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Application of Genomics for Molecular Breeding in Rice

  • Chapter
Genomics-Assisted Crop Improvement

Abstract

Rice is arguably the most important food crop of the world and due to its small genome size compared to other major cereals, rice was selected as model crop species for decoding of its full genome. The international rice genome sequencing project (IRGSP), a consortium of laboratories from ten different countries, has generated a very high quality map based sequence of the 12 chromosomes of japonica rice cultivar ‘Nipponbare’ and made it available in the public domain. A whole genome draft sequence of indica type rice variety ‘93-11’ has also been reported by the Beijing Genomics Institute. Annotation and comparative analysis of these and other partial genomic sequences has provided a wealth of information to the rice geneticists and breeders. Simple Sequence Repeat (SSR) markers are now easily available for any region of the rice genome. SSR markers have also been derived from the expressed sequence tags (ESTs) and unigene sequences, which correspond to the expressed component of the genome and thus have greater potential in comparative genome analysis. Furthermore, millions of single nucleotide polymorphism (SNP) and insertion-deletion (InDel) markers have already been identified in rice. Saturation of the genome with such sequence based SSR and SNP markers is accelerating fine mapping and map-based cloning of genes, and thus, development of gene-based allele-specific markers. Rice improvement programs are expected to benefit greatly from the use of these markers in near future.

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References

  • 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

    Article  PubMed  CAS  Google Scholar 

  • Bao JS, Zheng XW, Xia YW, He P, Shu QY, Lu X, Chen Y, Zhu LH (2000) QTL mapping for the paste viscosity characteristics in rice (Oryza sativa L.). Theor Appl Genet 100:280–284

    Article  CAS  Google Scholar 

  • Bradbury LMT, Fitzgerald TL, Henry RJ, Jin Q, Waters DLE (2005) The gene for fragrance in rice. Plant Biotech J 3:363–370

    Article  CAS  Google Scholar 

  • Bres-Patry C, Loreux M, Clement G, Bangratz M, Ghesquiere A (2001) Heredity and genetic mapping of domestication-related traits in a temperate japonica weedy rice. Theor Appl Genet 102:118–126

    Article  CAS  Google Scholar 

  • Causse MA, Fulton TM, Cho YG, Ahn SN, Chunwongse J, Wu K, Xiao J, Yu Z, Ronald PC, Harrington SE, Second G, McCouch SR, Tanksley SD (1994) Saturated molecular map of the rice genome based on an interspecific backcross population. Genetics 138:1251–1274

    PubMed  CAS  Google Scholar 

  • Chen X, Temnykh S, Xu Y, Cho YG, McCouch SR (1997) Development of a microsatellite framework map providing genome-wide coverage in rice (Oryza sativa L.). Theor Appl Genet 95:553–567

    Article  CAS  Google Scholar 

  • Chen M, Presting G, Barbazuk WB, Goicoechea JL, Blackmon B, Fang G, Kim H, Frisch D, Yu Y, Sun S et al (2002) An integrated physical and genetic map of the rice genome. Plant Cell 14:537–545

    Article  PubMed  CAS  Google Scholar 

  • Cho YG, Ishii T, Temnykh S, Chen X, Lipovich L, Park WD, Ayres N, Cartinhour S, McCouch SR (2000) Diversity of microsatellites derived from genomic libraries and GenBank sequences in rice (Oryza sativa L.). Theor Appl Genet 100:713–722

    Article  CAS  Google Scholar 

  • Coburn JR, Temnykh SV, Paul EM, McCouch SR (2002) Design and application of microsatellite marker panels for semiautomated genotyping of rice (Oryza sativa L.). Crop Sci 42:2092–2099

    Article  CAS  Google Scholar 

  • Feltus FA, Wan J, Schulze SR, Estill JC, Jiang N, Paterson AH (2004) Genome alignments of japonica and indica subspecies. Genome Res 14:1812–1819

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Harushima Y, Yano M, Shomura A, Sato M, Shimano T, Kuboki Y, Yamamoto T, Lin SY, Antonio BA, Parco A et al (1998) A high-density rice genetic linkage map with 2275 markers using a single F2 population. Genetics 148:479–494

    PubMed  CAS  Google Scholar 

  • International HapMap Consortium (2005) A haplotype map of the human genome. Nature 437:1299–1320

    Google Scholar 

  • Gorantla M, Babu PR, Lachagari VBR, Feltus FA, Paterson AH, Reddy AR (2005) Functional genomics of drought stress response in rice: Transcript mapping of annotated unigenes of an indica rice (Oryza sativa L. cv. Nagina 22). Curr Sci 89:496–514

    CAS  Google Scholar 

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

    Google Scholar 

  • Iwata N (1986) The relationship between cytologically identified chromosomes and linkage groups in rice. In: Rice genetics. Proceedings of the international rice genetic symposium, Los Baños, Philippines, Manila (Philippines) 27–31 May 1985; International rice research institute, pp 229–238

    Google Scholar 

  • Joseph M, Gopalakrishnan S, Sharma RK, Singh VP, Singh AK, Singh NK, Mohapatra T (2004) Combining bacterial blight resistance and Basmati quality characteristics by phenotypic and molecular marker-assisted selection in rice. Mol Breed 13:377–387

    Article  CAS  Google Scholar 

  • Kawasaki S, Borchert C, Deyholos M, Wang H, Brazille S, Kawai K, Galbraith D, Bohnert HJ (2001) Gene expression profiles during the initial phase of salt stress in rice. Plant Cell 13:889–906

    Article  PubMed  CAS  Google Scholar 

  • Kikuchi S, Satoh K, Nagata T, Kawagashira N, Doi K, Kishimoto N, Yazaki J, Ishikawa M, Yamada H, Ooka H et al (2003) Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice. Science 300:1566–1569

    Article  CAS  Google Scholar 

  • 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

    Article  PubMed  CAS  Google Scholar 

  • Kurata N, Nagamura Y, Yamamoto K, Harushima Y, Sue N, Wu J, Antonio BA et al (1994) A 300-kilobase interval genetic map of rice including 883 expressed sequences. Nat Genet 8:365–372

    Article  PubMed  CAS  Google Scholar 

  • Kuwada Y (1910) A cytological study of Oryza sativa L. Bot Mag (Tokyo) 24:267–280

    Google Scholar 

  • Liu S-P, Li X, Wang C-Y, Li X-H, He Y-Q (2003) Improvement of resistance to rice blast in Zhenzhan 97 by molecular marker-aided selection. Acta Bot Sin 45:1346–1350

    Google Scholar 

  • Liu X, Gu M, Han Y, Ji Q, Lu J, Gu S, Zhang R, Li X, Chen J, Korban SS, Xu M (2004) Developing gene-tagged molecular markers for functional analysis of starch-synthesizing genes in rice (Oryza sativa L.). Euphytica 135:345–353

    Article  CAS  Google Scholar 

  • Ma JF, Tamai K, Yamaji N, Mitani N, Konishi S, Katsuhara M, Ishiguro M, Murata Y, Yano M (2006) A silicon transporter in rice. Nature 440:688–691

    Article  PubMed  CAS  Google Scholar 

  • 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

    Article  CAS  Google Scholar 

  • McCouch SR, Chen XL, Panaud O, Temnykh S, Xu YB, Cho YG, Huang N, Ishii T, Blair M (1997) Microsatellite marker development, mapping and applications in rice genetics and breeding. Plant Mol Biol 35:89–99

    Article  PubMed  CAS  Google Scholar 

  • Miyao A et al (2003) Target site specificity of the Tos17 retrotransposon shows a preference for insertion within genes and against insertion in retrotransposon rich regions of the genome. Plant Cell 15:1771–1780

    Article  PubMed  Google Scholar 

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

    Article  CAS  Google Scholar 

  • Morinaga T (1937) On the microsporogenesis of the various interspecific hybrids of Oryza. A preliminary note. Jpn J Genet 13:245

    Google Scholar 

  • Morinaga T (1939) Cytogenetics in rice. (Oryza sativa L.). Bot Zool 7:179–183

    Google Scholar 

  • Nagao S, Takahashi M (1963) Trial construction of twelve linkage groups in Japanese rice (Genetical studies on rice plant, XXVII). J Fac Agric Hokkaido Univ 53:72–130

    Google Scholar 

  • Olufowote JO, Xu Y, Chen X, Park WD, Beachell HM, Dilday RH, Goto M, McCouch SR (1997) Comparative evaluation of within-cultivar variation of rice (Oryza sativa L.) using microsatellite and RFLP markers. Genome 38:1170–1176

    Google Scholar 

  • Parida S, Kumar KAR, Dalal V, Singh NK, Mohapatra T (2006) Unigene derived microsatellite markers for the cereal genomes. T Appl Genet 112:808–817

    Article  CAS  Google Scholar 

  • 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

    Article  PubMed  CAS  Google Scholar 

  • Sahi C, Singh A, Kumar K, Blumwald E, Grover A (2006) Salt stress response in rice: genetics, molecular biology, and comparative genomics. Funct Integr Genomics 6:263–284

    Article  PubMed  CAS  Google Scholar 

  • Saji S, Umehara Y, Antonio B, Yamane H, Tanoue H, Baba T, Aoki H, Ishige N, Wu JZ, Koike K, Matsumoto T, Sasaki T (2001) A physical map with yeast artificial chromosome (YAC) clones covering 63% of the 12 rice chromosomes. Genome 44:32–37

    Article  PubMed  CAS  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

    Article  CAS  Google Scholar 

  • Sasaki A, Ashikari M, Ueguchi-Tanaka M, Itoh H, Nishimura A, Datta SK, Ishiyama K, Saito T, Kobayashi M, Khush GS, Kitano H, Matsuoka M (2002) Green revolution: a mutant gibberellin-synthesis gene in rice. Nature 416:701–702

    Article  PubMed  CAS  Google Scholar 

  • Sharma TR, Madhav MS, Singh BK, Shanker P, Jana TK, Dalal V, Pandit A, Singh A, Gaikwad K, Upreti HC, Singh NK (2005) High-resolution mapping, cloning and molecular characterization of the Pi-kh gene of rice, which confers resistance to Magnaporthe grisea. Mol Gen Genomics 274:569–578

    Google Scholar 

  • Shastry SVS, Ranga Rao DR, Misra RN (1960) Pachytene analysis in Oryza. I. Chromosome morphology in Oryza sativa. Indian J Genet Plant Breed 20:5–21

    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 Xa21) using marker-assisted selection into indica rice cultivar PR106. Theor Appl Genet 102:1011–1015

    Article  CAS  Google Scholar 

  • Singh RK, Sharma RK, Singh AK, Singh VP, Singh NK, Tiwari SP, Mohapatra T (2004) Suitability of mapped sequence tagged microsatellite site markers for establishing distinctness, uniformity and stability in aromatic rice. Euphytica 135:135–143

    Article  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Tao Q, Chang YL, Wang JZ, Chen HM, Islam-Faridi MN, Scheuring C, Wang B, Stelly DM, Zhang HB (2001) Bacterial artificial chromosome-based physical map of the rice genome constructed by restriction fingerprint analysis. Genetics 158:1711–1724

    PubMed  CAS  Google Scholar 

  • Temnykh S, Park WD, Ayres N, Cartinhour S, Hauck N, Lipovich L, Cho YG, Ishii T, McCouch SR (2000) Mapping and genome organization of microsatellite sequences in rice (Oryza sativa L.). Theor Appl Genet 100:697–712

    Article  CAS  Google Scholar 

  • Temnykh S, Declerk G, Lukashover A, Lipovich L, Cartinhour S, McCouch SR (2001) Computational and experimental analysis of microsatellites in rice (Oryza sativa L.): frequency, length-variation, transposon associations and genetic marker potential. Genome Res 11:1441–1452

    Article  PubMed  CAS  Google Scholar 

  • Toojinda T, Tragoonrung S, Vanavichit A, Siangliw JL, Pa-In N, Jantaboon J, Siangliw M, Fukai S (2005) Molecular breeding for rainfed lowland rice in the Mekong region. Plant Prod Sci 8:330-333

    Google Scholar 

  • Wayne ML, McIntyre LM (2002) Combining mapping and arraying: an approach to candidate gene identification. Proc Natl Acad Sci USA 99:14903–14906

    Article  PubMed  CAS  Google Scholar 

  • Wu KS, Tanksley SD (1993) Abundance, polymorphism and genetic mapping of microsatellites in rice. Mol Gen Genet 241:225–235

    Article  PubMed  CAS  Google Scholar 

  • Wu J, Maehara T, Shimokawa T, Yamamoto S, Harada C, Takazaki Y, Ono N, Mukai Y, Koike K, Yazaki J, Fujii F, Shomura A, Ando T, Kono I, Waki K, Yamamoto K, Yano M, Matsumoto T, Sasaki T (2002) A comprehensive rice transcript map containing 6591 expressed sequence tag sites. Plant Cell 14:525–535

    Article  PubMed  CAS  Google Scholar 

  • Wu J, Mizuno H, Hayashi-Tsugane M, Ito Y, Chiden Y, Fujisawa M, Katagiri S, Saji S, Yoshiki S, Karasawa W, Yoshihara R, Hayashi A, Kobayashi H, Ito K, Hamada M, Okamoto M, Ikeno M, Ichikawa Y, Katayose Y, Yano M, Matsumoto T, Sasaki T (2003) Physical maps and recombination frequency of six rice chromosomes. Plant J 36:720–730

    Article  PubMed  CAS  Google Scholar 

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

    PubMed  CAS  Google Scholar 

  • Xu K, Xu X, Fukao T, Canlas P, Maghirang-Rodriguez R, Heuer S, Ismail AM, Bailey-Serres J, Ronald PC, Mackill DJ (2006) Sub1A is an ethylene-response-factor-like gene that confers submergence tolerance to rice. Nature 442:705–708

    Article  PubMed  CAS  Google Scholar 

  • Yang GP, Saghai Maroof MA, Xu CG, Zhang Q, Biyashev M (1994) Comparative analysis of microsatellite DNA polymorphism in landraces and cultivars of rice. Mol Gen Genet 245:187–194

    Article  PubMed  CAS  Google Scholar 

  • Yu J, Hu S, Wang J, Wong GK, Li S, Liu B, Deng Y, Dai L, Zhou Y, Zhang X et al (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science 296:79–92

    Article  PubMed  CAS  Google Scholar 

  • Zhao X, Kochert G (1992) Characterization and genetic mapping of a short, highly repeated, interspersed DNA sequence from rice (Oryza sativa L.). Mol Gen Genet 231:353–359

    Article  PubMed  CAS  Google Scholar 

  • Zhao XP, Kochert G (1993) Phylogenetic distribution and genetic mapping of a (GGC)n microsatellite from rice (Oryza sativa L.). Plant Mol Biol 21:607–614

    Article  PubMed  CAS  Google Scholar 

  • Zou JH, Pan XB, Chen ZX, Xu JY, Lu JF, Zhai WX, Zhu LH (2000) Mapping quantitative trait loci controlling sheath blight resistance in rice cultivars (Oryza sativa L.) Theor Appl Genet 101:569–573

    Google Scholar 

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Authors and Affiliations

  1. National Research Centre on Plant Biotechnology (NRCPB), Indian Agricultural Research Institute (IARI), New Delhi-110 012, India

    Nagendra K. Singh & Trilochan Mohapatra

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  1. Nagendra K. Singh
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  2. Trilochan Mohapatra
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Editors and Affiliations

  1. ICRISAT, Patancheru, India

    Rajeev K. Varshney

  2. University of Bologna, Italy

    Roberto Tuberosa

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Singh, N.K., Mohapatra, T. (2007). Application of Genomics for Molecular Breeding in Rice. In: Varshney, R.K., Tuberosa, R. (eds) Genomics-Assisted Crop Improvement. Springer, Dordrecht. https://doi.org/10.1007/978-1-4020-6297-1_8

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