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Oryza

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Wild Crop Relatives: Genomic and Breeding Resources

Abstract

Rice (Oryza sativa L) is an important cereal for one-third of the world’s population. Its productivity is continually threatened by a series of biotic and abiotic stresses. There is thus an urgent need to broaden the gene pool of rice for developing varieties with high yield and resistance to several stresses. Wild species of Oryza are a reservoir of genes for tolerance to various biotic and abiotic stresses and also possess yield-enhancing loci. Morphological, cytological, and molecular divergence studies have been used to identify ten genome types in 22 Oryza species. Interspecific hybrids and alien introgression lines have been produced. Genes for resistance to grassy stunt virus, tungro virus, brown planthopper, bacterial blight, blast, tolerance to soil toxicity, and cytoplasmic male sterility have been transferred from wild species and varieties released. Many of the genes/QTL introgressed from wild species have been tagged with DNA markers. Xa21, a gene for bacterial blight resistance has been pyramided along with other genes through MAS and 12 varieties/hybrids released. Molecular analysis has shown limited introgression of short segments from distant genomes. Parental genomes and alien chromosomes segments have been characterized using genomic in situ hybridization. BAC libraries from different wild species have been established. BAC end sequence, physical framework of different genomes of Oryza, and alignment with the rice reference genome have provided valuable information on evolutionary mechanisms and on genome organization, structural rearrangements, repeats, transposable elements, SSR, miRNA, and single nucleotide variation. Long terminal repeated (LTR)-retrotransposons are considered as the predominant class of repeat elements that increase the genome size in some species. Introgression of genes with broad spectrum of resistance to stresses, yield-enhancing loci/QTLs, and identification of genes controlling homoeologous pairing to introgress wild species genes from distant genomes need to be explored. BAC libraries and CSSL of wild relatives are important genetic resource for functional genomics and for mapping and cloning of agronomically important genes/QTLs harbored in wild species of Oryza. With the advances in tissue culture techniques, molecular markers, and genomics, the scope for utilization of wild species in genetic enhancement of rice seems more promising than before.

This chapter is dedicated to our dearest teacher Dr. Gurdev S. Khush.

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References

  • Abbasi FM, Brar DS, Carpena AL, Fukui K, Khush GS (1999) Detection of auto-syndetic and allosyndetic pairing among A and E genomes of Oryza through genomic in situ hybridization. Rice Genet Newsl 16:24–25

    Google Scholar 

  • Aggarwal PK (2003) Molecular approaches in evolutionary studies and speciation in genus Oryza – present status. In: Nanda JS, Sharma SD (eds) Monograph on genus Oryza. Science, Enfield, NH, USA, pp 139–170

    Google Scholar 

  • Aggarwal RK, Brar DS, Khush GS, Jackson MT (1996) Oryza schlechteri Pilger has a distinct genome based on molecular analysis. Rice Genet Newsl 13:58–59

    Google Scholar 

  • Aggarwal RK, Brar DS, Khush GS (1997) Two new genomes in the Oryza complex identified on the basis of molecular divergence analysis using total genomic DNA hybridization. Mol Gen Genet 254:1–12

    PubMed  CAS  Google Scholar 

  • Aggarwal RK, Brar DS, Nandi S, Huang N, Khush GS (1999) Phylogenetic relationships among Oryza species revealed by AFLP markers. Theor Appl Genet 98:1320–1328

    CAS  Google Scholar 

  • Ahn SN, Tanskley SD (1993) Comparative linkage maps of the rice and maize genomes. Proc Natl Acad Sci USA 90:7980–7984

    PubMed  CAS  Google Scholar 

  • Amante-Bordeos A, Sitch LA, Nelson R, Dalmacio RD, Oliva NP, Aswidinnoor H et al (1992) Transfer of bacterial blight and blast resistance from the tetraploid wild rice Oryza minuta to cultivated rice. Theor Appl Genet 84:345–354

    Google Scholar 

  • Ammiraju JSS, Luo M, Goicoechea JL, Wang W, Kudrna D, Mueller C et al (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

    PubMed  Google Scholar 

  • Ammiraju JSS, Zuccolo A, Yu Y, Song X, Piegu B, Chevalier F et al (2007) Evolutionary dynamics of an ancient retrotransposon family provides insights into evolution of genome size in the genus Oryza. Plant J 52:342–351

    PubMed  CAS  Google Scholar 

  • Asghar M, Brar DS, Hernandez JE, Ohmido N, Khush GS (1998) Characterization of parental genomes in a hybrid between Oryza sativa L and O. officinalis Wall ex Watt. through fluorescence in situ hybridization. Rice Genet Newsl 15:83–84

    Google Scholar 

  • Aswidinnoor H, Nelson RJ, Dallas JF, McIntre CL, Leung H, Gustafson JP (1991) Cloning and characterization of repetitive DNA sequences from genomes of Oryza minuta and Oryza australiensis. Genome 34:790–798

    PubMed  CAS  Google Scholar 

  • Bellon MR, Brar DS, Lu BR, Pham JL (1998) Rice genetic resources. In: Dowlwig NG, Greenfield SM, Fischer KS (eds) Sustainability of rice in the global food system. Pacific Basin Study Center and IRRI, Philippines, pp 251–282

    Google Scholar 

  • Bennetzen JL, Ma J, Devos KM (2005) Mechanisms of recent genome size variation in flowering plants. Ann Bot 95:127–132

    PubMed  CAS  Google Scholar 

  • Bimpong IK (2005) Nematode resistance of backcross derivatives of Oryza sativa L crosses with Oryza glaberrima Steud and molecular characterization of introgression. MSc Thesis, University of the Philippines, Los Baños (UPLB), Laguna, Philippines

    Google Scholar 

  • Bimpong IK (2009) Identification and mapping of QTLs for drought tolerance introgressed from Oryza glaberrima Steud. into indica rice (O. sativa L.). PhD Thesis, University of the Philippines, Los Baños (UPLB), Laguna, Philippines

    Google Scholar 

  • Brar DS, Khush GS (1986) Wide hybridization and chromosome manipulation in cereals. In: Evans DH, Sharp WR, Ammirato PV (eds) Handbook of plant cell culture, vol 4, Techniques and applications. MacMillan, New York, USA, pp 221–263

    Google Scholar 

  • Brar DS, Khush GS (1997) Alien introgression in rice. Plant Mol Biol 35:35–47

    PubMed  CAS  Google Scholar 

  • Brar DS, Khush GS (2002) Transferring genes from wild species into rice. In: Kang MS (ed) Quantitative genetics, genomics and plant breeding. CABI, Wallingford, UK, pp 197–217

    Google Scholar 

  • Brar DS, Khush GS (2006) Cytogenetic manipulation and germplasm enhancement of rice (Oryza sativa L.). In: Singh RJ, Jauhar PP (eds) Genetic resources, chromosome engineering and crop improvement. CRC, Boca Raton, FL, USA, pp 115–158

    Google Scholar 

  • Brar DS, Elloran R, Khush GS (1991) Interspecific hybrids produced through embryo rescue between cultivated and eight wild species of rice. Rice Genet Newsl 8:91–93

    Google Scholar 

  • Brar DS, Elloran R, Luang M, Khush GS (1995) Search for apomixis in wild species of rice. In: Proceedings of international conference on harnessing apomixis, University of Texas, College Station, TX, USA, p 39

    Google Scholar 

  • Brar DS, Dalmacio R, Elloran R, Aggarwal R, Angeles R, Khush GS (1996) Gene transfer and molecular characterization of introgression from wild Oryza species into rice. In: Rice genetics III. IRRI, Manila, Philippines, pp 477–486

    Google Scholar 

  • Brar DS, Elloran RM, Talag JD, Abbasi F, Khush GS (1997) Cytogenetic and molecular characterization of an intergeneric hybrid between Oryza sativa L. and Porteresia coarctata (Roxb.) Tateoka. Rice Genet Newsl 14:43–44

    Google Scholar 

  • Chang TT (1972) International cooperation in conserving and evaluation of rice germplasm resources. In: Rice breeding. IRRI, Manila, Philippines, pp 177–185

    Google Scholar 

  • Chang TT (1976) The origin, evolution, cultivation, dissemination and diversification of the Asian and African rices. Euphytica 25:425–441

    Google Scholar 

  • Chang TT (2003) Origin, domestication and diversification. In: Smith CW, Dilday RH (eds) Rice: origin, history, technology and production. Wiley, Hoboken, NJ, USA, pp 3–25

    Google Scholar 

  • Chatterjee D (1948) A modified key and enumeration of the species of Oryza Linn. Indian J Agric Sci 18(185):192

    Google Scholar 

  • Cheema KK, Bains NS, Mangat GS, Das A, Brar DS, Khush GS et al (2008a) Introgression of quantitative trait loci for improved productivity from Oryza rufipogon into O. sativa. Euphytica 160:401–409

    CAS  Google Scholar 

  • Cheema KK, Grewal NK, Vikal Y, Das A, Sharma R, Lore JS et al (2008b) A novel bacterial blight resistance gene from Oryza nivara mapped to 38 Kbp region on chromosome 4L and transferred to O. sativa L. Genet Res 90:397–407

    CAS  Google Scholar 

  • Chen MS, San Miguel P, Bennetzen JL (1998) Sequence organization and conservation in sh2/a1-homologous regions of sorghum and rice. Genetics 148:435–443

    PubMed  CAS  Google Scholar 

  • Cheng Z, Han H, Yu H, Tang S, Jlang J, Gu M et al (2001a) Development and application of a complete set of rice telotrisomics. Genetics 157:361–368

    PubMed  CAS  Google Scholar 

  • Cheng ZK, Presting GG, Buell CR, Wing RA, Jiang JM (2001b) High-resolution pachytene chromosome mapping of bacterial artificial chromosomes anchored by genetic markers reveals the centromere location and the distribution of genetic recombination along chromosome 10 of rice. Genetics 157:1749–1757

    PubMed  CAS  Google Scholar 

  • Cheng C, Tsuchimoto S, Ohtsubo H, Ohtsubo E (2002) Evolutionary relationships among rice species with AA genome based on SINE insertion analysis. Gen Genet Syst 77:323–334

    CAS  Google Scholar 

  • Cheng C, Motohasi R, Tsuchimoto S, Fukuta Y, Ohtsubo H, Ohtsubo E (2003) Polyphyletic origin of cultivated rice: based on interspersion pattern of SINEs. Mol Biol Evol 20:67–75

    PubMed  CAS  Google Scholar 

  • Dalmacio RD, Brar DS, lshii T, Sitch LA, Virmani SS, Khush GS (1995) Identification and transfer of a new cytoplasmic male sterility source from Oryza perrenis into indica rice (O. sativa). Euphytica 82:221–225

    Google Scholar 

  • Dalmacio RD, Brar DS, Virmani S, Khush GS (1996) Male sterile line in rice (Oryza sativa) developed with O. glumaepatula cytoplasm. Int Rice Res Notes 21:22–23

    Google Scholar 

  • Devos KM (2005) Updating the ‘crop circle’. Curr Opin Plant Biol 8:155–162

    PubMed  CAS  Google Scholar 

  • Devos KM, Gale MD (1997) Comparative genetics in the grasses. Plant Mol Biol 35:3–15

    PubMed  CAS  Google Scholar 

  • Dingkuhn M, Jones MP, Johnson DE, Sow A (1998) Growth and yield potential of Oryza sativa and O. glaberrima upland rice cultivars and their interspecific progenies. Field Crops Res 57:57–69

    Google Scholar 

  • Doi K, Sobrizal, Ikeda K, Sanchez PL, Kurakazu T, Nagai Y (2003) Developing and evaluating rice chromosome segment substitution lines. In: Mew TW, Brar DS, Peng S, Dawe D, Hardy H (eds) Rice science: innovations and impact on livelihood. International Rice Research Institute and CASE and CAAS, Beijing, China, pp 289–296

    Google Scholar 

  • Ellis JL (1985) Oryza indandamanica Ellis, a new rice plant from islands of Andamans. Bot Bull Surv India 27:225–227

    Google Scholar 

  • Fukui K, Ohmido N, Khush GS (1994) Variability in the rDNA loci in genus Oryza detected through fluorescence in situ hybridization. Theor Appl Genet 87:893–899

    CAS  Google Scholar 

  • Furukawa T, Maekawa M, Oki T, Suda I, Iida S, Shimada H et al (2007) The Rc and Rd genes are involved in pro-anthocyanidin synthesis in rice pericarp. Plant J 49:91–102

    PubMed  CAS  Google Scholar 

  • Gale M, Moore G, Devos K (2001) Rice: a central genome for the genetics of all cereals. In: Khush GS, Brar DS, Hardy B (eds) Rice genetics IV. International Rice Research Institute and Science Publications, Los Baños, Laguna, Philippines, pp 79–88

    Google Scholar 

  • Garris AJ, Tai TH, Coburn J, Kresovich S, McCouch S (2005) Genetic structure and diversity in Oryza sativa L. Genetics 169:1631–1638

    PubMed  CAS  Google Scholar 

  • Ge S, Sang T, Lu BR, Hong DY (1999) Phylogeny of rice genomes with emphasis on origins of allotetraploid species. Proc Natl Acad Sci USA 96:14400–14405

    PubMed  CAS  Google Scholar 

  • Glaszmann JC (1987) lsozymes and classification of Asian rice varieties. Theor Appl Genet 74:21–30

    CAS  Google Scholar 

  • Goff SA, Ricke D, Lan TH, Presting G, Wang R et al (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science 296:92–100

    PubMed  CAS  Google Scholar 

  • Grillo MA, Li C, Fowlkes AM, Briggeman TM, Zhou A, Schemske DW et al (2009) Genetic architecture for the adaptive origin of annual wild rice, Oryza nivara. Evolution 63:870–883

    PubMed  CAS  Google Scholar 

  • Grover A, Pental D (1992) Interrelationships of Oryza species based on electrophoretic patterns of alcohol dehydrogenase. Can J Bot 70:352–358

    CAS  Google Scholar 

  • Gu K, Tian D, Yang F, Wu L, Sreekala C, Wang GL, Yin Z (2003) High-resolution genetic mapping of Xa27(t), a new bacterial blight resistance gene in rice, O. sativa L. Theor Appl Genet 108:800–807

    PubMed  Google Scholar 

  • Gu K, Yang B, Tian DS, Wu LF, Wang DJ, Sreekala C et al (2005) R gene expression induced by a type III effector triggers disease resistance in rice. Nature 435:1122–1125

    PubMed  CAS  Google Scholar 

  • Han B, Xue Y, Li J, Deng XW, Zhang Q (2007) Rice functional genomics research in China. Philos Trans R Soc B 362:1009–1021

    CAS  Google Scholar 

  • Hayashi Y, Kozuka J, Shimamoto K (1988) Hybrids of rice (Oryza sativa L.) and wild Oryza species obtained by cell fusion. Mol Gen Genet 214:6–10

    Google Scholar 

  • Hechanova S (2008) Molecular characterization of introgression and putative genes for bacterial blight resistance in wide-cross derivatives of rice (Oryza sativa L.). MSc Thesis, University of the Philippines, Los Baños (UPLB), Laguna, Philippines

    Google Scholar 

  • Hirabayashi H, Kaji R, Okamoto M, Ogawa T, Brar DS, Angeles ER et al (2003) Mapping QTLs for brown planthopper (BPH) resistance introgressed from O. officinalis in rice. In: Khush GS, Brar DS, Hardy B (eds) Advances in rice genetics. International Rice Research Institute, Manila, Philippines, pp 268–270

    Google Scholar 

  • Hirsh CD, Wu Y, Yan H, Jiang J (2009) Lineage-specific adaptive evolution of the centromeric protein CENH3 in diploid and allotetraploid Oryza species. Mol Biol Evol 26:2877–2885

    Google Scholar 

  • Hu CH (1961) Comparative karyological studies of wild and cultivated species of Oryza. Taiwan Provincial College of Agriculture, Taiwan

    Google Scholar 

  • Huang Z, He G, Shu L, Li X, Zhang Q (2001) Identification and mapping of two brown planthopper resistance genes in rice. Theor Appl Genet 102:929–934

    CAS  Google Scholar 

  • Huang X, Feng Q, Quian Q, Zhao Q, Wang L, Wang A et al (2009) High throughput genotyping by whole genome resequencing. Genome Res 19:1068–1076

    PubMed  CAS  Google Scholar 

  • Hue NTN (2004) Homoeologous chromosome pairing and alien introgression analyses in wide-cross derivatives of Oryza through fluorescence in situ hybridization. PhD Thesis, University of the Philippines, Los Baños, Laguna, Philippines

    Google Scholar 

  • International Rice Genome Sequencing Project (2005) The map-based sequence of the rice genome. Nature 436:793–800

    Google Scholar 

  • Ishii T, Brar DS, Multani DS, Khush GS (1994) Molecular tagging of genes for brown planthopper resistance and earliness introgressed from Oryza australiensis into cultivated rice O. sativa. Genome 37:217–221

    PubMed  CAS  Google Scholar 

  • Izawa T, Konishi S, Shomura A, Yano M (2009) DNA changes tell us about rice domestication. Curr Opin Plant Biol 12:1–8

    Google Scholar 

  • Jackson MT (1997) Conservation of rice genetic resources: the role of the International Rice Gene Bank at IRRI. Plant Mol Biol 35:61–67

    PubMed  CAS  Google Scholar 

  • Jelodar NB, Blackhall NW, Hartman TPV, Brar DS, Khush GS, Davey MR et al (1999) Intergeneric somatic hybrids of rice [Oryza sativa L. (+) Porteresia coarctata (Roxb.) Tateoka]. Theor Appl Genet 99:570–577

    CAS  Google Scholar 

  • Jena KK, Khush GS (1989) Monosomic alien addition lines of rice: production, morphology, cytology and breeding behavior. Genome 32:449–455

    Google Scholar 

  • Jena KK, Khush GS (1990) Introgression of genes from Oryza officinalis Well ex Watt to cultivated rice O. sativa L. Theor Appl Genet 80:737–745

    Google Scholar 

  • Jena KK, Khush GS, Kochert G (1992) RFLP analysis of rice (Oryza sativa L.) introgression lines. Theor Appl Genet 84:608–616

    Google Scholar 

  • Jena KK, Khush GS, Kochert G (1994) Comparative RFLP mapping of a wild rice, Oryza officinalis and cultivated rice O. sativa. Genome 37:382–389

    PubMed  CAS  Google Scholar 

  • Jena KK, Jeung JU, Lee JH, Choi HC, Brar DS (2006) High-resolution mapping of a new brown planthopper (BPH) resistance gene, Bph18(t), and marker-assisted selection for BPH resistance in rice (Oryza sativa L.). Theor Appl Genet 112:288–297

    PubMed  CAS  Google Scholar 

  • Jeung JU, Kim BR, Cho YC, Han SS, Moon HP, Lee YT et al (2007) A novel gene, Pi40(t) linked to the DNA markers derived from NBS-LRR motifs confers broad spectrum of blast resistance in rice. Theor Appl Genet 115:1163–1177

    PubMed  CAS  Google Scholar 

  • Jiang J, Gill BS, Wang GL, Ronald PC, Ward DC (1995) Metaphase and interphase fluorescence in situ hybridization mapping of the rice genome with bacterial artificial chromosomes. Proc Natl Acad Sci USA 92:4487–4491

    PubMed  CAS  Google Scholar 

  • Jin J, Huang W, Gao J, Yang J, Shi M, Zhu M et al (2008) Genetic control of rice plant architecture under domestication. Nat Genet 40:1365–1369

    PubMed  CAS  Google Scholar 

  • Jones MP, Dingkuhn M, Aluko GK, Semon M (1997) Interspecific Oryza sativa L. x O. glaberrima Steud. progenies in upland rice improvement. Euphytica 92:237–246

    Google Scholar 

  • Joshi SP, Gupta VS, Aggarwal RK, Ranjekar PS, Brar DS (2000) Genetic diversity and phylogenetic relationships as revealed by inter simple sequence repeat (ISSR) polymorphism in the genus Oryza. Theor Appl Genet 100:1311–1320

    CAS  Google Scholar 

  • Katayama T (1967) Cytogenetic studies on the genus Oryza, The F1 hybrids of the crosses BBCC x CC, BBCC x a diploid strain of O. punctata and CC x a diploid strain of O. punctata. Proc Jpn Acad 43:327–331

    Google Scholar 

  • Kato S, Kosaka H, Hara S (1928) On the affinity of rice varieties as shown by fertility of hybrid plants. Bull Sci Fac Agri Kyushu Univ 3:132–147

    Google Scholar 

  • Khush GS (1973) Cytogenetics of aneuploids. Academic, New York, USA

    Google Scholar 

  • Khush GS (1977) Disease and insect resistance in rice. Adv Agron 29:265–341

    Google Scholar 

  • Khush GS (1997) Origin, dispersal, cultivation and variation of rice. Plant Mol Biol 35:25–34

    PubMed  CAS  Google Scholar 

  • Khush GS, Brar DS (1992) Overcoming the barriers of hybridization. Theor Appl Genet 16:47–61

    Google Scholar 

  • Khush GS, Brar DS (2001) Rice genetics from Mendel to functional genomics. In: Khush GS, Brar DS, Hardy B (eds) Rice genetics IV. International Rice Research Institute and Science Publications, Los Baños, Laguna, Philippines, pp 3–19

    Google Scholar 

  • Khush GS, Brar DS (2002) Rice. In: Chopra VL, Prakash S (eds) Evolution and adaptation of cereal crops. Science, Enfield, NH, USA, pp 1–41

    Google Scholar 

  • Khush GS, Brar DS, Virk PS, Tang SX, Mallik SS, Busto GA et al (2003). Classifying rice germplasm by isozyme polymorphism and origin of cultivated rice, IRRI Discussion Paper 46. International Rice Research Institute, Manila, Philippines, p 279

    Google Scholar 

  • Khush GS, Ling KC (1974) Inheritance of resistance to grassy stunt virus and its vector in rice. J Hered 65:134–136

    Google Scholar 

  • Khush GS, Singh RJ, Sur SC, Librojo AL (1984) Primary trisomics of rice: origin, morphology, cytology and use in linkage mapping. Genetics 107:141–163

    PubMed  CAS  Google Scholar 

  • Khush GS, Bacalangco E, Ogawa T (1990) A new gene for resistance to bacterial blight from O. longistaminata. Rice Genet Newsl 7:121–122

    Google Scholar 

  • Khush GS, Brar DS, Bennett J, Virmani SS (1994) Apomixis for rice improvement. In: Khush GS (ed) Apomixis: exploiting hybrid vigor in rice. International Rice Research Institute, Manila, Philippines, pp 1–21

    Google Scholar 

  • Khush GS, Brar DS, Bennett J (1998) Apomixis in rice and prospects for its use in heterosis breeding. In: Virmani SS, Siddiq EA, Muralidharan K (eds) Advances in hybrid rice technology. International Rice Research Institute, Manila, Philippines, pp 297–309

    Google Scholar 

  • Khush GS, Angeles R, Virk PS, Brar DS (2004) Breeding rice for resistance to tungro virus at IRRI. SABRAO J 36:101–106

    Google Scholar 

  • Kikuchi S, Satoh K, Nagata T, Kawagashira N, Doi K, Kishimoto N et al (2003) Collecting, mapping and annotation of over 28,000 cDNA clones from japonica rice. Science 301:376–379

    Google Scholar 

  • Kim HR, San Miguel P, Nelson W, Collura K, Wissotski M, Walling JG et al (2007) Comparative physical mapping between Oryza sativa (AA genome type) and O. punctata (BB genome type). Genetics 176:379–390

    PubMed  CAS  Google Scholar 

  • Kim HR, Hurwitz B, Yu Y, Collura K, Gill N, San Miguel P et al (2008) Construction, alignment and analysis of twelve framework physical map that represent the ten genome types of genus Oryza. Genome Biol 9:R45.1–R45.14

    Google Scholar 

  • Kisaka H, Lee H, Kisaka M, Kanno A, Kang K, Kameya T (1994) Production and analysis of asymmetric hybrid plants between monocotyledon (Oryza sativa L.) and dicotyledon (Daucus carota L.). Theor Appl Genet 89:365–371

    Google Scholar 

  • Kisaka H, Kisaka M, Kanno A, Kameya T (1998) Intergeneric somatic hybridization of rice (Oryza sativa L) and barley (Hordeum vulgare L) by protoplast fusion. Plant Cell Rep 17:362–367

    CAS  Google Scholar 

  • Kobayashi N, Ikeda R, Domingo IT, Vaughan DA (1993) Resistance to infection of rice tungro viruses and vector resistance in wild species of rice (Oryza spp.). Jpn J Breed 43:377–387

    Google Scholar 

  • Konishi S, Izawa T, Lin SY, Ebana K, Fukuta Y, Sasaki T et al (2006) An SNP caused loss of seed shattering during rice domestication. Science 312:1392–1396

    PubMed  CAS  Google Scholar 

  • Krishnan A, Guiderdoni E, An G, Hsing YC, Han C, Lee MC et al (2009) Mutant resources in rice for functional genomics of the grasses. Plant Physiol 149:165–170

    PubMed  CAS  Google Scholar 

  • Kurata N, Fukui K (2003) Chromosome research in genus Oryza. In: Nanda JS, Sharma SD (eds) Monograph on Genus Oryza. Science, Enfield, NH, USA, pp 213–261

    Google Scholar 

  • Kurata N, Omura T (1978) Karyotype analysis in rice. I. A new method for identifying all chromosome pairs. Jpn J Genet 53:251–255

    Google Scholar 

  • Kurata N, Omura T (1982) Karyotype analysis in rice. 3. Karyological comparisons among 4 Oryza species. Jpn J Breed 32:253–258

    Google Scholar 

  • Kurata N, Iwata N, Omura T (1981) Karyotype analysis in rice. II. Identification of extra chromosomes in trisomic plants and banding structure on some chromosomes. Jpn J Genet 56:41–50

    Google Scholar 

  • Kuwada Y (1910) A cytological study of Oryza sativa L. Shokubutsugaksu Zasshi 24:267–281

    Google Scholar 

  • Larkin PJ, Banks PM, Bhati R, Brettell RIS, Davies PA, Ryan SA, Scowcroft WR, Spindler LH, Tanner GJ (1989) From somatic variation to variant plants: mechanisms and applications. Genome 31:705–711

    Google Scholar 

  • Launert E (1965) A survey of the genus Leersia in Africa (Gramineae, Oryzoideae, Oryzeae). Sneck Biol 46:129–153

    Google Scholar 

  • Li HW, Chen CC, Weng TS, Wuu KD (1961) Cytogenetic studies of O. sativa and its related species. I hybrids O. paraguaiensis Wedd x O. brachyantha Chev et Roehr; O. paraguaiensis Wedd x O. australiensis Domin and O. australiensis Domin x O. alta Swallen. Bot Bull Acad Sin 2:79–86

    Google Scholar 

  • Li HW, Chen CC, Weng TS, Wuu KD (1963) Cytogenetics studies of Oryza sativa and its related species 4 interspecific crosses involving O. australiensis with O. sativa and O. minuta. Bot Bull Acad Sin 4:6574

    Google Scholar 

  • Li C, Zhou A, Sang T (2006) Rice domestication by reducing shattering. Science 311:1936–1939

    PubMed  CAS  Google Scholar 

  • Lin SC, Yuan LP (1980) Hybrid rice breeding in China. In: Innovative approaches to rice breeding. International Rice Research Institute, Manila, Philippines, pp 35–51

    Google Scholar 

  • Lin Z, Griffith ME, Li X, Zhu Z, Tan L, Fu Y et al (2007) Origin of seed shattering in rice (O. sativa L.). Planta 226:11–20

    PubMed  CAS  Google Scholar 

  • Ling KC, Aguiero VM, Lee SH (1970) A mass screening method for testing resistance to grassy stunt disease of rice. Plant Dis Rep 56:565–569

    Google Scholar 

  • Liu B, Liu Z, Li XW (1999) Production of a highly asymmetric somatic hybrid between rice and Zizania latifolia (Griseb): evidence for intergenome exchange. Theor Appl Genet 98:1099–1103

    Google Scholar 

  • Liu G, Lu G, Zeng L, Wang GL (2002) Two broad spectrum blast resistance genes, Pi9(t) and Pi2(t) are physically linked on rice chromosome 6. Mol Genet Genome 267:472–480

    CAS  Google Scholar 

  • Londo JP, Chiang YC, Hung KH, Chiang TY, Schaal BA (2006) Phylogeography of Asian wild rice, Oryza rufipogon, reveals multiple independent domestications of cultivated rice. O. sativa. Proc Natl Acad Sci USA 103:9578–9583

    PubMed  CAS  Google Scholar 

  • Lu B, Sharma SD (2003) Exploration, collection and conservation of wild Oryza species. In: Nanda JS, Sharma SD (eds) Monograph on genus Oryza. Science, Enfield, NH, USA, pp 263–283

    Google Scholar 

  • Lu B, Naredo EB, Juliano AB, Jackson MT (1998) Taxonomic status of Oryza glumaepetula Steud III. Assessment of genomic affinity among AA genome species from the New World, Asia and Australia. Genet Resour Crop Evol 45:215–223

    Google Scholar 

  • Lu G, Jantasuriyarat C, Zhou B, Wang GL (2004) Isolation and characterization of novel defense responsive genes involved in compatible and incompatible reactions between rice and Magnaporthe grisea. Theor Appl Genet 108:525–534

    PubMed  CAS  Google Scholar 

  • Lu T, Huang X, Zhu C, Huang T, Zhao Q, Xie K et al (2008) RICD: a rice indica cDNA database resource for rice functional genomics. BMC Plant Biol 8:118

    PubMed  Google Scholar 

  • Lu F, Ammiraju JSS, Sanyal A, Zhang S, Song R, Chen J et al (2009) Comparative sequence analysis of MONOCULM1-orthologous regions in 14 Oryza genomes. Proc Natl Acad Sci USA 106:2071–2076

    PubMed  CAS  Google Scholar 

  • Ma J, Bennetzen JL (2004) Rapid recent growth and divergence of rice nuclear genomes. Proc Natl Acad Sci USA 101:12404–12410

    PubMed  CAS  Google Scholar 

  • Ma J, Wing RA, Bennetzen JL, Jackson SA (2007) Evolutionary history and positional shift of a rice centromere. Genetics 177:1217–1220

    PubMed  CAS  Google Scholar 

  • Mahajan R (2007) Molecular mapping and transfer of bacterial blight resistance from Oryza glaberrima and O. barthii to O. sativa. PhD Thesis, Punjab Agricultural University, Ludhiana, India

    Google Scholar 

  • Min A (2009) Mapping genes for bacterial blight resistance transferred from wild species, Oryza rufipogon Griff. into rice (O. sativa L.). MSc Thesis, University of the Philippines, Los Baños (UPLB), Laguna, Philippines

    Google Scholar 

  • Moncada P, Martinez CP, Borrero J, Chatel M, Gauch H Jr, Guimaraes E et al (2001) Quantitative trait loci for yield and yield components in an Oryza sativa x Oryza rufipogon BC2F2 population evaluated in an upland environment. Theor Appl Genet 102:41–52

    CAS  Google Scholar 

  • Moore G, Devos KM, Wang Z, Gale MD (1995) Cereal genome evolution: grasses, line up and form a circle. Curr Biol 5:737–739

    PubMed  CAS  Google Scholar 

  • Morinaga T (1939) Cytogenetics of rice. Bot Zool (Shokubutsu oyobidobutsu) 7:197–201 (in Japanese)

    Google Scholar 

  • Morinaga T (1943) Cytogenetic studies on Oryza sativa L. IV the cytogenetics of F1 hybrids of O. minuta Presl. and O. latifolia Desv. Jpn J Bot 11:1–16

    Google Scholar 

  • Morinaga T (1954) Classification of rice varieties on the basis of affinity. In: Reports for the 5th meeting of international rice commission’s working party on rice breeding, Ministry of Agriculture and Forestry, Tokyo, Japan, pp 1–14

    Google Scholar 

  • Morinaga T, Kuriyama H (1959) Genomic constitution of Oryza officinalis. Jpn J Breed 9:259

    Google Scholar 

  • Morishima H (2001) Evolution and domestication of rice. In: Khush GS, Brar DS, Hardy B (eds) Rice genetics IV. International Rice Research Institute and Science Publications, Los Baños, Laguna, Philippines, pp 63–77

    Google Scholar 

  • Multani DS, Jena KK, Brar DS, Delos Reyes BC, Angeles ER, Khush GS (1994) Development of monosomic alien addition lines and introgression of genes from Oryza australiensis Domin. to cultivated rice O. sativa L. Theor Appl Genet 88:102–109

    Google Scholar 

  • Multani DS, Khush GS, Delos Reyes BG, Brar DS (2003) Alien genes introgression and development of monosomic alien additional lines from Oryza latifolia Desv. to rice. Theor Appl Genet 107:395–405

    PubMed  CAS  Google Scholar 

  • Nandi HK (1936) The chromosome morphology, secondary association and origin of cultivated rice. J Genet 33:315–336

    Google Scholar 

  • Naredo EB, Vaughan DA, Cruz FS (1993) Comparative spikelet morphology of Oryza schlechteri Pilger and related species of Leersia and Oryza (Poaceae). J Plant Res 106:109–112

    Google Scholar 

  • Nayar NM (1973) Origin and cytogenetics of rice. Adv Genet 17:153–292

    Google Scholar 

  • Nezu M, Katayama TC, Kihari H (1960) Genetic studies on the genus Oryza I, crossability and chromosomal affinity among 17 species. Seiken Zho 11:1–23

    Google Scholar 

  • Ng NQ, Hawkes JG, William JT, Chang TT (1981) The recognition of a new species of rice (Oryza) from Australia. Bot J Linn Soc 82:327–330

    Google Scholar 

  • Nguyen BD, Brar DS, Bui BC, Nguyen TV, Pham LN, Nguyen HT (2003) Identification and mapping of the QTL for aluminum tolerance introgressed from new source, Oryza rufipogon Griff. into indica rice, (Oryza sativa L.). Theor Appl Genet 106:583–593

    PubMed  CAS  Google Scholar 

  • Nishimura Y (1961) Studies on the reciprocal translocations in rice and barley. Bull Natl Inst Agri Sci Jpn Ser D9:171–235

    Google Scholar 

  • Ogawa T (2003) Genome research in genus Oryza. In: Nanda JS, Sharma SD (eds) Monograph on Genus Oryza. Science, Enfield, NH, USA, pp 172–212

    Google Scholar 

  • Oka HI (1958) Varietal variation and classification of cultivated rice. Indian J Genet 18:78–89

    Google Scholar 

  • Oka HI (1961) Report of trip for investigation of rice in Latin American countries. International Rice Research Institute Library, Manila, Philippines (unpublished)

    Google Scholar 

  • Oka HI (1974) Experimental studies on the origin of cultivated rice. Genetics 78:475–486

    PubMed  CAS  Google Scholar 

  • Oka HI (1988) Origin of cultivated rice. In: Developments in crop science, vol 14. Japan Scientific Societies Press, Tokyo, Japan

    Google Scholar 

  • Oka HI, Morishima H (1982) Phylogenetic differentiation of cultivated rice. XXIII. Potentiality of wild progenitors to evolve the indica and japonica types of rice cultivars. Euphytica 31:41–50

    Google Scholar 

  • Panaud O, Vitte C, Hivert J, Muzlak S, Talag J, Brar DS et al (2002) Characterization of transposable elements in the genome of rice (Oryza sativa L.) using representational difference analysis (RDA). Mol Genet Genome 268:113–120

    CAS  Google Scholar 

  • Piegu B, Guyot R, Picault N, Roulin A, Saniyal A, Kim H et al (2006) Doubling genome size without polyploidization: dynamics of retrotransposition-driven genomic expansions in Oryza australiensis, a wild relative of rice. Genome Res 16:1262–1269

    PubMed  CAS  Google Scholar 

  • Rahman Md L, Jiang W, Chu SH, Qiao Y, Ham TH, Woo MO et al (2009) High resolution mapping of two rice brown planthopper resistance genes, Bph20(t) and Bph21(t), originating from Oryza minuta. Theor Appl Genet 119:1237–1244

    PubMed  Google Scholar 

  • Ramos JM (2005) Introgression of genes for tungro virus disease resistance from Oryza rufipogon Griff. into rice (O.sativa L.). MSc Thesis, University of the Philippines, Los Baños (UPLB), Laguna, Philippines

    Google Scholar 

  • Ramos JM, Ona IP, Torres GS, Hechanova SS, Vera Cruz CM, Brar DS (2009) Introgression of genes for blast resistance from African rice (Oryza glaberrima) into indica rice (O. sativa L.). In: Proceedings 6th international rice genetics symposium, Manila (Abstr) P3–11

    Google Scholar 

  • Rau NS (1929) Further contribution to the cytology of some crop plants of South India. Bot Soc 8:201–206

    Google Scholar 

  • Reintar RS (2007) Molecular characterization of introgression from Oryza longistaminata A. Chev. et Roehr. into rice (Oryza sativa L.). MSc Thesis, University of the Philippines, Los Baños (UPLB), Laguna, Philippines

    Google Scholar 

  • Ronald PC, Albano B, Tabien R, Abenes L, Wu K, McCouch S et al (1992) Genetic and physical analysis of rice bacterial blight resistance locus, Xa2I. Mol Gen Genet 236:113–120

    PubMed  CAS  Google Scholar 

  • Roschevicz R (1931) A contribution to the knowledge of rice. Bull Appl Bot Genet Plant Breed 27:1–33

    Google Scholar 

  • Rutgers JN (1992) Searching for apomixis in rice. In: Proceedings of apomixis workshop. USDA-ARS, Atlanta, GA, USA, pp 36–39

    Google Scholar 

  • Sallaud C, Gay C, Larmande P, Bes M, Piffanelli P et al (2004) High throughput T-DNA insertion mutagenesis in rice: a first step towards in silico reverse genetics. Plant J 39:450–464

    PubMed  CAS  Google Scholar 

  • Salse J, Piegu B, Cooke R, Delseny M (2004) New in silico insight into the synteny between rice (Oryza sativa L.) and maize (Zea mays L.) highlights reshuffling and identifies new duplications in the rice genome. Plant J 38:396–409

    PubMed  CAS  Google Scholar 

  • Sampath S (1962) The genus Oryza: its taxonomy and species relationship. Oryza 1:1–29

    Google Scholar 

  • Sanchez AC, Brar DS, Huang N, Li Z, Khush GS (2000) Sequence tagged site marker-assisted selection for three bacterial blight resistance genes in rice. Crop Sci 40:792–797

    CAS  Google Scholar 

  • Sang T, Ge S (2007) The puzzle of rice domestication. Integr Plant Biol 49:760–768

    CAS  Google Scholar 

  • Sarkar R, Raina SN (1992) Assessment of genomic relationships in the genus Oryza based on seed-protein profile analysis. Theor Appl Genet 85:127–131

    Google Scholar 

  • Second G (1982) Origin of the genic diversity of cultivated rice (Oryza spp): study of the polymorphism scored at 40 isozyme loci. Jpn J Genet 57:25–57

    Google Scholar 

  • Sen SK (1963) Analysis of rice pachytene chromosomes. Nucleus 6:107–120

    Google Scholar 

  • Septiningsih EM, Prasetiyano J, Lubis E, Tai TH, Tjurbayat T, Moeljopawiro S et al (2003) Identification of quantitative trait loci for yield and yield components in an advanced backcross population derived from the Oryza sativa variety IR64 and the wild relative O. rufipogon. Theor Appl Genet 107:1419–1432

    PubMed  CAS  Google Scholar 

  • Sharma SD, Shastry SVS (1965a) Taxonomic studies in genus Oryza. III. O. rufipogon Griff, sensu stricto and O. nivara Sharma et Shastry nom. Indian J Genet 25:157–167

    Google Scholar 

  • Sharma SD, Shastry SVS (1965b) Taxonomic studies in genus Oryza. IV. The Ceylones Oryza spp. affin. O. officinalis Wall ex Watt. Indian J Genet 25:168–172

    Google Scholar 

  • Sharma SD, Tripathy S, Biswal J (2000) Origin of O. sativa and its ecotypes. In: Nanda JS (ed) Rice breeding and genetics: research priorities and challenges. Science, Enfield, NH, USA, pp 349–369

    Google Scholar 

  • Shastry SVS, Rangao Rao DR, Misra RN (1960) Pachytene analysis in Oryza. I. chromosome morphology in Oryza sativa L. Indian J Genet 20:15–21

    Google Scholar 

  • Shim J (2007) Development of Oryza minuta J.S. PRESL. ex C.B.PRESL. specific clones using representational difference analysis (RDA), alien introgression and genomic relationship in Oryza. PhD Thesis, University of the Philippines, Los Baños (UPLB), Laguna, Philippines

    Google Scholar 

  • Shin YB, Katayama T (1979) Cytogenetical studies on the genus Oryza XI Alien addition lines of O. sativa with single chromosomes of O. officinalis. Jpn J Genet 54:1–10

    Google Scholar 

  • Shishido R, Apisitwanich S, Ohmido N, Okinaka Y, Mori K, Fukui K (1998) Detection of specific chromosome reduction in rice somatic hybrids with the A. B., and C genomes by multi-color genomic in situ hybridization. Theor Appl Genet 97:1013–1018

    Google Scholar 

  • Singh K, Ishii T, Parco A, Huang N, Brar DS, Khush GS (1996a) Centromere mapping and orientation of the molecular linkage map of rice (Oryza sativa L). Proc Natl Acad Sci USA 93:6163–6168

    PubMed  CAS  Google Scholar 

  • Singh K, Multani DS, Khush GS (1996b) Secondary trisomics and telotrisomics of rice: origin, characterization, and use in determining the orientation of chromosome map. Genetics 143:517–529

    PubMed  CAS  Google Scholar 

  • Singh S, Sidhu JS, Huang N, Vikal Y, Li Z, Brar DS, Dhaliwal HS, Khush GS (2001) Pyramiding three bacterial blight resistance genes (xa5, xa13 and Xa2I) using marker assisted selection into indica rice cultivar PR106. Theor Appl Genet 102:1011–1015

    CAS  Google Scholar 

  • Sitch LA (1990) Incompatibility barriers operating in crosses of Oryza sativa with related species and genera. In: Gustafson JP (ed) Genetic manipulation in plant improvement II. Plenum, New York, USA, pp 77–94

    Google Scholar 

  • Song WY, Wang GL, Chen LL, Kim HS, Pi YL, Holsten T et al (1995) A receptor kinase-like protein encoded by the rice disease resistance gene, Xa21. Science 270:1804–1806

    PubMed  CAS  Google Scholar 

  • Soriano IR, Schmit V, Brar DS, Prot JC, Reversat G (1999) Resistance to rice root-knot nematode Meloidogyne graminicola identified in Oryza longistaminata and O. glaberrima. Nematology 1:395–398

    Google Scholar 

  • Suh JP, Roh JH, Cho YC, Han SS, Kim YG, Jena KK (2009) The Pi40 gene for durable resistance to rice blast and molecular analysis of Pi40 advanced backcross breeding lines. Phytopathology 99:243–250

    PubMed  CAS  Google Scholar 

  • Sweeny M, McCouch S (2007) The complex history of the domestication of rice. Ann Bot 100:951–957

    Google Scholar 

  • Sweeny MT, Thomson MJ, Pfeil BE, McCouch S (2006) Caught red-handed: Rc encodes a basic helic-loop-helix protein conditioning red pericarp in rice. Plant Cell 18:283–294

    Google Scholar 

  • Tan G, Ren X, Weng QM, Shi ZY, Zhu LL, He GC (2004a) Mapping of new resistance gene to bacterial blight in rice line introgressed from Oryza officinalis. Yi Chuan Xue Bao 31:724–729 (In Chinese)

    PubMed  CAS  Google Scholar 

  • Tan G, Weng QM, Ren X, Huang Z, Zhu LL, He GC (2004b) Two whitebacked planthopper resistance genes in rice share the same loci with those for brown planthopper resistance. Heredity 92:212–217

    PubMed  CAS  Google Scholar 

  • Tan L, Li X, Liu F, Sun X, Li C, Zhu Z et al (2008) Control of a key transition from prostate to erect growth in rice domestication. Nat Genet 40:13060–13064

    Google Scholar 

  • Tanksley SD, Nelson JC (1996) Advanced backcross QTL analysis: a method for the simultaneous discovery and transfer of valuable QTLs from unadapted germplasm into elite breeding lines. Theor Appl Genet 92:191–203

    Google Scholar 

  • Tateoka T (1962a) Taxonomic studies of Oryza. I. O. latifolia complex. Bot Mag 75:418–427

    Google Scholar 

  • Tateoka T (1962b) Taxonomic studies of Oryza. II. Several species complexes. Bot Mag 75:455–461

    Google Scholar 

  • Tateoka T (1963) Notes on some grasses. VIII. Relationship between Oryzeae and Ehrharteae, with special reference to leaf antomology and histology. Bot Gaz 124:264–270

    Google Scholar 

  • Tateoka T (1965) A taxonomic study of Oryza eichingeri and O. punctata. Bot Mag 78:156–163

    Google Scholar 

  • Terada R, Kyozuka J, Nishibayashi S, Shimamoto K (1987) Plantlet regeneration from somatic hybrids of rice (Oryza sativa L.) and barnyard grass (Echinochloa oryzicola Vasing). Mol Gen Genet 210:39–43

    Google Scholar 

  • Thomas CA (1971) The genetic organization of chromosomes. Annu Rev Genet 5:237–256

    PubMed  CAS  Google Scholar 

  • Till BJ, Cooper J, Tai TH, Colowit P, Greene EA, Henikoff S et al (2007) Discovery of chemically induced mutation in rice by TILLING. BMC Plant Biol 7:19

    PubMed  Google Scholar 

  • Ting Y (1957) The origin and evolution of cultivated rice in China. Acta Agron Sin 8:243–260 (in Chinese)

    Google Scholar 

  • Vaughan DA (1989) The genus Oryza L.: current status of taxonomy, IRRl Res Paper Sr 138. International Rice Research Institute, Manila, Philippines, p 21

    Google Scholar 

  • Vaughan DA (1994) The wild relatives of rice: a genetic resources handbook. International Rice Research Institute, Manila, Philippines, 137 p

    Google Scholar 

  • Vaughan DA (2003) Genepools of genus Oryza. In: Nanda JS, Sharma SD (eds) Monograph on genus Oryza. Science, Enfield, NH, USA, pp 113–138

    Google Scholar 

  • Vaughan DA, Sitch LA (1991) Gene flow from the jungle to farmers: wild-rice genetic resources and their uses. Bioscience 44:22–28

    Google Scholar 

  • Vaughan DA, Morishima H, Kadowaki K (2003) Diversity in the Oryza genus. Curr Opin Plant Biol 6:139–146

    PubMed  CAS  Google Scholar 

  • Vitte C, Ishii T, Lamy F, Brar DS, Panaud O (2004) Genomic paleontology provides evidence for two distinct origins of Asian rice (Oryza sativa L.) Mol Genet. Genome 272:504–511

    CAS  Google Scholar 

  • Wang ZY, Second G, Tanksley SD (1992) Polymorphism and phylogenetic relationships among species in the genus Oryza as determined by analysis of nuclear RFLPs. Theor Appl Genet 83:565–581

    Google Scholar 

  • Wang GL, Holsten TE, Song WY, Ronald PC (1995) Construction of a rice bacterial artificial chromosome library and identification of clones linked to the Xa21 disease resistant locus. PIant J 7:525–533

    CAS  Google Scholar 

  • Wang E, Wang J, Zhu X, Hao W, Wang L, Li Q et al (2008) Control of rice grain-filling and yield by a gene with a potential signature of domestication. Nat Genet 40:1370–1374

    PubMed  CAS  Google Scholar 

  • Wu JL, Wu C, Lei C, Baraoidan M, Bordeos A, Madamba RS et al (2005) Chemical and irradiation-induced mutants of indica rice IR64 for forward and reverse genetics. Plant Mol Biol 59:85–97

    PubMed  CAS  Google Scholar 

  • Wuu KD, Jui Y, Lu KCL, Chou C, Li HW (1963) Cytogenetic studies of Oryza sativa L and its related species. 3. Two intersectional hybrids, O. sativa Linn x O. brachyantha A. Chev et Roehr and O. minuta Presl x O. brachyantha A. Chev et Roehr. Bot Bull Acad Sin 4:5159

    Google Scholar 

  • Xiao J, Ahn GS, SN McCouch SR, Tanksley SD, Li J et al (1996) Genes from wild rice improve yield. Nature 384:223–224

    CAS  Google Scholar 

  • Xiao J, Li J, Grandillo S, Ahn SN, Yuan L, Tanksley SD et al (1998) Identification of trait-improving quantitative trait loci alleles from a wild rice relative, Oryza rufipogon. Genetics 150:899–909

    PubMed  CAS  Google Scholar 

  • Yamanaka S, Nakamura I, Nakai H, Sato Y (2003) Dual origin of the cultivated rice based on molecular markers of newly collected annual and perennial strains of wild rice species. Oryza nivara and O. rufipogon. Genet Resour Crop Evol 50:529–538

    CAS  Google Scholar 

  • Yan H, Min S, Zhu L (1999) Visualization of Oryza eichingeri chromosomes in intergeneric hybrid plants from O. sativa x O. eichingeri via fluorescence in situ hybridization. Genome 42:48–51

    Google Scholar 

  • Yasui K (1941) Diploid bud formation in a haploid Oryza with some remarks on the behavior of nucleolus in mitosis. Cytologia 11:515–525

    Google Scholar 

  • Yoon DB, Kang KH, Kim KJ, Ju HG, Kwon SJ, Suh JP et al (2006) Mapping quatitative trait loci for yield components and morphological traits in an advanced backcross population between Oryza grandiglumis and the O. sativa japonica cultivar Hwaseongbyeo. Theor Appl Genet 112:1052–1062

    PubMed  CAS  Google Scholar 

  • Yu J, Hu S, Wang J, Wang GK, Li S, Liu B et al (2002) A draft sequence of the rice genome (Oryza sativa L spp indica). Science 296:79–92

    PubMed  CAS  Google Scholar 

  • Yu J, Wang J, Lin W, Li S, Li H, Zhou J et al (2005) The genomes of Oryza sativa: a history of duplications. PLoS Biol 3(2):e38

    PubMed  Google Scholar 

  • Zhang Q, Lin SC, Zhao BY, Wang CL, Wang WC, Zhou YL et al (1998) Identification and tagging of a new gene for resistance to bacterial blight (Xanthomonas oryzae pv. oryzae) from O. rufipogon. Rice Genet Newsl 15:138–142

    Google Scholar 

  • Zhang Q, Li J, Xue Y, Han B, Deng XW (2008) Rice 2020: a call for an international coordinated effort in rice functional genomics. Mol Plant 1:715–719

    PubMed  CAS  Google Scholar 

  • Zhu Q, Zheng X, Luo J, Gaut BS, Ge S (2007) Multilocus analysis of nucleotide variation of Oryza sativa and its wild relatives: severe bottleneck during domestication of rice. Mol Biol Evol 24:875–882

    PubMed  CAS  Google Scholar 

  • Zuccolo A, Ammiraju JSS, Kim H, Sanyal A, Jackson SA, Wing RA (2008) Rapid and differential proliferation of the Ty3-Gypsy LTR-retrotransposon Atlantys in the genus Oryza. Rice 1:85–99

    Google Scholar 

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  1. Plant Breeding, Genetics and Biotechnology Division, International Rice Research Institute (IRRI), Manila, Philippines

    Darshan S. Brar

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  1. Institute of Nutraceutical Research, Clemson University, Jordan Hall 109, Clemson, 29634, South Carolina, USA

    Chittaranjan Kole

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Brar, D.S., Singh, K. (2011). Oryza. In: Kole, C. (eds) Wild Crop Relatives: Genomic and Breeding Resources. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-14228-4_7

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