Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Al-Babili S, Beyer P (2005)Golden Rice – five years on the road – five years to go? Trends Plant Sci 10:565–573
Ammiraju JS, Luo M, Goicoechea JL, Wang W, Kudrna D, Mueller C, Talag J, Kim H, Sisneros NB, Blackmon B, Fang E, Tomkins JB, Brar D, Mackill D, McCouch S, Kurata N, Lambert G, Galbraith DW, Arumuganathan K, Rao K, Walling JG, Gill N, Yu Y, Sanmiguel P, Soderlund C, Jackson S, Wing RA (2006)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. Genome Res 16:140–147
An G, Jeong DH, Jung KH, Lee S (2005)Reverse genetic approaches for functional genomics of rice. Plant Mol Biol 59:111–123
Ashikari M, Sasaki A, Ueguchi-TanakaM, Itoh H, Nishimura A, Datta SK, Ishiyama K, Saito T, Kobayashi M, Khush GS, Kitano H, Matsuoka M (2002) Mutation in a gibberellin biosynthetic gene, GA20 oxidase, contributed to the rice “Green Revolution”. Breed Sci 52:143–150
Ashikari M, Sakakibara H, Lin S, Yamamoto T, Takashi T, Nishimura A, Angeles ER, Qian Q, Kitano H, Matsuoka M (2005)Cytokinin oxidase regulates rice grain production. Science 309:741–745
Bennett MD, Leitch IJ (1995)Nuclear DNA amounts in angiosperms. Annal Bot 76:113–176
Bennett MD, Leitch IJ (2005)Nuclear DNA amounts in angiosperms: progress, problems, and prospects. Annal Bot 95:45–90
Causse MA, Fulton TM, Cho YG, Ahn SN, Chunwongse J, Wu K, Xiao J, Yu Z, Ronald PC, Harrington SE, Second G, MaCouch SR, Tanksley SD (1994)Saturated molecular map of the rice genome based on an interspecific backcross population. Genetics 138:1251–1274
Devos KM (2005)Updating the ’crop circle’. Curr Opin Plant Biol 8:155–162
Doebley J, Stec A, Hubbard L (1997)The evolution of apical dominance in maize. Nature 386:485–488
Doi K, Izawa T, Fuse T, Yamanouchi U, Kubo T, Shimatani Z, Yano M, Yoshimura A (2004)Ehd1, a B-type response regulator in rice, confers short-day promotion of flowering and controls FT-like gene expression independently of Hd1. Genes Dev 18:926–936
Ebitani T, Takeuchi Y, Nonoue Y, Yamamoto T, Takeuchi K, Yano M (2005) Construction and evaluation of chromosome segment substitution lines carrying overlapping chromosome segments ofindica rice cultivar ‘Kasalath’ in a genetic background ofjaponica elite cultivar ‘Koshihikari’. Breed Sci 55: 65–73
El-Assal SED, Alonso-Blanco C, Peeters AJM, Raz V, Koornneef MA (2001)QTL for flowering time in Arabidopsis reveals a novel allele of CRY2. Nat Genet 29:435–440
Frary A, Nesbitt TC, Grandillo S, Knaap E, Cong B, Liu J, Meller J, Elber R, Alpert KB, Tanksley SD. (2000)fw2.2: a quantitative trait locus key to the evolution of tomato fruit size. Science 289:85–88
Fridman E, Pleban T, Zamir D (2000)A recombination hotspot delimits a wild-species quantitative trait locus for tomato sugar content to 484 bp within an invertase gene. Proc Natl Acad Sci USA 97:4718–4723
Greco R, Ouwerkerk PB, Taal AJ, Favalli C, Beguiristain T, Puigdomenech P, Colombo L, Hoge J H, Pereira A (2001)Early and multiple Ac transpositions in rice suitable for efficient insertional mutagenesis. Plant Mol Biol 46:215–227
Harushima Y, Yano M, Shomura A, Sato M, Shimano T, Kuboki Y, Yamamoto T, Lin SY, Antonio BA, Parco A, Kajiya H, Huang N, Yamamoto K, Nagamura Y, Kurata N, Khush GS, Sasaki T (1998)A high-density rice genetic linkage map with 2275 markers using a single F2 population. Genetics 148:479–494
Hiei Y, Ohta S, Komari T, Kumashiro T (1994)Efficient transformation of rice (Oryza sativa L.) mediated by Agrobacterium and sequence analysis of the boundaries of the T-DNA. Plant J 6:271–282
Hirochika, H (2001)Contribution of the Tos17 retrotransposon to rice functional genomics. Curr Opin Plant Biol 4:118–122
International Rice Genome Sequencing Project (2005)The map-based sequence of the rice genome. Nature 436:793–800
Iwata N, Omura T (1975)Studies on the trisomics in rice plants (Oryza sativa L.). III. Relation between trisomics and genetic linkage groups. Jpn J Breed 25:363–368
Jaiswal P, Ni J, Yap I, Ware D, Spooner W, Youens-Clark K, Ren L, Liang C, Zhao W, Ratnapu K, Faga B, Canaran P, Fogleman M, Hebbard C, Avraham S, Schmidt S, Casstevens TM, Buckler ES, Stein L, McCouch S (2006)Gramene: a bird’s eye view of cereal genomes. Nucl Acids Res 34 (Database issue):D717–723
Jeon JS, Lee S, Jung KH, Jun SH, Jeong DH, Lee J, Kim C, Jang S, Lee S, Yang J, Nam K, An K, Han MJ, Sung RJ, Choi HS, Yu JH, Yu JH, Choi JH, Cho SY, Cha SS, Kim SI, An G (2000)T-DNA insertional mutagenesis for functional genomics in rice. Plant J 22:561–570
Khush GS (2003)Productivity improvements in rice. Nutr Rev 61:114–116
Kikuchi S, Satoh K, Nagata T, Kawagashira N, Doi K, Kishimoto N, Yazaki J, Ishikawa M, Yamada H, Ooka H, Hotta I, Kojima K, Namiki T, Ohneda E, Yahagi W, Suzuki K, Li CJ, Ohtsuki K, Shishiki T, Otomo Y, Murakami K, Iida Y, Sugano S, Fujimura T, Suzuki Y, Tsunoda Y, Kurosaki T, Kodama T, Masuda H, Kobayashi M, Xie Q, Lu M, Narikawa R, Sugiyama A, Mizuno K, Yokomizo S, Niikura J, Ikeda R, Ishibiki J, Kawamata M, Yoshimura A, Miura J, Kusumegi T, Oka M, Ryu R, Ueda M, Matsubara K, Kawai J, Carninci P, Adachi J, Aizawa K, Arakawa T, Fukuda S, Hara A, Hashizume W, Hayatsu N, Imotani K, Ishii Y, Itoh M, Kagawa I, Kondo S, Konno H, Miyazaki A, Osato N, Ota Y, Saito R, Sasaki D, Sato K, Shibata K, Shinagawa A, Shiraki T, Yoshino M, Hayashizaki Y, Yasunishi A (2003)Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice. Science 301:376–379
Kinoshita T (1995)Report of committee on gene symbolization, nomenclature and linkage groups. Rice Genet Newsl 12:9–153
Kojima S, Takahashi Y, Kobayashi Y, Monna L, Sasaki T, Araki T, Yano M (2002)Hd3a, a rice ortholog of the Arabidopsis FT gene, promotes transition to flowering downstream of Hd1 under short-day condition. Plant Cell Physiol 43:1096–1105
Konishi S, Izawa T, Lin SY, Ebana K, Fukuta Y, Sasaki T, Yano M (2006)An SNP caused loss of seed shattering during rice domestication. Science 312:1392–1396
Kurata N, Yamazaki Y (2006)An integrated biological and genome information database for rice. Plant Physiol 140:12–17
Kurata N, Nagamura Y, Yamamoto K, Harushima Y, Sue N, Wu J, Antonio BA, Shomura A, Shimizu T, Lin SY, Inoue T, Fukuda A, Shimano T, Kobuki Y, Toyama T, Miyamoto Y, Kirihara T, Hayasaka K, Miyao A, Monna L, Zhong HS, Tamura Y, Wang ZX, Momma T, Umehara Y, Yano M, Sasaki T, Minobe Y (1994)A 300 kilobase interval genetic map of rice including 883 expressed sequences. Nat Genet 8:365–372
Li C, Zhou A, Sang T (2006)Rice domestication by reducing shattering. Science 311:1936–1939
Lin HX, Yamamoto T, Sasaki T, Yano M (2000)Characterization and detection of epistatic interactions of three QTLs, Hd1, Hd2, and Hd3, controlling heading date in rice using nearly isogenic lines. Theor Appl Genet 01:1021–1028
Lin HX, Ashikari M, Yamanouchi U, Sasaki T, Yano M (2002)Identification and characterization of a quantitative trait locus, Hd9, controlling heading date in rice. Breed Sci 52:35–41
Lin HX, Liang ZW, Sasaki T, Yano M (2003)Fine mapping and characterization of quantitative trait loci Hd4 and Hd5 controlling heading date in rice. Breed Sci 53:51–59
Liu JP, Van Eck J, Cong B, Tanksley SD (2002)A new class of regulatory genes underlying the cause of pear-shaped tomato fruit. Proc Natl Acad Sci USA 99:13302–13306
Ma L, Chen C, Liu X, Jiao Y, Su N, Li L, Wang X, Cao M, Sun N, Zhang X, Bao J, Li J, Pedersen S, Bolund L, Zhao H, Yuan L, Wong GK, Wang J, Deng XW, Wang J (2005)A microarray analysis of the rice transcriptome and its comparison to Arabidopsis. Genome Res 15:1274–1283
McCouch SR, Kochert G, Yu ZH, Wang ZY, Khush GS, Coffman WR, Tanksley SD (1988)Molecular mapping of rice chromosomes. Theor Appl Genet 76:815–829
McCouch SR, Teytelman L, Xu Y, Lobos KB, Clare K, Walton M, Fu B, Maghirang R, Li Z, Xing Y, Zhang Q, Kono I, Yano M, Fjellstrom R, DeClerck G, Schneider D, Cartinhour S, Ware D, Stein L (2002)Development and mapping of 2240 new SSR markers for rice (Oryza sativa L.). DNA Res 9: 199–207
Nagao S, Takahashi M (1963)Trial construction of twelve linkage groups in Japanese rice (Genetical studies on rice plant, XXVII). J Facul Agr Hokkaido Univ Sapporo 53:72–130
Nishimura A, Ashikari M, Lin S, Takashi T, Angeles ER, Yamamoto T, Matsuoka M (2005)Isolation of a rice regeneration quantitative trait loci gene and its application to transformation systems. Proc Natl Acad Sci USA 102: 11940–11944
Paterson AH, Lander ES, Hewitt JD, Peterson S, Lincoln SE, Tanksley SD (1988)Resolution of quantitative traits into Mendelian factors by using a complete linkage map of restriction fragment length polymorphisms. Nature 335: 721–726
Ren ZH, Gao JP, Li LG, Cai XL, Huang W, Chao DY, Zhu MZ, Wang ZY, Luan S, Lin HX (2005)A rice quantitative trait locus for salt tolerance encodes a sodium transporter. Nat Genet 37:1141–1146
Rensink WA, Buell CR (2005)Microarray expression profiling resources for plant genomics. Trends Plant Sci 10:603–609
Saito A, Yano M, Kishimoto N, Nakagahra M, Yoshimura A, Saito K, Kuhara S, Ukai Y, Kawase M, Nagamine T, Yoshimura S, Ideta O, Ohsawa R, Hayano Y, Iwata N, Sugiura M (1991)Linkage map of restriction fragment length polymorphism loci in rice. Jpn J Breed 41:665–670
Sasaki A, Ashikari, M, Ueguchi-Tanaka M, Itoh H, Nishimura A, Datta S, Ishiyama K, Saito T, Kobayashi M, Khush GS, Kitano H, Matsuoka M (2002)Rice gibberellin synthesis gene. Nature 416:701–702
Spielmeyer W, Ellis MH, Chandler PM (2002)Semidwarf (sd-1), “green revolution” rice, contains a defective gibberellin 20-oxidase gene. Proc Natl Acad Sci USA 99:9043–9048
Takahashi Y, Shomura A, Sasaki T, Yano M (2001)Hd6, a rice quantitative trait locus involved in photoperiod sensitivity, encodes the alpha subunit of protein kinase CK2. Proc Natl Acad Sci USA 98:7922–7927
Vaughan DA, Morishima H, Kadowaki K (2003)Diversity in the Oryza genus. Curr Opin Plant Biol 6, 139–146
Yamazaki Y, Jaiswal P (2005)Biological ontologies in rice databases. An introduction to the activities in Gramene and Oryzabase. Plant Cell Physiol 46: 63–68
Yamamoto T, Lin HX, Sasaki T, Yano M (2000)Identification of heading date quantitative trait locus Hd6 and characterization of its epistatic interactions with Hd2 in rice using advanced backcross progeny. Genetics 154:885–891
Yano M, Sasaki T (1997)Genetic and molecular dissection of quantitative traits in rice. Plant Mol Biol 35:145–153
Yano M, Katayose Y, Ashikari M, Yamanouchi U, Monna L, Fuse T, Baba T, Yamamoto K, Umehara Y, Nagamura Y, Sasaki T (2000)Hd1, a major photoperiod sensitivity quantitative trait locus in rice, is closely related to the Arabidopsis flowering time gene CONSTANS. Plant Cell 12:2473–2483
Ye X, Al-Babili S, Kloti A, Zhang J, Lucca P, Beyer P, Potrykus I (2000) Engineering the provitamin A (beta-carotene) biosynthetic pathway into (carotenoid-free) rice endosperm. Science 287:303–305
White PT (1994)Rice: the essential harvest. Natl Geogr 185:48–79
Wing RA, Ammiraju JS, Luo M, Kim H, Yu Y, Kudrna D, Goicoechea JL, Wang W, Nelson W, Rao K, Brar D, Mackill DJ, Han B, Soderlund C, Stein L, SanMiguel P, Jackson S (2005)The Oryza map alignment project: the golden path to unlocking the genetic potential of wild rice species. Plant Mol Biol 59:53–62
Author information
Authors and Affiliations
Rights and permissions
Copyright information
© 2007 Springer Science+Business Media, LLC
About this chapter
Cite this chapter
Ashikari, M., Matsuoka, M., Yano, M. (2007). Application of Functional Genomics Tools for Crop Improvement. In: Rice Functional Genomics. Springer, New York, NY. https://doi.org/10.1007/0-387-48914-2_16
Download citation
DOI: https://doi.org/10.1007/0-387-48914-2_16
Publisher Name: Springer, New York, NY
Print ISBN: 978-0-387-48903-2
Online ISBN: 978-0-387-48914-8
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)