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  1. 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
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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
  11. 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
  12. 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
  13. 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
  14. 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
  15. 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
  16. 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
  17. 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
  18. 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
  19. 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
  20. 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
  21. 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
  22. 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
  23. 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
  24. 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
  25. 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
  26. 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
  27. 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
  28. Regulatory small RNAs (approximately 20 to 24 nt in length) are produced through pathways that involve several key evolutionarily conserved protein families; the variants of these proteins found in plants are ...

    Authors: Stacey A. Simon, Jixian Zhai, Jia Zeng and Blake C. Meyers
    Citation: Rice 2008 1:9008
  29. 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
  30. Flowering time is a key trait for geographical and seasonal adaptation of plants and is an important consideration for rice breeders. Recently identified genetic factors provide new insights into this complex ...

    Authors: Hiroyuki Tsuji, Shojiro Tamaki, Reina Komiya and Ko Shimamoto
    Citation: Rice 2008 1:9005
  31. The Committee on Gene Symbolization, Nomenclature and Linkage (CGSNL) of the Rice Genetics Cooperative has revised the gene nomenclature system for rice (Oryza) to take advantage of the completion of the rice gen...

    Authors: Susan R. McCouch
    Citation: Rice 2008 1:9004
  32. 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
  33. 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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