References
- Brar, D. S. and Khush, G. S. (1997). Alien introgression in rice. Plant Molecular Biology 35, 35-47.
- Cai, H. W. and Morishima, H. (2002). QTL clusters reflect character associations in wild and cultivated rice. Theoretical and Applied Genetics 104, 1217-1228.
- Caicedo AL, SH Williamson, A Fledel-Alon, TL York, N Polato, KM Olsen, R Nielsen, SR McCouch, CD Bustamante and MD Purugganan (2007) Demography and selection shapes genome-wide patterns of nucleotide polymorphism in domesticated rice. PLOS Genetics (submitted)
- Cheng, C. Y., Motohashi, R., Tsuchimoto, S., Fukita, Y., Ohtsubo, H. and Ohtsubo, E. (2003). Polyphyletic origin of cultivated rice: base on the interspersion pattern of SINEs. Mol Biol Evol 20, 67-75.
- Cho, Y. C., Suh, J. P., Choi, I. S., Hong, H. C., Baek, M. K., Kang, K. H., Kim, Y. G., Ahn, S. N., Choi, H. C., Hwang, H. G. et al. (2003). QTLs analysis of yield and its related traits in wild rice relative Oryzarufipogon. Treat of Crop Res In Korea 4.
- Chu, Y. E., Morishima, H. and Oka, H. I. (1969). Reproductive barriers distrbuted in cultivated rice species and their wild relatives. Japan J. Genet 44, 207-223.
- Dalmacio, R. D., Brar, D. S., Ishii, T., Sitch, T. A., Virmani, S. S. and Khush, G. S. (1995). Identification and transfer of a new cytoplasmic male sterility source from Oryza perennis into indica rice (O. sativa). Euphytica 82, 221-225.
- Doi, K., Yoshimura, A. and Iwata, N. (1998). RFLP mapping and QTL analysis of heading date and pollen sterility using backcross populations between Oryza sativa L. and OryzaglaberrimaSteud. Breeding Science 48, 395-399.
- Edwards, J. D., Temnykh, S., Jain, S., Cho, Y. I., Koh, H. J. and McCouch, S. R. (2005). Origins and distribution of allelic diversity in populations of wild and cultivated rice. Genetics Submitted 09/05.
- Garris, A. J., McCouch, S. R. and 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, 759-69.
- Garris, A. J., Tai, T. H., Coburn, J. R., Kresovich, S. and McCouch, S. (2005). Genetic structure and diversity in Oryza sativa L. Genetics 169, 1631-1638.
- Glaszmann, J. C. (1987). Isozymes and Classification of Asian Rice Varieties. Theoretical and Applied Genetics 74, 21-30.
- Harushima, Y., Nakagahra, M., Yano, M., Sasaki, T. and Kurata, N. (2002). Diverse variation of reproductive barriers in three intraspecific rice crosses. Genetics 160, 313-322.
- Higham and Lu, 1998
- Hu H, J Mu, HJ Zhang, YZ Tao and B Han (2006) Differentiation of a miniature inverted transposable element (MITE) system in Asian rice cultivars and its inference for a diphyletic origin of two sub-species of Asian cultivated rice. J Integrat Plant Biol 48:260-267.
- Ishii, T., Bautista, N. S., Shimadzutsu, K., Kobayashi, N., Uchida, N. and Kamijima, O. (2003). Wild-QTL-allele effect in the background of japonica Nipponbare and indica (IR35) cultivars. In Advances in Rice Genetics, eds. G. S. Khush D. S. Brar and B. Hardy), pp. 173-175.
- Jiang and Liu, 2006
- Lee, S. J., Oh, C. S., Suh, J. P., McCouch, S. R. and Ahn, S. N. (2005). Identification of QTLs for domestication-related and agronomic traits in an Oryza sativa x O. rufipogonBC1F7 population. Plant Breeding 124, 209-219.
- Li DJ, CQ Sun, YC Fu, C Li, ZF Zhu, I Chen, HW Cai and XK Wang (2002). Identification and mapping of genes for improving yield from Chinese common wild rice (O. rufipogon Griff.) using advanced backcross QTL analysis. Chinese Sci. Bull. 47:1533-1537.
- Li, J., Thomson, M. J. and McCouch, S. R. (2004). Fine mapping of a grain weight QTL in the peri-centromeric region of rice chromosome 3. Genetics 168, 2187-2195.
- Li et al., 2005
- Li, J. and Yuan, L. (2000). Hybrid rice: genetics, breeding, and seed production. Plant Breeding Reviews 17, 150-158.
- Li, Z. K., Fu, B. Y., Gao, Y. M., Xu, J. L., Ali, J., Lafritte, H. R., Jiang, Y. Z., Rey, J. D., Vijayakumar, C. H. M., Maghirang, R. et al. (2005). Genome-wide introgression lines and their use in genetic and molecular dissection of complex phenotypes in rice (Oryza sativa L.). Molecular Biology 59, 33-52.
- Londo et al., 2006
- Lu, H., Redus, M. A., Coburn, J. R., Rutger, J. N., McCouch, S. R. and Tai, T. H. (2004). Population structure and breeding patterns of 145 US rice cultivars based on SSR marker analysis. Crop Sci 45, 66-76.
- Ma, J. and Bennetzen, J. L. (2004). Rapid recent growth and divergence of rice nuclear genomes. Proceedings of the National Academy of Sciences of the United States of America 10.1073/pnas.0403715101.
- Marri, P. R., Sarla, N., Reddy, L. V. and Siddiq, E. A. (2005). Identification and mapping of yield and yield related QTLs from an Indian accession of Oryza rufipogon. BMC Genetics UK 6, Art. No. 33.
- Matsuo et al., 1997
- Matsuoka, Y., Vigouroux, Y., Goodman, M. M., Sanchez, G. J., Buckler, E. and Doebley, J. (2002). A single domestication for maize shown by multilocus microsatellite genotyping. Proceedings of the National Academy of Sciences of the United States of America 99, 6080-6084.
- McCouch, S. R. (2004). Diversifying Selection in Plant Breeding. PLoS Biology 2, e347.
- McCouch et al., 2007
- Moncada, M., Martinez, 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 Oryzarufipogon BC2F2 population evaluated in an upland environment. Theor Appl Genet 102, 41-52.
- Morishima, H., Sano, Y. and Oka, H. I. (1984). Differentiation of perennial and annual types due to habitat conditions in the wild rice Oryza perennis. Plant Syst Evol 144, 119-135.
- Nguyen, B. D., Brar, D. S., Bui, B. C., Nguyen, T. V., Pham, L. N. and Nguyen, H. T. (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, 583-593.
- Ni, J., Colowit, P. M. and Mackill, D. J. (2002). Evaluation of genetic diversity in rice subspecies using microsatellite markers. Crop Science 42, 601-607.
- Oka, H. I. (1988). Functions and genetic base of reproductive barriers. In Origin of Cultivated Rice., (ed. H. I. Oka), pp. 156-159;181-209. Amsterdam: Tokyo/Elsevier Science/Japan Scientific Societies Press.
- Oka, H. I. and Morishima, H. (1967). Variations in the breeding systems of a wild rice, Oryzaperennis. Evolution 21, 249-258.
- Pei, 1998
- Roy, S. C. (1921). A preliminary classification of the wild rices of the Central Province and Berar. Agric. J. India 16, 365-380.
- Sano, Y. (1993). Constraints in using wild relatives in breeding: lack of basic knowledge on crop gene pools. In International Crop Science, vol. I (ed. D. R. Buxton), pp. 437-443. Madison, WI: Crop Science Society of America.
- Second, G. (1982). Origin of the genetic diversity of cultivated rice (Oryza spp.): Study of the polymorphism scored at 40 isozyme loci. Japanese Journal of Genetics 57, 25-57.
- Second, G. (1991). Molecular markers in rice systematics and the evaluation of genetic resources. Biotechnology in Agriculture and Forestry 14, 468-494.
- Septiningsih, E. M., Prasetiyono, J., Lubis, E., Tai, T. H., Tjubaryat, T., Moeljopawiro, S. and McCouch, S. R. (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, 1419-32.
- Septiningsih, E. M., Trijatmiko, K. R., Moeljopawiro, S. and McCouch, S. R. (2003b). Identification of quantitative trait loci for grain quality in an advanced backcross population derived from the Oryza sativa variety IR64 and the wild relative O. rufipogon. Theor Appl Genet 107, 1433-41.
- Tanksley, S. D. and McCouch, S. R. (1997). Seed banks and molecular maps: unlocking genetic potential from the wild. Science 277, 1063-1066.
- Thomson, M. J., Edwards, J. D., Septiningsih, E. M., Harrington, S. and McCouch, S. R. (2005). Substitution mapping of dth1.1, a flowering time QTL associated with transgressive variation in rice, reveals a cluster of QTLs. Genetics 172: 2501-2514
- Thomson, M. J., Tai, T. H., McClung, A. M., Hinga, M. E., Lobos, K. B., Xu, Y., Martinez, C. and McCouch, S. R. (2003). Mapping quantitative trait loci for yield, yield components, and morphological traits in an advanced backcross population between Oryzarufipogon and the Oryza sativa cultivar Jefferson. Theor Appl Genet 107, 479-493.
- Vaughan, D. A., Kadowaki, K.-I., Kaga, A. and Tomooka, N. (2005). On the Phylogeny and Biogeography of the GenusOryza. Breeding Science 55, 113-122.
- Vitte et al. 2004
- Xiao, J., Li, J., Grandillo, S., Ahn, S. N., Yuan, L., Tanksley, S. D. and McCouch, S. R. (1998). Identification of trait-improving quantitative trait loci alleles from a wild rice relative, Oryzarufipogon. Genetics 150, 899-909.
- Xie, X., Song, M. H., Jin, F., Suh, J. P., McCouch, S. R. and Ahn, S. N. (2005). Fine mapping of a grain weight quantitative trait locus on rice chromosome 8 using near isogenic lines derived from a cross between Oryza sativa and O. rufipogon. Theor Appl Genet 113:885-894
- Xiong, L. Z., Liu, K. D., Dai, X. K., Xu, C. G. and 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.
- Zhao, 1998