, Volume 154, Issue 3, pp 317–339 | Cite as

Through the genetic bottleneck: O. rufipogon as a source of trait-enhancing alleles for O. sativa

  • Susan R. McCouch
  • Megan Sweeney
  • Jiming Li
  • Hui Jiang
  • Michael Thomson
  • Endang Septiningsih
  • Jeremy Edwards
  • Pilar Moncada
  • Jinhua Xiao
  • Amanda Garris
  • Tom Tai
  • Cesar Martinez
  • Joe Tohme
  • M. Sugiono
  • Anna McClung
  • Long Ping Yuan
  • Sang-Nag Ahn


This paper summarizes results from a decade of collaborative research using advanced backcross (AB) populations to a) identify quantitative trait loci (QTL) associated with improved performance in rice and to b) clone genes underlying key QTLs of interest. We demonstrate that AB-QTL analysis is capable of (1) successfully uncovering positive alleles in wild germplasm that were not obvious based on the phenotype of the parent (2) offering an estimation of the breeding value of exotic germplasm, (3) generating near isogenic lines that can be used as the basis for gene isolation and also as parents for further crossing in a variety development program and (4) providing gene-based markers for targeted introgression of alleles using marker-assisted-selection (MAS). Knowledge gained from studies examining the population structure and evolutionary history of rice is helping to illuminate a long-term strategy for exploiting and simultaneously preserving the well-partitioned gene pools in rice.


Inter-specific cross Transgressive variation Quantitative trait loci (QTL) Rice (Oryza sativa L.) Marker assisted selection Molecular breeding 



Advanced backcross


Quantitative trait loci




Near isogenic line


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This research was supported by grants from the Rockefeller Foundation; the U.S. Department of Agriculture (USDA) Plant Genome Research Program (National Research Initiative grant No. 96-35300-3645 and No. 00-35300-9216); CRIS Project 6225-21000-006; NSF Plant Genome awards DBI-0110004 and DBI-0319553, sub-award 2003-1054-01; RiceTec, Inc.; a graduate assistantship to Michael Thomson provided by the Cornell Plant Cell and Molecular Biology Program (DOE/NSF/USDA Interagency Training Grant); a graduate assistantship to Amanda Garris provided by USDA/CSRS Competitive Grant 97-35300-5101 representing Food and Agricultural Sciences National Needs Graduate Fellowship in Plant Biotechnology; Ph.D. support for Pilar Moncada from the National Federation of Coffee Growers (Cenicafe) of Colombia; support for QTL analysis in Korea from the Crop Functional Genomics Center of the of the 21st Century Frontier Research Program (Project code: CG3112) and from Bio Green 21 of the Rural Development Administration, Republic of Korea. We are grateful to the International Center for Tropical Agriculture (CIAT) in Cali, Colombia for population development and phenotypic evaluation of the Caiapo population; to the China National Hybrid Rice Research and Development Center, Changsha, China for population development and phenotypic evaluation of the Ce64 hybrid families; to ICABIOGRAD in Indonesia for population development and phenotypic evaluation of the IR64 population; and to the USDA-ARS Beaumont Rice Research Unit, Beaumont, TX for phenotypic evaluation of the Jefferson population.

We are grateful to Junjian Ni for the curation of QTLs in the Gramene database and for contributing to the development of Fig. 3; to Lois Swales for formatting the manuscript and creating figures from rough sketches; to all the many scientists and staff in the national breeding programs and in the McCouch lab without whose help and dedication we could not have developed the populations, collected the phenotypic data or done the fine-mapping that has been so critical to the success of these projects.


  1. Aluko G, Martinez C, Tohme J, Castano C, Bergman C, Oard J (2004) QTL mapping of grain quality traits from the interspecific cross Oryza sativa × O. glaberrima. Theor Appl Genet 109:630–639Google Scholar
  2. Aquino RC, Jennings PR (1966) Inheritance and significance of dwarfism in an Indica rice variety. Crop Sci 6:551–554CrossRefGoogle Scholar
  3. Ashikari M, Sasaki A, Ueguchi-Tanaka M, Itoh H, Nishimura A, Datta S, Ishiyama K, Saito T, Kobayashi M, Khush GS, Kitano H, Matsuoka M (2002) Loss-of-function of a rice gibberellin biosynthesis gene,H GA20 oxidase (GA20 ox-2), let to the rice ‘green revolution’. Breed Sci 52:143–150CrossRefGoogle Scholar
  4. Bergman CJ, Delgado JT, McClung AM, Fjellstrom R (2001) An improved method for using a microsatellite in the rice waxy gene to determine amylose class. Cereal Chem 78:257–260Google Scholar
  5. Bernacchi D, Beck-Bunn T, Emmatty D, Inai S (1998) Advanced backcross QTL analysis of tomato. II. Evaluation of near-isogenic lines carrying single-donor introgressions for desireable wild QTL alleles derived from Lycopersicon hirsutum and L. pimpinellifolium. Theor Appl Genet 97:170–180CrossRefGoogle Scholar
  6. Brar DS, Khush GS (1997) Alien introgression in rice. Plant Mol Biol 35:35–47PubMedCrossRefGoogle Scholar
  7. Bradbury LM, Henry RJ, Jin QS, Reinke RF, Waters DL (2005) A perfect marker for fragrance genotyping in rice. Mol Breed 16:279–283CrossRefGoogle Scholar
  8. Brondani C, Rangel N, Brondani V, Ferreira E (2002) QTL mapping and introgression of yield-related traits from Oryza glumaepatula to cultivated rice (Oryza sativa) using microsatellite markers. Theor Appl Genet 104:1192–1203PubMedCrossRefGoogle Scholar
  9. Bruskiewich, RM, Cosico AB, Eusebio W, Portugal AM, Ramos LM, Reyes MT, Sallan MA, Ulat VJ, Wang X, Mcnally KL, Sackville Hamilton R, Mclaren CG (2003) Linking genotype to phenotype: the International Rice Information System (IRIS). Bioinformatics 19(Suppl 1):i63–65PubMedCrossRefGoogle Scholar
  10. Burr FA, Burr B, Scheffler BE, Blewitt M, Wienand U, Matz EC (1996) The maize repressor-like gene intensifier1 shares homology with the r1/b1 multigene family of transcription factors and exhibits missplicing. Plant Cell 8:1249–1259PubMedCrossRefGoogle Scholar
  11. Cao G, Zhu J, He CX, Gao YJ, Yan J, Wu P (2001) Impact of epistasis and QTL x environmental interaction on the developmental behavior of plant height in rice (Oryza sativa L.). Theor Appl Genet 103:153–160CrossRefGoogle Scholar
  12. Cheng CY, Motohashi R, Tsuchimoto S, Fukuta Y, Ohtsubo H, Ohtsubo E (2003) Polyphyletic origin of cultivated rice: based on the interspersion pattern of SINEs. Mol Biol Evol 20:67–75PubMedCrossRefGoogle Scholar
  13. Cho YC, Suh JP, Choi IS, Hong HC, Baek MK, Kang KH, Kim YG, Ahn SN, Choi HC, Hwang HG, Moon HP (2003) QTLs analysis of yield and its related traits in wild rice relative Oryza rufipogon. Treat of Crop Res In Korea 4Google Scholar
  14. Choi HC (1978) Recent advances in rice breeding in Korea. Korean J Breed 10:201–238Google Scholar
  15. Choi HO, Bae SH, Chung GS, Cho CY (1974) A New Short-Statured Rice Variety “Tongil”. Res. Rep. of the O.R.D. in Korea 16:1–12Google Scholar
  16. Churchill GA, Doerge RW (1994) Empirical threshold values for quantitative trait mapping. Genetics 139:963–971Google Scholar
  17. Clark JI, Brooksbank C, Lomax J (2005) It’s all GO for plant scientists. Plant Physiol 138:1268–1279PubMedCrossRefGoogle Scholar
  18. Dalmacio RD, Brar DS, Ishii T, Sitch TA, Virmani SS, Khush GS (1995) Identification and transfer of a new cytoplasmic male sterility source from Oryza perennis into indica rice (O. sativa). Euphytica 82:221–225CrossRefGoogle Scholar
  19. Deng QY, Yuan LP, Liang FS, Li J, Wang LG, Wang B (2004) Studies on yield-enhancing genes from wild rice and their marker-assisted selection in hybrid rice. Hybrid Rice 19:6–10Google Scholar
  20. Dilday RH (1990) Contribution of ancestral lines in the␣development of new cultivars of rice. Crop Sci 30:905–911CrossRefGoogle Scholar
  21. Dobzhansky T (1936) Studies on hybrid sterility. II. Localization of sterility factors in Drosophila pseudoobscura hybrids. Genetics 21:113–135PubMedGoogle Scholar
  22. Edwards JD (2005) Origins and distribution of allelic diversity in populations of wild and cultivated rice and phenotypic consequences of admixture at a complex flowering time locus. CornellGoogle Scholar
  23. European-Plant-Science-Organization-(EPSO) (2005) European plant science: a field of opportunities. J Exp Bot 56:1699–1709CrossRefGoogle Scholar
  24. Fan C, Xing YZ, Mao HL, Lu TT, Han B, Xu C, Li X, Zhang Q (2006) GS3, a major QTL for grain length and weight and minor QTL for grain width and thickness in rice, encodes a putative transmembrane protein. Theor Appl Genet DOI 10.1007/s00122-006-0218-1Google Scholar
  25. Foster KW, Rutger JN (1978) Inheritance of semi dwarfism in rice Oryza sativa. Genetics 88:559–574PubMedGoogle Scholar
  26. Frey KJ, Hammond EG, Lawrence PK (1975) Inheritance of oil percentage in interspecific crosses of hexaploid oats. Crop Sci 15:94–95CrossRefGoogle Scholar
  27. Gale MD, Devos KM (1998) Comparative genetics in the grasses. Proc Natl Acad Sci 95:1971–1974PubMedCrossRefGoogle Scholar
  28. Garris AJ, Tai TH, Coburn JR, Kresovich S, McCouch S (2005) Genetic structure and diversity in Oryza sativa L. Genetics 169:1631–1638PubMedCrossRefGoogle Scholar
  29. Gealy DR, Tai TH, Sneller CH (2002) Identification of red rice, rice, and hybrid populations using microsatellite markers. Weed Sci 50:333–339CrossRefGoogle Scholar
  30. Glaszmann JC (1987) Isozymes and Classification of Asian Rice Varieties. Theor Appl Genet 74:21–30CrossRefGoogle Scholar
  31. Gu XY, Kianian SF, Foley ME (2005a) Phenotypic selection for dormancy introduced a set of adaptive haplotypes from weedy into cultivated rice. Genetics 171:695–704CrossRefGoogle Scholar
  32. Gu XY, Kianian SF, Hareland GA, Hoffer BL, Foley ME (2005b) Genetic analysis of adaptive syndromes interrelatd with seed dormancy in weedy rice (Oryza sativa). Theor Appl Genet 110:1108–1118CrossRefGoogle Scholar
  33. Harlan J (1992) Crops & man. In: 2nd Harlan J (ed) American society of agronomy, Inc.; Crop Science Society of America, Inc.: Madison, Wisconsin, p 288Google Scholar
  34. Harlan JR (1976) Genetic resources in wild relatives of crops. Crop Sci 16:329–333CrossRefGoogle Scholar
  35. Harlan JR (1975) Our vanishing genetic resources. Science 188:618–621CrossRefGoogle Scholar
  36. Harushima Y, Nakagahra M, Yano M, Sasaki T, Kurata N (2002) Diverse variation of reproductive barriers in three intraspecific rice crosses. Genetics 160:313–322PubMedGoogle Scholar
  37. Hawkes JG (1958) Significance of wild species and primitive forms for potato breeding. Euphytica 7:257–270Google Scholar
  38. Hedden P (2003) The genes of the green revolution. Trend Genet 19:5–9CrossRefGoogle Scholar
  39. Hedden P, Phillips AL (2000) Gibberellin metabolism: new insights revealed by the genes. Trends Plant Sci 5:523–530PubMedCrossRefGoogle Scholar
  40. Huang XQ, Coster H, Ganal MW, Roder MS (2003) Advanced backcross QTL analysis for the identification of quantitative trait loci alleles from wild relatives of wheat (Triticum aestivum L.). Theor Appl Genet 106:1379–1389PubMedGoogle Scholar
  41. Iida S, Terada R (2005) Modification of endogenous natural genes by gene targeting in rice and other higher plants. Plant Mol Biol 59:205–219PubMedCrossRefGoogle Scholar
  42. 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 37:217–221PubMedGoogle Scholar
  43. Iyer-Pascuzzi A, McCouch S (2006) Functional markers for xa5 mediated resistance in rice (Oryza sativa, L.). Mol Breed (in press)Google Scholar
  44. Jaiswal J, Avraham S, Ilic K, Kellogg E, McCouch S, Pujar A, Reiser L, Rhee S, Sachs M, Schaeffer M, Stein L, Stevens P, Vincent L, Ware D, Zapata F (2006a) Plant Ontology (PO): a controlled vocabulary of plant structures and growth stages. Comp Funct Genom 6:388–397CrossRefGoogle Scholar
  45. Jaiswal P, Ni J, Yap IV, 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 T, Buckler E, Stein L, McCouch S (2006b) Gramene: a bird’s eye view of␣cereal genomics. Nucleic Acids Res 34:D717–D723Google Scholar
  46. Jena KK, Khush GS, Kochert G (1992) RFLP analysis of rice (Oryza sativa L.). Theor Appl Genet 84:608–616CrossRefGoogle Scholar
  47. Jennings PR (1964) Plant type as a rice breeding objective. Crop Sci 4:13–15CrossRefGoogle Scholar
  48. Jia Y, McAdams SA, Bryan GT, Hershey HP, Valent B (2000) Direct interaction of resistance gene and avirulence gene products confers rice blast resistance. EMBO J 19:4004–4014PubMedCrossRefGoogle Scholar
  49. Jia Y, Redus MA, Wang Z, Rutger J (2004) Development of SNLP marker from the Pi-ta blast resistance gene by Tri-Primer PCR. Euphytica 138:97–105CrossRefGoogle Scholar
  50. Kato, S, Kosaka H, Hara S (1928) On the affinity of rice varieties as shown by the fertility of rice plants. Central Agricultural Inst Kyushu Imperial Univ 2:241–276Google Scholar
  51. Khush GS (2001) Green Revolution: the way forward. Nat Rev Genet 2:815–822PubMedCrossRefGoogle Scholar
  52. Kinoshita T (1998) Linkage mapping using mutant genes in rice. Rice Genet Newslett 15:13–74Google Scholar
  53. Kubo T, Takano-Kai N, Yoshimura A (2001) RFLP mapping of genes for long kernel and awn on chromosome 3 in rice. Rice Genet Newslett 18:26–28Google Scholar
  54. Lee SJ, Oh CS, Suh JP, McCouch SR, Ahn SN (2005) Identification of QTLs for domestication-related and agronomic traits in an Oryza sativa x O. rufipogon BC1F7 population. Plant Breed 124:209–219CrossRefGoogle Scholar
  55. Li J, Thomson MJ, McCouch SR (2004a) Fine mapping of a grain weight QTL in the peri-centromeric region of rice chromosome 3. Genetics 168:2187–2195PubMedCrossRefGoogle Scholar
  56. Li J, Xiao J, Grandillo S, Jiang L, Wan Y, Deng Q, Yuan L, McCouch S (2004b) QTL detection for rice grain quality traits using an interspecific backcross population derived from cultivated Asian (O. sativa L.) and African (O. glaberrima S.) rice. Genome 47:697–704Google Scholar
  57. Li J, Yuan L (2000) Hybrid rice: genetics, breeding, and seed production. Plant Breed Rev 17:150–158Google Scholar
  58. Li Z, Pinson SR, Park WD, Paterson AH, Stansel JW (1997) Epistasis for three grain yield components in rice (Oryza sativa L.). Genetics 145:453–465PubMedGoogle Scholar
  59. Li ZK, Fu BY, Gao YM, Xu JL, Ali J, Lafitte JR, Jiang YZ, Rey JD, Vijayakumar CHM, Maghirang R, Zheng TQ, Zhu LH (2005) Genome-wide introgression lines and their use in genetic and molecular dissection of complex phenotypes in rice (Oryza sativa L.). Plant Mol Biol 59:33–52PubMedCrossRefGoogle Scholar
  60. Ling WH, Cheng ZX, Ma J, Wang T (2001) Red and black rice decrease atherosclerotic plaque formaion and increase antioxidant status in rabbits. J Nutr 131:1421–1426PubMedGoogle Scholar
  61. Londo JP, Chiang Y-C, Hung K-H, Chiang T-Y, Schaal BA (2006) Phylogeography of Asian wild rice, Oryza rufipogon, reveals multiple independent domestications of cultivated rice, Oryza sativa. Proc Natl Acad Sci 103:9578–9583PubMedCrossRefGoogle Scholar
  62. Lu BR, Zheng KL, Qian HR, Zhuang JY (2002) Genetic differentiation of wild relatives of rice as assessed by RFLP analysis. Theor Appl Genet 106:101–106PubMedGoogle Scholar
  63. Lu H, Redus MA, Coburn JR, Rutger JN, McCouch SR, Tai TH (2004) Population structure and breeding patterns of 145 US rice cultivars based on SSR marker analysis. Crop Sci 45:66–76CrossRefGoogle Scholar
  64. Ma J, Bennetzen JL (2004) Rapid recent growth and divergence of rice nuclear genomes. Proc Nat Acad Sci USA101:12404–12410PubMedCrossRefGoogle Scholar
  65. Marri PR, Sarla N, Reddy LV, Siddiq EA (2005) Identification and mapping of yield and yield related QTLs from an Indian accession of Oryza rufipogon. BMC Genet UK 6:33 DOI: 10.1186/1471-2156-1186-1133Google Scholar
  66. Matsuo T, Futsuhara Y, Kikuchi F, Yamaguchi H (1997) Science of the rice plant. In: Matsuo T, Futsuhara Y, Kikuchi F, Yamaguchi H (eds) Food and Agriculture Policy Research Center, TokyoGoogle Scholar
  67. McClung AM, Marchetti MA, Webb BD, Bollich CN (1997) Registration of ’Jefferson” rice. Crop Sci 37:629–630CrossRefGoogle Scholar
  68. 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 9:199–207PubMedCrossRefGoogle Scholar
  69. Moncada M, Martínez C, Tohme J, Guimaraes E, Chatel M, Borrero J, Gauch H, McCouch S (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 102:41–52CrossRefGoogle Scholar
  70. Monna L, Kitazawa N, Yoshino R, Suzuki J, Masuda H, Maehara Y, Tanji M, Sato M, Nasu S, Minobe Y (2002) Positional cloning of rice semidwarfing gene, sd-1: rice “green revolution gene” encodes a mutant enzyme involved in gibberellin synthesis. DNA Res 9:11–17PubMedCrossRefGoogle Scholar
  71. Morishima H, Sano Y, Oka HI (1984) Differentiation of perennial and annual types due to habitat conditions in the wild rice Oryza perennis. Plant Syst Evol 144:119–135CrossRefGoogle Scholar
  72. Muller HJ (1942) Isolating mechanisms, evolution and temperature. Biol Sump 6:71–125Google Scholar
  73. Nguyen BD, Brar DS, Bui BC, Nguyen TV, Pham LN, Nguyen HT (2003) Identification and mapping of the QTL for aluminum tolerance introgressed from the new source, Oryza rufipogon Griff., into indica rice (Oryza sativa L.). Theor Appl Genet 106:583–593PubMedGoogle Scholar
  74. Ni J, Colowit PM, Mackill DJ (2002) Evaluation of genetic diversity in rice subspecies using microsatellite markers. Crop Sci 42:601–607CrossRefGoogle Scholar
  75. Oka HI (1988) Origin of cultivated rice. In: Oka HI (ed) Elsevier Science/Japan Scientific Societies Press, Tokyo, p 254Google Scholar
  76. Oka HI, Morishima H (1967) Variations in the breeding systems of a wild rice, Oryza perennis. Evolution 21:249–258CrossRefGoogle Scholar
  77. Oki T, Masuda M, Kobayashi M, Nishiba Y, Furuta S, Suda I, Sato T (2002) Polymeric Procyanidins as Radical-Scavenging Components in Red-Hulled Rice. J Agriculture Food Chem 50:7524–7529CrossRefGoogle Scholar
  78. Payne CT, Zhang F, Lloyd AM (2000) GL3 Encodes a bHLH Protein That Regulates Trichome Development in Arabidopsis Through Interaction With GL1 and TTG1. Genetics 156:1349–1362PubMedGoogle Scholar
  79. Peloquin SJ (1983) Utilization of exotic germplasm in potato breeding: germplasm transfer with haploids and 2n gametes. In: Conservation and utilization of exotic germplasm to improve varieties.; Plant Breeding Research Forum: WHERE? pp 147–167Google Scholar
  80. Peng J, Richards DE, Hartley NM, Murphy GP, Devos KM, Flintham JE, Beales J, Fish LJ, Worland AJ, Pelica F, Sudhakar D, Christou P, Snape JW, Gale MD, Harberd NP (1999) ‘Green Revolution’ genes encode mutant gibberellin response modulators. Nature 400:256–261PubMedCrossRefGoogle Scholar
  81. Pillen K, Zacharias A, Leon J (2003) Advanced backcross QTL analysis in barley (Hordeum vulgare L.). Theor Appl Genet 107:340–352PubMedCrossRefGoogle Scholar
  82. Rao GU, Ben Chaim A, Borovsky Y, Paran I (2003) Mapping of yield-related QTLs in pepper in an interspecific cross of Capisicum annum and C. frutescens. Theor Appl Genet 106:1457–1466PubMedGoogle Scholar
  83. Redona ED, Mackill DJ (1998) Quantitative trait locus analysis for rice panicle and grain characteristics. Theor Appl Genet 96:957–963CrossRefGoogle Scholar
  84. Rick CM (1983) Conservation and use of exotic tomato germplasm. In: Conservation and utilization of exotic germplasm to improve varieties. Report of the 1983 Plant Breeding Research Forum pp 147–167Google Scholar
  85. Rick CM XVII (1967) Int Hort Congr 3:217–229Google Scholar
  86. Roy SC (1921) A preliminary classification of the wild rices of the Central Province and Berar. Agric J India 16:365–380Google Scholar
  87. Sano Y (1993) Constraints in using wild relatives in breeding: lack of basic knowledge on crop gene pools. In: Buxton DR (ed) International crop science. Crop Science Society of America, Madison, WI, pp 437–443Google Scholar
  88. Sasaki A, Ashikari M, Ueguchi-Tanaka M, Itoh H, Nishimura A, Swapan D, Ishiyama K, Saito T, Kobayashi M, Khush GS, Kitano H, Matsuoka M (2002) A mutant gibberellin-synthesis gene in rice. Nature 416:701–702PubMedCrossRefGoogle Scholar
  89. Sato Y, Nishio T (2003) Mutation detection in rice waxy mutants by PCR-RF-SSCP. Theor Appl Genet 107:560–567PubMedCrossRefGoogle Scholar
  90. Second G (1991) Molecular markers in rice systematics and the evaluation of genetic resources. Biotech Agric Forest 14:468–494Google Scholar
  91. Second G (1982) Origin of the genetic diversity of cultivated rice (Oryza spp.): Study of the polymorphism scored at 40 isozyme loci. Japanese J Genet 57:25–57Google Scholar
  92. Septiningsih EM, Prasetiyono J, Lubis E, Tai TH, Tjubaryat T, Moeljopawiro S, McCouch SR (2003a) 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 107:1419–1432CrossRefGoogle Scholar
  93. Septiningsih EM (2002) Identification of near-isogenic line development and fine mapping of quantitative trait loci from the rice cultivar IR64 and its wild relative Oryza rufipogon. PhD Thesis, CornellGoogle Scholar
  94. Shirley B (1998) Flavinoids in seeds and grains: physiological function, agronomic importance and the genetics of biosynthesis. Seed Sci Res 8:415–422CrossRefGoogle Scholar
  95. Spelt C, Quatrocchio F, Mol J, Koes R (2002) ANTHOCYANIN1 of petunia controls pigment synthesis, vacuolar pH, and seed coat development by genetically distinct mechanisms. Plant Cell 14:2121–2135PubMedCrossRefGoogle Scholar
  96. 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 99:9043–9048PubMedCrossRefGoogle Scholar
  97. Steele KA, Price AH, Shashidhar HE, Witcombe JR (2005) Marker-assisted selection to introgress rice QTLs controlling root traits into an Indian upland rice variety. Theor Appl Genet 112:208–221PubMedCrossRefGoogle Scholar
  98. Sun CQ, Wang XK, Yoshimura A, Doi K (2002) Genetic differentiation for nuclear mitochrodrial and chloroplast genomes in common wild rice (Oryza rufipogon Griff.) and cultivated rice (Oryza sativa L.). Theor Appl Genet 104:1335–1345PubMedCrossRefGoogle Scholar
  99. Sweeney M, Thomson MJ, Pfeil B, McCouch S (2006) Caught red-handed: Rc encodes a basic helix-loop-helix protein conditioning red pericarp in rice. The Plant Cell 18:283–294PubMedCrossRefGoogle Scholar
  100. Tanksley SD, McCouch SR (1997) Seed banks and molecular maps: unlocking genetic potential from the wild. Science 277:1063–1066PubMedCrossRefGoogle Scholar
  101. Tanksley SD, Nelson JC (1996) Advanced backcross QTL analysis: a method for the simultaneous discovery and tranfer of valuable QTLs from unadapted germplasm into elite breeding lines. Theor Appl Genet 92:191–203CrossRefGoogle Scholar
  102. Temnykh S, Declerck G, Lukashova A, Lipovich L, Cartinhour S, McCouch S (2001) Computational and experimental analysis of microsatellites in rice (Oryza sativa L.): frequency, length variation, transposon associations, and genetic marker potential. Genome Res 11:1441–1452PubMedCrossRefGoogle Scholar
  103. Terada R, Urawa H, Inagaki Y, Tsugane K, Iida S (2002) Efficient gene tarteting by homologous recombination in rice. Nat Biotechnol 20:983–984CrossRefGoogle Scholar
  104. Thomson MJ, Edwards JD, Septiningsih EM, Harrington S, McCouch SR (2006) Substitution mapping of dth1.1, a flowering time QTL associated with transgressive variation in rice, reveals a cluster of QTLs. Genetics: Genetics: doi 10.1534/genetics.1105.050500Google Scholar
  105. Thomson MJ, Tai TH, McClung AM, Hinga ME, Lobos KB, Xu Y, Martinez C, McCouch SR (2003) Mapping quantitative trait loci for yield, yield components, and␣morphological traits in an advanced backcross population between Oryza rufipogon and the Oryza sativa cultivar Jefferson. Theor Appl Genet 107:479–493PubMedCrossRefGoogle Scholar
  106. Vaughan DA, Kadowaki KI, Kaga A, Tomooka N (2005) On the Phylogeny and Biogeography of the Genus Oryza. Breed Sci 55:113–122CrossRefGoogle Scholar
  107. Wang YM, Dong ZY, Zhang ZJ, Lin Y, Shen D, Zhou D, Liu B (2005) Extensive de Novo genomic variation in rice induced by introgression from wild rice (Zizania latifolia Griseb.). Genetics 170Google Scholar
  108. 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 150:899–909PubMedGoogle Scholar
  109. Xiao J, Li J, Yuan L, Tanksley SD (1996) Identification of QTLs affecting traits of agronomic importance in a recombinant inbred population derived from a subspecific cross. Theor Appl Genet 92:230–244CrossRefGoogle Scholar
  110. Xing Y-Z, Tan Y-F, Hua J-P, Sun X-L, Xu C-G, Zhang Q (2002) Characterization of the main effects, epistatic effects and their environmental interactions of QTLs on the genetic basis of yield traits in rice. Theor Appl Genet 105:248–247PubMedCrossRefGoogle Scholar
  111. Xing YZ, Tan YF, Xu CG, Hua JP, Sun XL (2001) Mapping quantitative trait loci for grain appearance traits of rice using a recombinant inbred line population. Acta Botanica Sinica 43:721–726Google Scholar
  112. Xiong LZ, Liu KD, Dai XK, Xu CG, Zhang Q (1999) Identification of genetic factors controlling domestication-related traits of rice using an F2 population of a cross between Oryza sativa and O. rufipogon. Theor Appl Genet 98:243–251CrossRefGoogle Scholar
  113. Yamanaka S, Nakamura I, Watanabe KN, Sato YI (2004) Identification of SNPs in the waxy gene among glutinous rice cultivars and their evolutionary significance during the domestication process of rice. Theor Appl Genet 108:1200–1204PubMedCrossRefGoogle Scholar
  114. Yu SB, Li JX, Xu CG, Li XH, Tan YF, Zhang Q (2002) Identification of quantitative trait loci and epistatic interactions for plant height and heading date in rice. Theor Appl Genet 104:619–625PubMedCrossRefGoogle Scholar
  115. Yu SB, Li JX, Xu CG, Tan YF, Gao YJ, Li XH, Zhang Q, Sagai X, Maroof MA (1997) Importance of epistasis as the genetic basis of heterosis in an elite rice hybrid. Proc Natl Acad Sci 94:9226–9231PubMedCrossRefGoogle Scholar
  116. Zeng W (1994) Precision mapping of quantitative trait loci. Genetics 136:1457–1468PubMedGoogle Scholar
  117. Zheng HG, Qian HR, Shen BZ, Zhuang JY, Lin HX, Lu J (1994) RFLP-based Phylogenetic analysis of wide compatibility varieties in Oryza sativa L. Theor Appl Genet 88:65–69CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2006

Authors and Affiliations

  • Susan R. McCouch
    • 1
  • Megan Sweeney
    • 1
  • Jiming Li
    • 2
  • Hui Jiang
    • 1
  • Michael Thomson
    • 1
    • 3
  • Endang Septiningsih
    • 1
    • 3
  • Jeremy Edwards
    • 1
    • 4
  • Pilar Moncada
    • 1
    • 5
  • Jinhua Xiao
    • 1
    • 6
  • Amanda Garris
    • 1
    • 7
  • Tom Tai
    • 8
  • Cesar Martinez
    • 9
  • Joe Tohme
    • 9
  • M. Sugiono
    • 10
  • Anna McClung
    • 11
  • Long Ping Yuan
    • 12
  • Sang-Nag Ahn
    • 13
  1. 1.Department of Plant Breeding & GeneticsCornell UniversityIthacaUSA
  2. 2.Pioneer Hybrid InternationalJohnstonUSA
  3. 3.International Rice Research InstituteLos Baños, LagunaPhilippines
  4. 4.University of ArizonaTucsonUSA
  5. 5.CenicafeManizales, CaldasColombia
  6. 6.Monsanto CorpSt. LouisUSA
  7. 7.USDA/ARSGenevaUSA
  8. 8.University of CaliforniaDavisUSA
  9. 9.CIATCaliColombia
  10. 10.ICABIOGRADBogorIndonesia
  11. 11.USDA-ARS, DBNRRC & Beaumont Rice Research UnitBeaumontUSA
  12. 12.China National Hybrid Rice Research & Development CenterChangshaP.R. China
  13. 13.Dept of Agronomy, College of AgricultureChungnam National UniversityDaejeonRepublic of Korea

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