Use of Naturally Occurring Alleles for Crop Improvement

  • Anjali S. Iyer-Pascuzzi
  • Megan T. Sweeney
  • Neelamraju Sarla
  • Susan R. McCouch

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Ahn SN, Suh JP, Oh CS, Lee SJ, Suh HS (2002) Development of introgression lines of weedy rice in the background of Tongil-type rice. Rice Genet Newsl 19:14Google Scholar
  2. Aida Y, Tsunematsu H, Doi K, Yoshimura A (1997) Development of a series of introgression lines of japonica in the background of indica rice. Rice Genet Newsl 14:41–43Google Scholar
  3. Andaya VC, Mackill DJ (2003) QTLs conferring cold tolerance at the booting stage of rice using recombinant inbred lines from a japonica x indica cross. Theor Appl Genet 106:1084–1090PubMedGoogle Scholar
  4. Andersen JR, Lubberstedt T (2003) Functional markers in plants. Trends Plant Sci 8:554–560PubMedCrossRefGoogle Scholar
  5. Ashikari M, Wu J, Yano M, Sasaki A, Yosimura A (1999) Rice gibberellin-insensitive dwarf mutant gene Dwarf1 encodes the alpha-subunit of GTP-binding protein. Proc Natl Acad Sci USA 96:10284–10289PubMedCrossRefGoogle Scholar
  6. 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) Mutation in a gibberellin biosynthesis gene, GA20 oxidase, contributed to the rice ‘Green Revolution’. Breed Sci 52:143–150CrossRefGoogle Scholar
  7. Ashikari M, Sakakibara H, Lin H, Yamamoto T, Takashi T, Nishimura A, Angeles ER, Qian Q, Kitano H, Matsuoka M, Ashikari M (2005) Cytokinin oxidase regulates rice grain production. Science 309:741–745PubMedCrossRefGoogle Scholar
  8. Barton NH (2000) Genetic hitchhiking. Phil Trans Royal Soc London B 355:1553–1562CrossRefGoogle Scholar
  9. Berner DK, Hoff BJ (1986) Inheritance of scent in American long grain rice. Crop Sci 26:876–878Google Scholar
  10. Bradbury LM, Henry RJ, Jin QS, Reinke RF, Waters DL (2005) A perfect marker for fragrance genotyping in rice. Mol Breed 1665:279–283CrossRefGoogle Scholar
  11. Brar DS, Khush GS (1997) Alien introgression in rice. Plant Mol Biol 35:35–47PubMedCrossRefGoogle Scholar
  12. Burr B, Burr FA, Thompson KH, Albertson MC, Stube CW (1988) Gene mapping with recombinant inbreds in maize. Genetics 118:519–526PubMedGoogle Scholar
  13. Buttery RG, Ling LC, Juliano BO, Turnbaugh JG (1983) Cooked rice aroma and 2-acetyl-1-pyrroline. J Agric Food Chem 31:823–826CrossRefGoogle Scholar
  14. Cai HW, Morishima H (2002) QTL clusters reflect character associations in wild and cultivated rice. Theor Appl Genet 104:1217–1228PubMedCrossRefGoogle Scholar
  15. Causse MA, Fulton TM, Cho YG, Ahn SN, Chunwongse J, Wu K, Xiao J, Yu Z, Ronald PC, Harrington SE, et al (1994) Saturated molecular map of the rice genome based on an interspecific backcross population. Genetics 138:1251–1274PubMedGoogle Scholar
  16. Champoux MC, Sarkarung S, Mackill DJ, O’Toole JC, Huang N, McCouch SR (1995) Locating genes associated with root morphology and drought avoidance via linkage to molecular markers. Theor Appl Genet 90:969–981CrossRefGoogle Scholar
  17. Chang TT (1976) Origin, Evolution, cultivation, dissemination, and diversification of Asian and African rices. Euphytica 25:425–441CrossRefGoogle Scholar
  18. 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 95:553–567CrossRefGoogle Scholar
  19. Cordeiro GM, Christopher MJ, Henry RJ, Reinke RF (2002) Identification of microsatellite markers for fragrance in rice by analysis of the rice genome sequence. Mol Breed 9:245–250CrossRefGoogle Scholar
  20. Doi K, Sobrizal K, Ikeda K, Sanchez PL, Kurakazu T (2002) Developing and evaluating rice chromosome segment substitution lines, In: IRRI Conference (September 16–19, 2002). International Rice Research Institute, Beijing, China. pp. 275–287Google Scholar
  21. Ebitani T, Takeuchi Y, Nonoue Y, Yamamoto T, Takeuchi K, Yano M (2005) Construction and evaluation of chromosome segment substitution lines carrying overlapping chromosome segments of indica rice cultivar ‘Kasalath’ in a genetic background of japonica elite cultivar ‘Koshihikari’. Breeding Sci 55:65–73CrossRefGoogle Scholar
  22. Edwards J, McCouch SR (2005) Molecular markers for use in plant breeding and germplasm evaluation. In: Proceedings of Red Bio (June 21–24, 2004). Dominican RepublicGoogle Scholar
  23. Engle LM, Chang TT, Ramirez DA (1969) The cytogenetics of sterility in F1 hybrids of indica x indica and indica x japonica varieties of rice (Orzya sativa L.). Philipp Agric 53:289–307Google Scholar
  24. Futsuhara Y, Kikuchi F (1997) Dwarf characters. In: Matsuo T, Futsuhara Y, Kikuchi F, Yamaguchi H (eds) Science of the Rice Plant, vol 3, Genetics. Food and Agriculture Policy Research Center, Tokyo, pp 300–308Google Scholar
  25. Garris AJ, McCouch SR, Kresovich S (2003) Population structure and its effect on haplotype diversity and linkage disequilibrium surrounding the xa5 locus of rice (Oryza sativa L.). Genetics 165:759–769PubMedGoogle Scholar
  26. Garris AJ, Tai TH, Coburn JR, Kresovich S, McCouch S (2005) Genetic structure and diversity in Oryza sativa L. Genetics 169:1631–1638PubMedCrossRefGoogle Scholar
  27. Ghesquiere A, Sequier J, Second G, Lorieux M (1997) First steps toward a rational use of African rice, Oryza glaberrima in rice breeding: A contig line concept. Euphytica 96:31–39CrossRefGoogle Scholar
  28. Glaszmann JC (1987) Isozymes and classification of Asian rice varieties. Theor Appl Genet 74:21–30CrossRefGoogle Scholar
  29. Gu K, Yang B, Tian D, Wu L, Wang D, Sreekala C, Yang F, Chu Z, Wang GL, White FF, Yin Z (2005) R gene expression induced by a type-III effector triggers disease resistance in rice. Nature 435:1122–1125PubMedCrossRefGoogle Scholar
  30. Guiderdoni EJ, Glaszmann JC, Courtois B (1988) Segregation of 12 isozyme gene among doubled haploid lines derived from a japonicax indica cross of rice (Oryza sativa L.). Euphytica 42:45–53CrossRefGoogle Scholar
  31. Harushima Y, Yano M, Shomura A, Sato M, Shimano T, Kuboki Y, Yamamoto T, Lin SY, Antonio BA, Parco A, Kajiya H, Huang N, Yamamoto K, Nagamura Y, Kurata N, Khush GS, Sasaki T (1998) A high-density rice genetic linkage map with 2,275 markers using a single F2 population. Genetics 148:479–494PubMedGoogle Scholar
  32. Hedden P (2003) The genes of the green revolution. Trends Genet 19:5–9PubMedCrossRefGoogle Scholar
  33. Hittalmani S, Huang N, Courtois B, Venuprasad R, Shashidhar HE, Zhuang JY, Zheng KL, Liu GF, Wang GC, Sidhu JS, Srivantaneeyakul S, Singh VP, Bagali PG, Prasanna HC, McLaren G, Khush GS (2003) Identification of QTL for growth- and grain yield-related traits in rice across nine locations of Asia. Theor Appl Genet 107:679–690PubMedCrossRefGoogle Scholar
  34. Hudson RR, Kaplan NL (1988) The coalescent process in models with selection and recombination. Genetics 120:831–840PubMedGoogle Scholar
  35. Hudson RR, Saez EG, Ayala FJ (1997) DNA variation at the Sodlocus of Drosophila melanogaster: An unfolding story of natural selection. Proc Natl Acad Sci USA 94:7725–7729PubMedCrossRefGoogle Scholar
  36. Ikeda R, Khush GS, Tabien RE (1990) A new resistance gene to bacterial blight derived from O. longistaminata. Jpn J Breed 40:280–281Google Scholar
  37. Ikeda A, Ueguchi-Tanaka M, Sonoda Y, Kitano H, Koshioka M, Futsuhara Y, Matsuoka M, Yamaguchi J (2001) slender rice, a constitutive gibberellin response mutant, is caused by a null mutation of the SLR1 gene, an ortholog of the height-regulating gene GAI/RGA/RHT/D8. Plant Cell 13:999–1010PubMedCrossRefGoogle Scholar
  38. Ishikawa S, Ae N, Yano M (2005) Chromosomal regions with quantitative trait loci controlling cadmium concentration in brown rice (Oryza sativa). New Phytol 168:345–350PubMedCrossRefGoogle Scholar
  39. Iyer AS, McCouch SR (2004) The rice bacterial blight resistance gene xa5 encodes a novel form of disease resistance. Mol Plant Microbe Interact 17:1348–1354PubMedGoogle Scholar
  40. Iyer-Pascuzzi A, McCouch SR (2006) Functional markers for xa5 mediated resistance in rice (Oryza sativa L.). Mol Breed (In Press, DOI 10.1007/s11032-006-9055-9)Google Scholar
  41. Jain S, Jain R, McCouch S (2004) Genetic analysis of Indian aromatic and quality rice (Oryza sativa L.) germplasm using panels of fluorescently-labeled microsatellite markers. Theor Appl Genet 109:965–977PubMedCrossRefGoogle Scholar
  42. 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
  43. Jiang L, Cao YJ, Wang CM, Zhai HQ, Wan JM, Yoshimura A (2003) Detection and analysis of QTL for seed dormancy in rice (Oryza sativa L.) using RIL and CSSL population. Acta Genetica Sinica 30:453–458PubMedGoogle Scholar
  44. Jiang GH, Xia ZH, Zhou YL, Wan J, Li DY, Chen RS, Zhai WX, Zhu LH (2006) Testifying the rice bacterial blight resistance gene xa5 by genetic complementation and further analyzing xa5 (Xa5) in comparison with its homolog TFIIAgamma1. Mol Genet Genomics 275:354–366PubMedCrossRefGoogle Scholar
  45. Jorde LB (2000) Linkage disequilbrium and the search for complex disease genes. Genome Res 10:1435–1444PubMedCrossRefGoogle Scholar
  46. Katayama TC (1993) Historical review of taxonomical studies. In: Matsuo T, Hoshikawa K (eds) Science of the Rice Plant, vol 1, Morphology. Food and Agriculture Policy Research Center, Tokyo, pp 35–41Google Scholar
  47. Kato S, Kosaka H, Hara S (1928) On the affinity of rice varieties as shown by fertility of hybrid plants. Bull Sci Fac Agric Kyushu Univ, Fukuoka, Japan 3:132–147Google Scholar
  48. Khush GS, Ling KC (1974) Inheritance of resistance to Grassy stunt virus and its vector in rice. J Hered 65:135–136Google Scholar
  49. Koornneef M, Alonso-Blanco C, Vreugdenhil D (2004) Naturally occurring genetic variation in Arabidopsis thaliana. Annu Rev Plant Biol 55:141–172PubMedCrossRefGoogle Scholar
  50. Kreitman M, Akashi H (1995) Molecular evidence for natural selection. Annu Rev Ecol Syst 26:403–422CrossRefGoogle Scholar
  51. Kruglyak L (1999) Prospects for whole-genome linkage disequilibrium mapping of common disease genes. Nat Genet 22:139–144PubMedCrossRefGoogle Scholar
  52. Kubo T, Aida Y, Nakamura K, Tsunematsu H, Doi K, Yoshimura A (2002) Reciprocal chromosome segment substitution series derived from Japonica and Indica cross of rice (Oryza sativaL.). Breed Sci 52:319–325CrossRefGoogle Scholar
  53. Kurakazu T, Sorbrizal N, Ikeda K, Sanchez PL, Doi K, Angeles RR, Khush GS, Yoshimura A (2001) Oryza meridionalischromosomal segment introgression lines in cultivated rice, O. sativa L. Rice Genet Newsl 18:81–82Google Scholar
  54. Lanceras JC, Huang ZL, Naivikul O, Vanavichit A, Ruanjaichon V, Tragoonrung S (2000) Mapping of genes for cooking and eating qualities in Thai jasmine rice (KDML105). DNA Res 7:93–101PubMedCrossRefGoogle Scholar
  55. Lanceras JC, Pantuwan G, Jongdee B, Toojinda T (2004) Quantitative trait loci associated with drought tolerance at reproductive stage in rice. Plant Physiol 135:384–399PubMedCrossRefGoogle Scholar
  56. Lee M, Sharopova N, Beavis WD, Grant D, Katt M, Blair D, Hallauer A (2002) Expanding the genetic map of maize with the intermated B73 × Mo17 (IBM) population. Plant Mol Biol 48:453–461PubMedCrossRefGoogle Scholar
  57. Li J, Yuan L (2000) Hybrid Rice: Genetics, breeding and seed production. Plant Breed Rev 17:15–120Google Scholar
  58. Li ZK, Yu SB, Lafitte HR, Huang N, Courtois B, Hittalmani S, Vijayakumar CH, Liu GF, Wang GC, Shashidhar HE, Zhuang JY, Zheng KL, Singh VP, Sidhu JS, Srivantaneeyakul S, Khush GS (2003) QTL × environment interactions in rice. I. heading date and plant height. Theor Appl Genet 108:141–153PubMedCrossRefGoogle 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. Long AD, Lyman RF, Langley CH, Mackay TFC (1998) Two sites in the Delta gene region contribute to naturally occurring variation in bristle number in Drosophila melanogaster. Genetics 149:999–10173PubMedGoogle Scholar
  61. Lorieux M, Petrov M, Huang N, Guiderdoni E, Ghesquiere A (1996) Aroma in rice: genetic analysis of a quantitative trait. Theor Appl Genet 93:1145–1151CrossRefGoogle Scholar
  62. Lu BR, Naredo EB, Juliano AB, Jackson MT (1998) Taxonomic status of Oryza glumaepatula Steud. III. Assesment of genomic affinity among AA gemone species from the New World, Asia, and Australia. Gen Res Crop Evol 45:215–223Google Scholar
  63. Lu C, Shen L, Tan Z, Xu Y, He P, Chen Y, Zhu L (1997) Comparative mapping of QTLs for agronomic traits of rice across environments by using a doubled-haploid population. Theor Appl Genet 94:145–150CrossRefGoogle Scholar
  64. Ma J, Bennetzen JL (2004) Rapid recent growth and divergence of rice nuclear genomes. Proc Natl Acad Sci U S A 101:12404–12410PubMedCrossRefGoogle 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 6:33PubMedCrossRefGoogle Scholar
  66. Matsuo T (1952) Genecological studies on cultivated rice. Bull Natl Inst Gr Sci Jpn D3:1–111Google Scholar
  67. McCouch SR, Kochert G (1988) Molecular mapping of rice chromosomes. Theor Appl Genet 76:815–829CrossRefGoogle 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. McCouch SR, Sweeney M, Li J, Jiang H, Thomson M, Septiningsih E, Edwards J, Moncada P, Xiao J, Garris A, Tai T, Martinez C, Tohme J, Sugiono M, McClung A, Yuan LP, Ahn SN (2006) Through the genetic bottleneck: O. rufipogon as a source of trait-enhancing alleles for O. sativa. Euphytica, (In Press, DOI 10.1007/s10681-006-9210-8)Google Scholar
  70. Moncada M, Martìnez 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
  71. 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
  72. Morishima H, Oka HI (1970) A survey of genetic variations in the populations of wild Oryzaspecies and their cultivated relatives. Jpn J Genet 45:371–385Google Scholar
  73. Mu J, Zhou H, Zhao S, Xu C, Yu S, Zhang Q (2004) Development of contiguous introgression lines covering entire genome for the sequenced japonica rice. In: Fischer T, Turner N, Angus J, McIntyre L, Robertson M, Borrell A (eds) New directions for a diverse planet: Proceedings for the 4th International Crop Science Congress, Brisbane, Australia, 26 September – 1 October 2004 (http://www.cropscience.org.au/icsc2004/poster/3/2/1/781_yusb.htm)Google Scholar
  74. Nandi S, Subudhi PK, Senadhira D, Manigbas NL, Sen-Mandi S, Huang N (1997) Mapping QTLs for submergence tolerance in rice by AFLP analysis and selective genotyping. Mol Gen Genet 255:1–8PubMedCrossRefGoogle Scholar
  75. Naredo MEB, Juliano AB, Lu BR, Jackson MT (1997) Hybridization of AA genome rice species from Asia and Australia I. Crosses and development of hybrids. Gen Res Crop Evol 44:17–23CrossRefGoogle Scholar
  76. Nielsen R (2001) Statistical tests of selective neutrality in the age of genomics. Heredity 86:641–647PubMedCrossRefGoogle Scholar
  77. Nordborg, M. Tavare, S. (2002) Linkage disequilibrium: what history has to tell us. Trend Genet 18:83–90CrossRefGoogle Scholar
  78. Ogawa T, Yamamoto T, Khush GS, Mew TW, Kaku H (1988) Near-isogenic lines as international differentials for resistance to bacterial blight of rice. Rice Genet Newsl 5:106–109Google Scholar
  79. Ohtsubo H, Cheng CY, Ohsawa I, Tsuchimoto S, Ohtsubo E (2004) Rice retroposon p-SINE1 and origin of cultivated rice. Breed Sci 54:1–11CrossRefGoogle Scholar
  80. 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 31:41–50Google Scholar
  81. Olsen KM, Caicedo AL, Polato N, McClung AM, McCouch SR, Purugganan MD (2006) Selection under domestication: evidence for a sweep in the rice Waxy genomic region. Genetics 173:975–983PubMedCrossRefGoogle Scholar
  82. Paine JA, Shipton CA, Chaggar S, Howells RM, Kennedy MJ, Vernon G, Wright SY, Hinchliffe E, Adams JL, Silverstone AL, Drake R (2005) Improving the nutritional value of Golden Rice through increased pro-vitamin A content. Nat Biotechnol 23:482–487PubMedCrossRefGoogle Scholar
  83. 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
  84. Puca AA, Daly MJ, Brewster SJ, Matise TC, Barrett J, Shea-Drinkwater M, Kang S, JOyce E, Nicoli J, Benson E, Kunkel LM, Perls T (2001) A genome-wide scan for linkage to human exceptional longevity identifies a locus on chromsome 4. Proc Natl Acad Sci USA 98:10505–10508PubMedCrossRefGoogle Scholar
  85. Reinke RF, Welsh LA, Reece JE, Lewin LG, Blakeney AB (1991) Procedures for quality selection of aromatic rice varieties. Int Rice Res Newsl 16:10–11Google Scholar
  86. Reiseberg LH, Widmer A, Arntz AM, Burke JM (2003) The genetic architecture necessary for transgressive segregation is common in both natural and domesticated populations. Philos Trans R Soc Lond 358:1141–1147CrossRefGoogle Scholar
  87. 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 37:1141–1146PubMedCrossRefGoogle Scholar
  88. Saito A, Yano M, Kishimoto N, Nakagahra M, Yoshimura A, Saito K, Kuhara S, Ukai Y, Kawase M, Nagamine T, Yoshimura S, Ideta O, Ohsawa R, Hayano Y, Iwata N, Sugiura M (1991) Linkage map of restriction fragment length polymorphism loci in rice. Jpn J Breed 41:665–670Google Scholar
  89. Sakamoto T, Miura K, Itoh H, Tatsumi T, Ueguchi-Tanaka M, Ishiyama K, Kobayashi M, Agrawal GK, Takeda S, Abe K, Miyao A, Hirochika H, Kitano H, Ashikari M, Matsuoka M (2004) An overview of gibberellin metabolism enzyme genes and their related mutants in rice. Plant Physiol 134:1642–1653PubMedCrossRefGoogle Scholar
  90. 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
  91. Second G (1982) Origin of the genic diversity of cultivated rice (Oryzaspp.): study of the polymorphism scored at 40 isozyme loci. Jpn J Genet 57:25–57Google Scholar
  92. Septiningsih EM (2002) Identification, near-isogenic line development and fine mapping of quantitative trait loci from the rice cultivar IR64 and its wild relative Oryza rufipogon. PhD thesis. Cornell University, Ithaca, NYGoogle Scholar
  93. Sergeeva LI, Keurentjes JJ, Bentsink L, Vonk J, van der Plas LH, Koornneef M, Vreugdenhil D (2006) Vacuolar invertase regulates elongation of Arabidopsis thaliana roots as revealed by QTL and mutant analysis. Proc Natl Acad Sci USA 103:2994–2999PubMedCrossRefGoogle Scholar
  94. Shen B, Zhuang JY, Zhang KQ, Xia QQ, Sheng CX, Zheng KL (2003) QTLs mapping of leaf traits and root vitality in a recombinant inbred line population of rice. Yi Chuan Xue Bao 30:1133–1139PubMedGoogle Scholar
  95. Sirithunya P, Tragoonrung S, Vanavichit A, Pa-In N, Vongsaprom C, Toojinda T (2002) Quantitative trait loci associated with leaf and neck blast resistance in recombinant inbred line population of rice (Oryza sativa). DNA Res 9:79–88PubMedCrossRefGoogle Scholar
  96. Sobrizal K, Ikeda P, Sanchez L, Doi K, Angeles ER, Khush GS, Yoshimura A (1999) Development of Oryza glumaepatula introgression lines in rice, O. sativa L. Rice Genet Newsl 16:107–108Google Scholar
  97. Song W-Y, Wang G-L, Chen L-L, Kim H-S, Pi L-Y, Holsten T, Gardner J, Wang B, Zhai W-X, Zhu L-H, Fauquet C, Ronald P (1995) A receptor kinase-like protein encoded by the rice disease resistance gene, Xa21. Science 27:1804–1806CrossRefGoogle Scholar
  98. Sood BC, Sidiq EA (1978) A rapid technique for scent determination in rice. Indian J Genetic Plant Breed 38: 271Google Scholar
  99. 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
  100. Sun X, Cao Y, Yang Z, Xu C, Li X, Wang S, Zhang Q (2004) Xa26, a gene conferring resistance to Xanthomonas oryzae pv. oryzae in rice, encodes an LRR receptor kinase-like protein. Plant J 37:517–527PubMedCrossRefGoogle Scholar
  101. 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. Plant Cell 18:283–294PubMedCrossRefGoogle Scholar
  102. Tabor H, Risch N, Myers R (2002) Candidate-gene approaches for studying coplex genetice traits: practical considerations. Nat Rev Genet 3:391–396PubMedCrossRefGoogle Scholar
  103. 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 92:191–203CrossRefGoogle Scholar
  104. Tanksley SD, McCouch SR (1997) Seed banks and molecular maps: unlocking genetic potential from the wild. Science 277:1063–1066PubMedCrossRefGoogle Scholar
  105. 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 100:697–712CrossRefGoogle Scholar
  106. 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
  107. Terada R, Urawa H, Inagaki Y, Tsugane K, Iida S (2002) Efficient gene targeting by homologous recombination in rice. Nat Biotechnol 20:983–984CrossRefGoogle Scholar
  108. Terwilliger JD, Weiss KM (1998) Linkage disequilibrium mapping of complex disease: fantasy or reality? Curr Opin Biotech 9:578–594PubMedCrossRefGoogle Scholar
  109. 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
  110. 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 172:2501–2514PubMedCrossRefGoogle Scholar
  111. Thornsberry JM, Goodman MM, Doebley J, Kresovich S, Nielsen D, Buckler ESt (2001) Dwarf8 polymorphisms associate with variation in flowering time. Nat Genet 28:286–289PubMedCrossRefGoogle Scholar
  112. Tian F, Li de J, Fu Q, Zhu ZF, Fu YC, Wang XK, Sun CQ (2006) Construction of introgression lines carrying wild rice (Oryza rufipogon Griff.) segments in cultivated rice (Oryza sativa L.) background and characterization of introgressed segments associated with yield-related traits. Theor Appl Genet 112:570–580PubMedCrossRefGoogle Scholar
  113. Toenniessen GH, O’Toole JC, DeVries J (2003) Advances in plant biotechnology and its adoption in developing countries. Curr Opin Plant Biol 6:191–198PubMedCrossRefGoogle Scholar
  114. Vaughan DA (1991) Biogeography of the genus Oryza across the Malay Archipelago. Rice Genet Newsl 8:73–75Google Scholar
  115. Vaughan DA, Morishima H, Kadowaki K (2003) Diversity in the Oryza genus. Curr Opin Plant Mol Biol 6:139–146CrossRefGoogle Scholar
  116. Vaughan DA, Kadowaki KI, Kaga A, Tomooka N (2005) On the Phylogeny and Biogeography of the Genus Oryza. Breed Sci 55:113–122CrossRefGoogle Scholar
  117. Virk P, Ford-Lloyd BV, Jackson MT, Newbury HJ. (1996) Predicting quantitative variation within rice germplasm using molecular markers. Heredity 76:296–304Google Scholar
  118. Wan JL, Zhai HQ, Wan JM, Yasui H, Yoshimura A (2003) Mapping QTL for traits associated with resistance to ferrous iron toxicity in rice (Oryza sativa L.), using japonica chromosome segment substitution lines. Yi Chuan Xue Bao 30:893–898PubMedGoogle Scholar
  119. Wan XY, Wan JM, Su CC, Wang CM, Shen WB, Li JM, Wang HL, Jiang L, Liu SJ, Chen LM, Yasui H, Yoshimura A (2004) QTL detection for eating quality of cooked rice in a population of chromosome segment substitution lines. Theor Appl Genet 110:71–79PubMedCrossRefGoogle Scholar
  120. Wan XY, Wan JM, Jiang L, Wang JK, Zhai HQ, Weng JF, Wang HL, Lei CL, Wang JL, Zhang X, Cheng ZJ, Guo XP (2006) QTL analysis for rice grain length and fine mapping of an identified QTL with stable and major effects. Theor Appl Genet 112:1258–1270PubMedCrossRefGoogle Scholar
  121. Wang GL, Mackill DJ, Bonman JM, McCouch SR, Champoux MC, Nelson RJ (1994) RFLP mapping of genes conferring complete and partial resistance to blast in a durably resistant rice cultivar. Genetics 136:1421–1434PubMedGoogle Scholar
  122. Wang ZY, Tanksley SD (1989) Restriction Fragment Length Polymorphism in Oryza sativa L. Genome 32:1113–1118Google Scholar
  123. Wang ZY, Second G, Tanksley SD (1992) Polymorphism and phylogenetic relationship among species in the genus Oryza as determined by analysis of nuclear RFLPs. Theor Appl Genet 83:565–581CrossRefGoogle Scholar
  124. Weir BS (1990) Genetic Data Analysis: Methods for Discrete Population Genetic Data, 377 pp. Sinaur Associates, Sunderland, MAGoogle Scholar
  125. Weiss K, Clark AG (2002) Linkage disequilibrium and the mapping of complex human traits. Trend Genet 18:19–24CrossRefGoogle Scholar
  126. Widjaja R, Craske JD, Wootton M (1996) Comparative studies on volatile components of non-fragrant and fragrant rices. J Sci Food Agric 70:151–161CrossRefGoogle Scholar
  127. Wing RA, Ammiraju JS, Luo M, Kim H, Yu Y, Kudrna D, Goicoechea JL, Wang W, Nelson W, Rao K, Brar D, Mackill DJ, Han B, Soderlund C, Stein L, SanMiguel P, Jackson S (2005) The Oryza map alignment project: the golden path to unlocking the genetic potential of wild rice species. Plant Mol Biol 59:53–62PubMedCrossRefGoogle Scholar
  128. 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
  129. Xing YZ, Tan YF, Hua JP, Sun XL, Xu CG, 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
  130. 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
  131. Xu Y, Zhu L, Xiao J, Huang N, McCouch SR (1997) Chromosomal regions associated with segregation distortion of molecular markers in F2, backcross, doubled haploid, and recombinant inbred populations in rice (Oryza sativa L.). Mol Gen Genet 253:535–545PubMedCrossRefGoogle Scholar
  132. Yamamoto T, Lin H, Sasaki T, Yano M (2000) Identification of heading date quantitative trait locus Hd6 and characterization of its epistatic interactions with Hd2 in rice using advanced backcross progeny. Genetics 154:885–891PubMedGoogle Scholar
  133. Yamanaka S, Nakamura I, Watanabe KN, Sato Y (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
  134. Yamanouchi U, Yano M, Lin H, Ashikari M, Yamada K (2002) A rice spotted leaf gene, Spl7, encodes a heat stress transcription factor protein. Proc Natl Acad Sci USA 99:7530–7535PubMedCrossRefGoogle Scholar
  135. Yang QH, Wang CM, Hu ML, Zhang YX, Zhai HQ, Wan JM (2005) Genetic analysis for nitrogen content and its change in rice flag leaf. Zhongguo Shuidao Kexue 19:7–12Google Scholar
  136. Yano M (2001) Genetic and molecular dissection of naturally occurring variation. Curr Opin Plant Biol 4:130–135PubMedCrossRefGoogle Scholar
  137. Yoshihashi T (2002) Quantitative analysis on 2-acetyl-1-pyrroline of an aromatic rice by stable isotope dilution method and model studies on its formation during cooking. J Food Sci 67:619–622CrossRefGoogle Scholar
  138. Yoshimura S, Yamanouchi U, Katayose Y, Toki S, Wang ZX, Kono I, Kurata N, Yano M, Iwata N, Sasaki T (1998) Expression of Xa1, a bacterial blight-resistance gene in rice, is induced by bacterial inoculation. Proc Natl Acad Sci USA 95:1663–1668PubMedCrossRefGoogle Scholar
  139. Yu CY, Liu YQ, Jiang L, Wang CM, Zhai HQ, Wan JM (2005) QTLs mapping and genetic analysis of tiller angle in rice (Oryza sativa L.). Acta Genetica Sinica 32:948–954PubMedGoogle Scholar
  140. Zhang N, Xu Y, Akash M, McCouch S, Oard J (2005) Identification of candidate markers associated with agronomic traits in rice using discriminant analysis. Theor Appl Genet 110:721–729PubMedCrossRefGoogle Scholar
  141. Zheng BS, Yang L, Zhang WP, Mao CZ, Wu YR, Yi KK, Liu FY, Wu P (2003) Mapping QTLs and candidate genes for rice root traits under different water-supply conditions and comparative analysis across three populations. Theor Appl Genet 107:1505–1515PubMedCrossRefGoogle Scholar
  142. Zheng BS, Yang L, Mao CZ, Zhang WP, Wu P (2006) QTLs and candidate genes for rice root growth under flooding and upland conditions. Yi Chuan Xue Bao 33:141–151PubMedGoogle Scholar
  143. Zheng HG, Babu RC, Pathan MS, Ali L, Huang N, Courtois B, Nguyen HT (2000) Quantitative trait loci for root-penetration ability and root thickness in rice: comparison of genetic backgrounds. Genome 43:53–61PubMedCrossRefGoogle Scholar
  144. Zhu Q, Ge S (2005) Phylogenetic relationships among A-genome species of the genus Oryzarevealed by intron sequences of four nuclear genes. New Phytol 167:249–265PubMedCrossRefGoogle Scholar
  145. Zhuang JY, Fan YY, Rao ZM, Wu JL, Xia YW, Zheng KL (2002) Analysis on additive effects and additive-by-additive epistatic effects of QTLs for yield traits in a recombinant inbred line population of rice. Theor Appl Genet 105:1137–1145PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2007

Authors and Affiliations

  • Anjali S. Iyer-Pascuzzi
    • 1
  • Megan T. Sweeney
    • 1
  • Neelamraju Sarla
    • 2
  • Susan R. McCouch
    • 1
  1. 1.Department of Plant Breeding and GeneticsCornell UniversityIthacaUSA
  2. 2.Directorate of Rice ResearchRajendranagarIndia

Personalised recommendations