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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 19:14
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 14:41–43
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 106:1084–1090
Andersen JR, Lubberstedt T (2003) Functional markers in plants. Trends Plant Sci 8:554–560
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 96:10284–10289
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 52:143–150
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 309:741–745
Barton NH (2000) Genetic hitchhiking. Phil Trans Royal Soc London B 355:1553–1562
Berner DK, Hoff BJ (1986) Inheritance of scent in American long grain rice. Crop Sci 26:876–878
Bradbury LM, Henry RJ, Jin QS, Reinke RF, Waters DL (2005) A perfect marker for fragrance genotyping in rice. Mol Breed 1665:279–283
Brar DS, Khush GS (1997) Alien introgression in rice. Plant Mol Biol 35:35–47
Burr B, Burr FA, Thompson KH, Albertson MC, Stube CW (1988) Gene mapping with recombinant inbreds in maize. Genetics 118:519–526
Buttery RG, Ling LC, Juliano BO, Turnbaugh JG (1983) Cooked rice aroma and 2-acetyl-1-pyrroline. J Agric Food Chem 31:823–826
Cai HW, Morishima H (2002) QTL clusters reflect character associations in wild and cultivated rice. Theor Appl Genet 104:1217–1228
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 138:1251–1274
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 90:969–981
Chang TT (1976) Origin, Evolution, cultivation, dissemination, and diversification of Asian and African rices. Euphytica 25:425–441
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
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 9:245–250
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. 275–287
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 55:65–73
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 Republic
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 53:289–307
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 300–308
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 165:759–769
Garris AJ, Tai TH, Coburn JR, Kresovich S, McCouch S (2005) Genetic structure and diversity in Oryza sativa L. Genetics 169:1631–1638
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 96:31–39
Glaszmann JC (1987) Isozymes and classification of Asian rice varieties. Theor Appl Genet 74:21–30
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 435:1122–1125
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 42:45–53
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 148:479–494
Hedden P (2003) The genes of the green revolution. Trends Genet 19:5–9
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 107:679–690
Hudson RR, Kaplan NL (1988) The coalescent process in models with selection and recombination. Genetics 120:831–840
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 94:7725–7729
Ikeda R, Khush GS, Tabien RE (1990) A new resistance gene to bacterial blight derived from O. longistaminata. Jpn J Breed 40:280–281
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 13:999–1010
Ishikawa S, Ae N, Yano M (2005) Chromosomal regions with quantitative trait loci controlling cadmium concentration in brown rice (Oryza sativa). New Phytol 168:345–350
Iyer AS, McCouch SR (2004) The rice bacterial blight resistance gene xa5 encodes a novel form of disease resistance. Mol Plant Microbe Interact 17:1348–1354
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)
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 109:965–977
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 138:97–105
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 30:453–458
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 275:354–366
Jorde LB (2000) Linkage disequilbrium and the search for complex disease genes. Genome Res 10:1435–1444
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 35–41
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 3:132–147
Khush GS, Ling KC (1974) Inheritance of resistance to Grassy stunt virus and its vector in rice. J Hered 65:135–136
Koornneef M, Alonso-Blanco C, Vreugdenhil D (2004) Naturally occurring genetic variation in Arabidopsis thaliana. Annu Rev Plant Biol 55:141–172
Kreitman M, Akashi H (1995) Molecular evidence for natural selection. Annu Rev Ecol Syst 26:403–422
Kruglyak L (1999) Prospects for whole-genome linkage disequilibrium mapping of common disease genes. Nat Genet 22:139–144
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 52:319–325
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 18:81–82
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 7:93–101
Lanceras JC, Pantuwan G, Jongdee B, Toojinda T (2004) Quantitative trait loci associated with drought tolerance at reproductive stage in rice. Plant Physiol 135:384–399
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 48:453–461
Li J, Yuan L (2000) Hybrid Rice: Genetics, breeding and seed production. Plant Breed Rev 17:15–120
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 108:141–153
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 59:33–52
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 149:999–10173
Lorieux M, Petrov M, Huang N, Guiderdoni E, Ghesquiere A (1996) Aroma in rice: genetic analysis of a quantitative trait. Theor Appl Genet 93:1145–1151
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 45:215–223
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 94:145–150
Ma J, Bennetzen JL (2004) Rapid recent growth and divergence of rice nuclear genomes. Proc Natl Acad Sci U S A 101:12404–12410
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 6:33
Matsuo T (1952) Genecological studies on cultivated rice. Bull Natl Inst Gr Sci Jpn D3:1–111
McCouch SR, Kochert G (1988) Molecular mapping of rice chromosomes. Theor Appl Genet 76:815–829
McCouch SR, Teytelman L, Xu Y, Lobos KB, Clare K, Walton M, Fu B, Maghirang R, Li Z, Xing Y, Zhang Q, Kono I, Yano M, Fjellstrom R, DeClerck G, Schneider D, Cartinhour S, Ware D, Stein L (2002) Development and mapping of 2240 new SSR markers for rice (Oryza sativa L.). DNA Res 9:199–207
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)
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 102:41–52
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 9:11–17
Morishima H, Oka HI (1970) A survey of genetic variations in the populations of wild Oryzaspecies and their cultivated relatives. Jpn J Genet 45:371–385
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)
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 255:1–8
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 44:17–23
Nielsen R (2001) Statistical tests of selective neutrality in the age of genomics. Heredity 86:641–647
Nordborg, M. Tavare, S. (2002) Linkage disequilibrium: what history has to tell us. Trend Genet 18:83–90
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 5:106–109
Ohtsubo H, Cheng CY, Ohsawa I, Tsuchimoto S, Ohtsubo E (2004) Rice retroposon p-SINE1 and origin of cultivated rice. Breed Sci 54:1–11
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
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 173:975–983
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 23:482–487
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 400:256–261
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 98:10505–10508
Reinke RF, Welsh LA, Reece JE, Lewin LG, Blakeney AB (1991) Procedures for quality selection of aromatic rice varieties. Int Rice Res Newsl 16:10–11
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 358:1141–1147
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
Saito A, Yano M, Kishimoto N, Nakagahra M, Yoshimura A, Saito K, Kuhara S, Ukai Y, Kawase M, Nagamine T, Yoshimura S, Ideta O, Ohsawa R, Hayano Y, Iwata N, Sugiura M (1991) Linkage map of restriction fragment length polymorphism loci in rice. Jpn J Breed 41:665–670
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 134:1642–1653
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 416:701–702
Second G (1982) Origin of the genic diversity of cultivated rice (Oryzaspp.): study of the polymorphism scored at 40 isozyme loci. Jpn J Genet 57:25–57
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, NY
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 103:2994–2999
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 30:1133–1139
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 9:79–88
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 16:107–108
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 27:1804–1806
Sood BC, Sidiq EA (1978) A rapid technique for scent determination in rice. Indian J Genetic Plant Breed 38: 271
Spielmeyer W, Ellis MH, Chandler PM (2002) Semidwarf (sd-1), “green revolution” rice, contains a defective gibberellin 20-oxidase gene. Proc Natl Acad Sci USA 99:9043–9048
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 37:517–527
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 18:283–294
Tabor H, Risch N, Myers R (2002) Candidate-gene approaches for studying coplex genetice traits: practical considerations. Nat Rev Genet 3:391–396
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
Tanksley SD, McCouch SR (1997) Seed banks and molecular maps: unlocking genetic potential from the wild. Science 277:1063–1066
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
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 11:1441–1452
Terada R, Urawa H, Inagaki Y, Tsugane K, Iida S (2002) Efficient gene targeting by homologous recombination in rice. Nat Biotechnol 20:983–984
Terwilliger JD, Weiss KM (1998) Linkage disequilibrium mapping of complex disease: fantasy or reality? Curr Opin Biotech 9:578–594
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 107:479–493
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 172:2501–2514
Thornsberry JM, Goodman MM, Doebley J, Kresovich S, Nielsen D, Buckler ESt (2001) Dwarf8 polymorphisms associate with variation in flowering time. Nat Genet 28:286–289
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 112:570–580
Toenniessen GH, O’Toole JC, DeVries J (2003) Advances in plant biotechnology and its adoption in developing countries. Curr Opin Plant Biol 6:191–198
Vaughan DA (1991) Biogeography of the genus Oryza across the Malay Archipelago. Rice Genet Newsl 8:73–75
Vaughan DA, Morishima H, Kadowaki K (2003) Diversity in the Oryza genus. Curr Opin Plant Mol Biol 6:139–146
Vaughan DA, Kadowaki KI, Kaga A, Tomooka N (2005) On the Phylogeny and Biogeography of the Genus Oryza. Breed Sci 55:113–122
Virk P, Ford-Lloyd BV, Jackson MT, Newbury HJ. (1996) Predicting quantitative variation within rice germplasm using molecular markers. Heredity 76:296–304
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 30:893–898
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 110:71–79
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 112:1258–1270
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 136:1421–1434
Wang ZY, Tanksley SD (1989) Restriction Fragment Length Polymorphism in Oryza sativa L. Genome 32:1113–1118
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 83:565–581
Weir BS (1990) Genetic Data Analysis: Methods for Discrete Population Genetic Data, 377 pp. Sinaur Associates, Sunderland, MA
Weiss K, Clark AG (2002) Linkage disequilibrium and the mapping of complex human traits. Trend Genet 18:19–24
Widjaja R, Craske JD, Wootton M (1996) Comparative studies on volatile components of non-fragrant and fragrant rices. J Sci Food Agric 70:151–161
Wing RA, Ammiraju JS, Luo M, Kim H, Yu Y, Kudrna D, Goicoechea JL, Wang W, Nelson W, Rao K, Brar D, Mackill DJ, Han B, Soderlund C, Stein L, SanMiguel P, Jackson S (2005) The Oryza map alignment project: the golden path to unlocking the genetic potential of wild rice species. Plant Mol Biol 59:53–62
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
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: 248–247
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 98:243–251
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 253:535–545
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 154:885–891
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 108:1200–1204
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 99:7530–7535
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 19:7–12
Yano M (2001) Genetic and molecular dissection of naturally occurring variation. Curr Opin Plant Biol 4:130–135
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 67:619–622
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 95:1663–1668
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 32:948–954
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 110:721–729
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 107:1505–1515
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 33:141–151
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 43:53–61
Zhu Q, Ge S (2005) Phylogenetic relationships among A-genome species of the genus Oryzarevealed by intron sequences of four nuclear genes. New Phytol 167:249–265
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 105:1137–1145
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Iyer-Pascuzzi, A.S., Sweeney, M.T., Sarla, N., McCouch, S.R. (2007). Use of Naturally Occurring Alleles for Crop Improvement. In: Rice Functional Genomics. Springer, New York, NY. https://doi.org/10.1007/0-387-48914-2_7
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DOI: https://doi.org/10.1007/0-387-48914-2_7
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