Rami, Julien Frouin, Chantal Hamelin and Manuel Ruiz

    Citation: Rice 2009 2:9028

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  20. Content type: Article

    To understand the basis of broad-spectrum disease resistance in rice, we isolated a gamma-ray-induced IR64 mutant G978 that showed enhanced resistance to blast and bacterial blight. The resistance is quantitat...

    Authors: Ma. Reina Suzette Madamba, Nobuko Sugiyama, Alicia Bordeos, Ramil Mauleon, Kouji Satoh, Marietta Baraoidan, Shoshi Kikuchi, Ko Shimamoto and Hei Leung

    Citation: Rice 2009 2:9027

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  21. Content type: Article

    Hybrid weakness is a reproductive barrier. In rice, the hybrid weakness caused by two complementary genes––HWC1 and HWC2––has been surveyed extensively. However, their gene products and the molecular mechanism th...

    Authors: Tsutomu Kuboyama, Toshiya Saito, Takashi Matsumoto, Jianzhong Wu, Hiroyuki Kanamori, Satoru Taura, Muneharu Sato, Wataru Marubashi and Katsuyuki Ichitani

    Citation: Rice 2009 2:9026

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  22. Content type: Article

    The genome sequencing of all major food and bioenergy crops is of critical importance in the race to improve crop production to meet the future food and energy security needs of the world. Next generation sequ...

    Authors: Steve Rounsley, Pradeep Reddy Marri, Yeisoo Yu, Ruifeng He, Nick Sisneros, Jose Luis Goicoechea, So Jeong Lee, Angelina Angelova, Dave Kudrna, Meizhong Luo, Jason Affourtit, Brian Desany, James Knight, Faheem Niazi, Michael Egholm and Rod A. Wing

    Citation: Rice 2009 2:9025

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  23. Content type: Article

    Rice oxalate oxidase genes (OXO) may play a role in resistance to Magnaporthe oryzae. Genome analyses showed four tandemly duplicated OXO genes, OsOXO1OsOXO4, which mapped to a blast resistance QTL in chromosome...

    Authors: Maria Gay C. Carrillo, Paul H. Goodwin, Jan E. Leach, Hei Leung and Casiana M. Vera Cruz

    Citation: Rice 2009 2:9024

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  24. Content type: Article

    Although the genetic diversity of rice germplasm has been well characterized globally, few studies have taken an in-depth view of a large number of rice landraces on a local scale. To better understand the rel...

    Authors: Michael J. Thomson, Nicholas R. Polato, Joko Prasetiyono, Kurniawan R. Trijatmiko, Tiur S. Silitonga and Susan R. McCouch

    Citation: Rice 2009 2:9023

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  25. Content type: Brief Communication

    Alternative splicing creates a diversity of gene products in higher eukaryotes. Twenty-five percent (1,583/6,371) of predicted alternatively spliced transcripts can be detected using the NSF45K rice whole-geno...

    Authors: Ki-Hong Jung, Laura E. Bartley, Peijian Cao, Patrick E. Canlas and Pamela C. Ronald

    Citation: Rice 2008 2:9020

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  26. Content type: Article

    Heading date determines rice’s adaptation to its area and cropping season. We analyzed the molecular evolution of the Hd6 quantitative trait locus for photoperiod sensitivity in a total of 20 cultivated varieties...

    Authors: Hiroko Yamane, Tomoko Ito, Harumi Ishikubo, Masaki Fujisawa, Harumi Yamagata, Kozue Kamiya, Yukiyo Ito, Masao Hamada, Hiroyuki Kanamori, Hiroshi Ikawa, Yuichi Katayose, Jianzhong Wu, Takuji Sasaki and Takashi Matsumoto

    Citation: Rice 2008 2:9019

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  27. Content type: Article

    Plant roots have a large range of functions, including acquisition of water and nutrients, as well as structural support. Dissecting the genetic and molecular mechanisms controlling rice root development is cr...

    Authors: J. Rebouillat, A. Dievart, J. L. Verdeil, J. Escoute, G. Giese, J. C. Breitler, P. Gantet, S. Espeout, E. Guiderdoni and C. Périn

    Citation: Rice 2008 2:9016

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  28. Content type: Article

    Coordinated transcriptional modulation of large gene sets depends on the combinatorial use of cis-regulatory motifs in promoters. We postulate that promoter content similarities are diagnostic for co-expressing g...

    Authors: Stuart Meier, Chris Gehring, Cameron Ross MacPherson, Mandeep Kaur, Monique Maqungo, Sheela Reuben, Samson Muyanga, Ming-Der Shih, Fu-Jin Wei, Samart Wanchana, Ramil Mauleon, Aleksandar Radovanovic, Richard Bruskiewich, Tsuyoshi Tanaka, Bijayalaxmi Mohanty, Takeshi Itoh…

    Citation: Rice 2008 1:9017

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  29. Content type: Review

    The increasing world population and global climate change have made optimizing crop plant return both crucial and urgent. Furthermore, improved understanding of crop yield potential as well as the implementati...

    Authors: Xian-Jun Song and Motoyuki Ashikari

    Citation: Rice 2008 1:9018

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  30. Content type: Article

    Metabolomics is a recently developed technology for comprehensive analysis of metabolites in organisms. Plant metabolites that are produced for the growth, development, and chemical defense of plants against c...

    Authors: Akira Oikawa, Fumio Matsuda, Miyako Kusano, Yozo Okazaki and Kazuki Saito

    Citation: Rice 2008 1:9009

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  31. Content type: Article

    Increasing the iron (Fe) and zinc (Zn) concentrations of staple foods, such as rice, could solve Fe and Zn deficiencies, which are two of the most serious nutritional problems affecting humans. Mugineic acid f...

    Authors: Hiroshi Masuda, Motofumi Suzuki, Kendi Claudio Morikawa, Takanori Kobayashi, Hiromi Nakanishi, Michiko Takahashi, Masahiko Saigusa, Satoshi Mori and Naoko K. Nishizawa

    Citation: Rice 2008 1:9007

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  32. Content type: Brief Communication

    Opportunities abound to apply crop science to solving many of the world’s food problems. International agricultural research centers (IARCs) provide a window through which students can see the need for improve...

    Authors: Ronald L. Phillips, Noel P. Magor, David Shires, Hei Leung, Susan R. McCouch and Duncan Macintosh

    Citation: Rice 2008 1:9003

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  33. Content type: Editorial

    Research into rice—the world’s most important food crop—is crucial for the development of technologies that will increase productivity for farmers who rely on rice for their livelihood. This is particularly th...

    Authors: Robert S. Zeigler and Adam Barclay

    Citation: Rice 2008 1:9001

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