請用此 Handle URI 來引用此文件：
http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/81944完整後設資料紀錄
| DC 欄位 | 值 | 語言 |
|---|---|---|
| dc.contributor.advisor | 邢禹依(Yue-Ie Hsing) | |
| dc.contributor.author | Cheng-Chieh Wu | en |
| dc.contributor.author | 吳正杰 | zh_TW |
| dc.date.accessioned | 2022-11-25T03:07:10Z | - |
| dc.date.available | 2023-08-30 | |
| dc.date.copyright | 2021-11-12 | |
| dc.date.issued | 2021 | |
| dc.date.submitted | 2021-08-30 | |
| dc.identifier.citation | 3K RGP. (2014). The 3,000 rice genomes project. GigaScience 3, 2047-2217X-2043-2047. Agnoun, Y., Biaou, S.S.H., Sié, M., Vodouhè, R.S., and Ahanchédé, A. (2012). The african rice Oryza glaberrima steud: knowledge distribution and prospects. International Journal of Biology 4, 158-180. Alam, O., Gutaker, R.M., Wu, C.-c., Hicks, K.A., Bocinsky, K., Castillo, C.C., Acabado, S., Fuller, D., d’Alpoim Guedes, J.A., and Hsing, Y.-i. (2021). Genome analysis traces regional dispersal of rice in Taiwan and Southeast Asia. Molecular Biology and Evolution. msab209, https://doi.org/10.1093/molbev/msab209 Alexander, D.H., Novembre, J., and Lange, K. (2009). Fast model-based estimation of ancestry in unrelated individuals. Genome Research 19, 1655-1664. Alexandrov, N., Tai, S., Wang, W., Mansueto, L., Palis, K., Fuentes, R.R., Ulat, V.J., Chebotarov, D., Zhang, G., and Li, Z. (2015). SNP-Seek database of SNPs derived from 3000 rice genomes. Nucleic Acids Research 43, D1023-D1027. Asano, K., Takashi, T., Miura, K., Qian, Q., Kitano, H., Matsuoka, M., and Ashikari, M. (2007). Genetic and molecular analysis of utility of sd1 alleles in rice breeding. Breeding Science 57, 53-58. Asano, K., Yamasaki, M., Takuno, S., Miura, K., Katagiri, S., Ito, T., Doi, K., Wu, J., Ebana, K., Matsumoto, T., Innan, H., Kitano, H., Ashikari, M., and Matsuoka, M. (2011). Artificial selection for a green revolution gene during japonica rice domestication. Proc Natl Acad Sci U S A 108, 11034-11039. Ashikari, M., Sasaki, A., Ueguchi-Tanaka, M., Itoh, H., Nishimura, A., Datta, S., Ishiyama, K., Saito, T., Kobayashi, M., and Khush, G.S. (2002). Loss-of-function of a rice gibberellin biosynthetic gene, GA20 oxidase (GA20ox-2), led to the rice ‘green revolution’. Breeding Science 52, 143-150. Bellwood, P. (1995). Austronesian prehistory in Southeast Asia: homeland, expansion and transformation. Canberra: ANU E Press, pp. 103-120 Bellwood, P. (2004). The origins and dispersals of agricultural communities in Southeast Asia, in Ian Glover and Peter Bellwood (ed.), Southeast Asia: From Prehistory to History, Routledge Curzon, London, pp. 21-40. Bellwood, P. (2007). Prehistory of the Indo-Malaysian Archipelago: revised edition. ANU Press. Bellwood, P. (2011). The Checkered Prehistory of Rice Movement Southwards as a Domesticated Cereal—from the Yangzi to the Equator. Rice 4, 93-103. Bellwood, P., Gamble, C., Le Blanc, S.A., Pluciennik, M., Richards, M., and Terrell, J.E. (2007). First Farmers: the Origins of Agricultural Societies. Cambridge Archaeological Journal 17, 87-109. Bettinger, R.L., Barton, L., and Morgan, C. (2010). The origins of food production in north China: A different kind of agricultural revolution. Evolutionary Anthropology: Issues, News, and Reviews: Issues, News, and Reviews 19, 9-21. Blust, R. (1995). The prehistory of the Austronesian-speaking peoples: a view from language. Journal of World Prehistory 9, 453-510. Bolger, A.M., Lohse, M., and Usadel, B. (2014). Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114-2120. Brooks, S.A., Yan, W., Jackson, A.K., and Deren, C.W. (2008). A natural mutation in rc reverts white-rice-pericarp to red and results in a new, dominant, wild-type allele: Rc-g. Theoretical and Applied Genetics 117, 575-580. Browning, B.L., and Browning, S.R. (2016). Genotype imputation with millions of reference samples. The American Journal of Human Genetics 98, 116-126. Chandraratna, M.F. (1955). Genetics of photoperiod sensitivity in rice. Journal of Genetics 53, 215-223. Chang, C.C., Chow, C.C., Tellier, L.C., Vattikuti, S., Purcell, S.M., and Lee, J.J. (2015). Second-generation PLINK: rising to the challenge of larger and richer datasets. Gigascience 4, s13742-13015-10047-13748. Chang, T.-T. (1976). The origin, evolution, cultivation, dissemination, and diversification of Asian and African rices. Euphytica 25, 425-441. Chen, J., Huang, Q., Gao, D., Wang, J., Lang, Y., Liu, T., Li, B., Bai, Z., Goicoechea, J.L., and Liang, C. (2013). Whole-genome sequencing of Oryza brachyantha reveals mechanisms underlying Oryza genome evolution. Nature Communications 4, 1-9. Cho, L.H., Yoon, J., and An, G. (2017). The control of flowering time by environmental factors. The Plant Journal 90, 708-719. Choi, J.Y., and Purugganan, M.D. (2018). Multiple origin but single domestication led to Oryza sativa. G3 (Bethesda) 8, 797-803. Choi, J.Y., Platts, A.E., Fuller, D.Q., Hsing, Y.I., Wing, R.A., and Purugganan, M.D. (2017). The Rice paradox: multiple origins but single domestication in asian rice. Mol Biol Evol 34, 969-979. Choi, J.Y., Zaidem, M., Gutaker, R., Dorph, K., Singh, R.K., and Purugganan, M.D. (2019). The complex geography of domestication of the African rice Oryza glaberrima. PLoS Genetics 15, e1007414. Cingolani, P., Platts, A., Wang le, L., Coon, M., Nguyen, T., Wang, L., Land, S.J., Lu, X., and Ruden, D.M. (2012). A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly (Austin) 6, 80-92. Clement, M., Posada, D., and Crandall, K.A. (2000). TCS: a computer program to estimate gene genealogies. Molecular Ecology 9, 1657-1659. Clement, M., Snell, Q., Walker, P., Posada, D., and Crandall, K. (2002). TCS: estimating gene genealogies. In Parallel and Distributed Processing Symposium, International, pp. 0184-0184. DAFTPG. (1989). The history of Taiwan rice development and production. Department of Agriculture and Forestry of the Taiwan Provincial Government (DAFTPG) (in Chinese), 837. Danecek, P., Auton, A., Abecasis, G., Albers, C.A., Banks, E., DePristo, M.A., Handsaker, R.E., Lunter, G., Marth, G.T., and Sherry, S.T. (2011). The variant call format and VCFtools. Bioinformatics 27, 2156-2158. Danecek, P., Bonfield, J.K., Liddle, J., Marshall, J., Ohan, V., Pollard, M.O., Whitwham, A., Keane, T., McCarthy, S.A., Davies, R.M., and Li, H. (2021). Twelve years of SAMtools and BCFtools. GigaScience 10. Deng, Z., Qin, L., Gao, Y., Weisskopf, A.R., Zhang, C., and Fuller, D.Q. (2015). From early domesticated rice of the middle Yangtze Basin to millet, rice and wheat agriculture: Archaeobotanical macro-remains from Baligang, Nanyang Basin, Central China (6700–500 BC). PLoS One 10, e0139885. Diamond, J. (2001). Polynesian origins: Slow boat to Melanesia? Nature 410, 167-168. Diamond, J. (2002). Evolution, consequences and future of plant and animal domestication. Nature 418, 700-707. Diamond, J., and Bellwood, P. (2003). Farmers and their languages: the first expansions. Science 300, 597-603. Doi, K., Izawa, T., Fuse, T., Yamanouchi, U., Kubo, T., Shimatani, Z., Yano, M., and Yoshimura, A. (2004). Ehd1, a B-type response regulator in rice, confers short-day promotion of flowering and controls FT-like gene expression independently of Hd1. Genes and Development 18, 926-936. Du, H., Yu, Y., Ma, Y., Gao, Q., Cao, Y., Chen, Z., Ma, B., Qi, M., Li, Y., and Zhao, X. (2017). Sequencing and de novo assembly of a near complete indica rice genome. Nature Communications 8, 1-12. Easson, D., White, E., and Pickles, S. (1993). The effects of weather, seed rate and cultivar on lodging and yield in winter wheat. The Journal of Agricultural Science 121, 145-156. Edgar, R.C. (2004a). MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 5, 113. Edgar, R.C. (2004b). MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research 32, 1792-1797. Endo-Higashi, N., and Izawa, T. (2011). Flowering time genes Heading date 1 and Early heading date 1 together control panicle development in rice. Plant and Cell Physiology 52, 1083-1094. Esquivel, J. (1633). Memoria de cosas pertenecientes a la isla hermosa, 345-354. Felsenstein, J. (2004). PHYLIP (Phylogeny Inference Package) version 3.6. Distributed by the author. http://www.evolution.gs.washington.edu/phylip.html. Fogg, W.H. (1983). The Origins of Chinese Civilization. In 4. Swidden Cultivation of Foxtail Millet by Taiwan Aborigines: A Cultural Analogue of the Domestication of Setaria italica in China, N.K. David, ed (University of California Press), pp. 95-116. Foster, K., and Rutger, J. (1978). Inheritance of semidwarfism in rice, Oryza sativa L. Genetics 88, 559-574. Fujino, K., Wu, J., Sekiguchi, H., Ito, T., Izawa, T., and Matsumoto, T. (2010). Multiple introgression events surrounding the Hd1 flowering-time gene in cultivated rice, Oryza sativa L. Molecular Genetics and Genomics 284, 137-146. Fuke, Y. (1955). Genetical study of the photoperiodic reaction in the rice plant. Bull. Natl. Inst. Agric. Sci. 5, 72-91. Fuller, D.Q. (2011). Pathways to Asian civilizations: Tracing the origins and spread of rice and rice cultures. Rice 4, 78-92. Fuller, D.Q., Qin, L., Zheng, Y., Zhao, Z., Chen, X., Hosoya, L.A., and Sun, G.-P. (2009). The domestication process and domestication rate in rice: spikelet bases from the Lower Yangtze. Science 323, 1607-1610. Fuller, D.Q., Denham, T., Arroyo-Kalin, M., Lucas, L., Stevens, C.J., Qin, L., Allaby, R.G., and Purugganan, M.D. (2014). Convergent evolution and parallelism in plant domestication revealed by an expanding archaeological record. Proc Natl Acad Sci U S A 111, 6147-6152. Fuller, D.Q., Sato, Y.-I., Castillo, C., Qin, L., Weisskopf, A.R., Kingwell-Banham, E.J., Song, J., Ahn, S.-M., and Van Etten, J. (2010). Consilience of genetics and archaeobotany in the entangled history of rice. Archaeological and Anthropological Sciences 2, 115-131. Furukawa, T., Maekawa, M., Oki, T., Suda, I., Iida, S., Shimada, H., Takamure, I., and Kadowaki, K.i. (2007). The Rc and Rd genes are involved in proanthocyanidin synthesis in rice pericarp. The Plant Journal 49, 91-102. Futsuhara, Y., Toriyama, K., and Tsunoda, K. (1967). Breeding of a new rice variety' reimei' by gamma-ray irradiation. Japanese Journal of Breeding 17, 85-90. Garris, A.J., Tai, T.H., Coburn, J., Kresovich, S., and McCouch, S. (2005). Genetic structure and diversity in Oryza sativa L. Genetics 169, 1631-1638. Gemayel, R., Vinces, M.D., Legendre, M., and Verstrepen, K.J. (2010). Variable tandem repeats accelerate evolution of coding and regulatory sequences. Annual Review of Genetics 44, 445-477. Gnanamanickam, S.S. (2009). Biological control of rice diseases. (Springer Science Business Media). Gu, B., Zhou, T., Luo, J., Liu, H., Wang, Y., Shangguan, Y., Zhu, J., Li, Y., Sang, T., Wang, Z., and Han, B. (2015). An-2 encodes a cytokinin synthesis enzyme that regulates awn length and grain production in rice. Mol Plant 8, 1635-1650. Gutaker, R.M., Groen, S.C., Bellis, E.S., Choi, J.Y., Pires, I.S., Bocinsky, R.K., Slayton, E.R., Wilkins, O., Castillo, C.C., and Negrão, S. (2020). Genomic history and ecology of the geographic spread of rice. Nature Plants 6, 492-502. Happart, G. (1842). 1650. Woordboek der Favorlangsche taal. Reprinted by WR van Hoëvell in Verhandelingen van het Koninklijk Bataviaasch Genootschap van Kunsten en Wetenschappen 18. Hargrove, T.R., and Cabanilla, V.L. (1979). The impact of semidwarf varieties on Asian rice-breeding programs. Bioscience 29, 731-735. He, Q., Kim, K.W., and Park, Y.J. (2017). Population genomics identifies the origin and signatures of selection of Korean weedy rice. Plant Biotechnology Journal 15, 357-366. Hori, K., Matsubara, K., and Yano, M. (2016). Genetic control of flowering time in rice: integration of Mendelian genetics and genomics. Theoretical and applied Genetics 129, 2241-2252. Hsieh, J.-s., Hsing, Y.-i.C., Hsu, T.-f., Li, P.J.-k., Li, K.-t., and Tsang, C.-h. (2011). Studies on ancient rice—where botanists, agronomists, archeologists, linguists, and ethnologists meet. Rice 4, 178-183. Hua, L., Wang, D.R., Tan, L., Fu, Y., Liu, F., Xiao, L., Zhu, Z., Fu, Q., Sun, X., Gu, P., Cai, H., McCouch, S.R., and Sun, C. (2015). LABA1, a domestication gene associated with long, barbed awns in wild rice. Plant Cell 27, 1875-1888. Huang, C.L., Hung, C.Y., Chiang, Y.C., Hwang, C.C., Hsu, T.W., Huang, C.C., Hung, K.H., Tsai, K.C., Wang, K.H., Osada, N., Schaal, B.A., and Chiang, T.Y. (2012a). Footprints of natural and artificial selection for photoperiod pathway genes in Oryza. Plant J 70, 769-782. Huang, X., Kurata, N., Wang, Z.-X., Wang, A., Zhao, Q., Zhao, Y., Liu, K., Lu, H., Li, W., and Guo, Y. (2012b). A map of rice genome variation reveals the origin of cultivated rice. Nature 490, 497-501. Huang, X., Zhao, Y., Wei, X., Li, C., Wang, A., Zhao, Q., Li, W., Guo, Y., Deng, L., Zhu, C., Fan, D., Lu, Y., Weng, Q., Liu, K., Zhou, T., Jing, Y., Si, L., Dong, G., Huang, T., Lu, T., Feng, Q., Qian, Q., Li, J., and Han, B. (2011). Genome-wide association study of flowering time and grain yield traits in a worldwide collection of rice germplasm. Nat Genet 44, 32-39. Huang, X., Wei, X., Sang, T., Zhao, Q., Feng, Q., Zhao, Y., Li, C., Zhu, C., Lu, T., Zhang, Z., Li, M., Fan, D., Guo, Y., Wang, A., Wang, L., Deng, L., Li, W., Lu, Y., Weng, Q., Liu, K., Huang, T., Zhou, T., Jing, Y., Li, W., Lin, Z., Buckler, E.S., Qian, Q., Zhang, Q.F., Li, J., and Han, B. (2010). Genome-wide association studies of 14 agronomic traits in rice landraces. Nat Genet 42, 961-967. IRGSP. (2005). The map-based sequence of the rice genome. Nature 436, 793-800. Ishii, T., Numaguchi, K., Miura, K., Yoshida, K., Thanh, P.T., Htun, T.M., Yamasaki, M., Komeda, N., Matsumoto, T., Terauchi, R., Ishikawa, R., and Ashikari, M. (2013). OsLG1 regulates a closed panicle trait in domesticated rice. Nat Genet 45, 462-465, 465e461-462. Ishikawa, R., Toki, N., Imai, K., Sato, Y., Yamagishi, H., Shimamoto, Y., Ueno, K., Morishima, H., and Sato, T. (2005). Origin of weedy rice grown in Bhutan and the force of genetic diversity. Genetic Resources and Crop Evolution 52, 395-403. Itoh, H., and Izawa, T. (2013). The coincidence of critical day length recognition for florigen gene expression and floral transition under long-day conditions in rice. Molecular Plant 6, 635-649. Itoh, H., Nonoue, Y., Yano, M., and Izawa, T. (2010). A pair of floral regulators sets critical day length for Hd3a florigen expression in rice. Nature genetics 42, 635. Itoh, H., Wada, K.C., Sakai, H., Shibasaki, K., Fukuoka, S., Wu, J., Yonemaru, J.i., Yano, M., and Izawa, T. (2018). Genomic adaptation of flowering‐time genes during the expansion of rice cultivation area. The Plant Journal 94, 895-909. Jacquemin, J., Bhatia, D., Singh, K., and Wing, R.A. (2013). The International Oryza Map Alignment Project: development of a genus-wide comparative genomics platform to help solve the 9 billion-people question. Current Opinion in Plant Biology 16, 147-156. Jin, J., Huang, W., Gao, J.P., Yang, J., Shi, M., Zhu, M.Z., Luo, D., and Lin, H.X. (2008). Genetic control of rice plant architecture under domestication. Nat Genet 40, 1365-1369. Jodon, N. (1940). Inheritance and linkage relationships of a chlorophyll mutation in rice. Agronomy Journal 32, 342-346. Kashiwagi, T., and Ishimaru, K. (2004). Identification and functional analysis of a locus for improvement of lodging resistance in rice. Plant Physiology 134, 676-683. Kashiwagi, T., Madoka, Y., Hirotsu, N., and Ishimaru, K. (2006). Locus prl5 improves lodging resistance of rice by delaying senescence and increasing carbohydrate reaccumulation. Plant Physiology and Biochemistry 44, 152-157. Kashiwagi, T., Togawa, E., Hirotsu, N., and Ishimaru, K. (2008). Improvement of lodging resistance with QTLs for stem diameter in rice (Oryza sativa L.). Theoretical and Applied Genetics 117, 749-757. Kato, S., Kosaka, H., and Hara, S. (1930). On the affinity of the cultivated varieties of rice plants, Oryza sativa L. J Dept Agric Kyushu Imp Univ 2, 241-276. Kawahara, Y., de la Bastide, M., Hamilton, J.P., Kanamori, H., McCombie, W.R., Ouyang, S., Schwartz, D.C., Tanaka, T., Wu, J., Zhou, S., Childs, K.L., Davidson, R.M., Lin, H., Quesada-Ocampo, L., Vaillancourt, B., Sakai, H., Lee, S.S., Kim, J., Numa, H., Itoh, T., Buell, C.R., and Matsumoto, T. (2013). Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data. Rice 6, 4. Keller, M., Karutz, C., Schmid, J., Stamp, P., Winzeler, M., Keller, B., and Messmer, M. (1999). Quantitative trait loci for lodging resistance in a segregating wheat× spelt population. Theoretical and Applied Genetics 98, 1171-1182. Khush, G.S. (1995). Modern varieties—their real contribution to food supply and equity. GeoJournal 35, 275-284. Khush, G.S. (1997). Origin, dispersal, cultivation and variation of rice. Plant Molecular Biology 35, 25-34. Khush, G.S. (1999). Green revolution: preparing for the 21st century. Genome 42, 646-655. Kikuchi, F. (1985). Genetic analysis of semi-dwarfism in high yielding rice varieties in Japan. Bull. Nat. Inst. Agr. Sc., Ser. D 36, 125-145. Kim, S.-R., Torollo, G., Yoon, M.-R., Kwak, J., Lee, C.-K., Prahalada, G., Choi, I.-R., Yeo, U.-S., Jeong, O., and Jena, K.K. (2018). Loss-of-Function Alleles of Heading Date 1 (Hd1) Are Associated With Adaptation of Temperate Japonica Rice Plants to the Tropical Region. Frontiers in plant science 9, 1827. Kinoshita, T. (1998). Report of the committee on gene symbolization, nomenclature and linkage groups. II. Linkage mapping using mutant genes in rice. Rice Genet Newsl 15, 13-74. Komiya, R., Ikegami, A., Tamaki, S., Yokoi, S., and Shimamoto, K. (2008). Hd3a and RFT1 are essential for flowering in rice. Development 135, 767-774. Korotkov, E.V., Kamionskya, A.M., and Korotkova, M.A. (2021). Detection of Highly Divergent Tandem Repeats in the Rice Genome. Genes 12, 473. Kovach, M.J., Sweeney, M.T., and McCouch, S.R. (2007). New insights into the history of rice domestication. Trends in Genetics 23, 578-587. Kudo, M. (1968). Genetical and thremmatological studies of characters, physiological or ecological, in the hybrids between ecological rice groups. Bull. Nat. Inst. Agric. Sci. D 19, 1-84. Kumar, S., Stecher, G., and Tamura, K. (2016). MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Molecular Biology and Evolution 33, 1870-1874. Lange, M.P., and Lange, T. (2006). Gibberellin biosynthesis and the regulation of plant development. Plant Biology 8, 281-290. Larson, G., Piperno, D.R., Allaby, R.G., Purugganan, M.D., Andersson, L., Arroyo-Kalin, M., Barton, L., Vigueira, C.C., Denham, T., and Dobney, K. (2014). Current perspectives and the future of domestication studies. Proceedings of the National Academy of Sciences 111, 6139-6146. Lee, J., Park, J.-J., Kim, S.L., Yim, J., and An, G. (2007). Mutations in the rice liguleless gene result in a complete loss of the auricle, ligule, and laminar joint. Plant Molecular Biology 65, 487-499. Li, C.B., Zhou, A.L., and Sang, T. (2006). Rice domestication by reducing shattering. Science 311, 1936-1939. Li, H. (2011). A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics 27, 2987-2993. Li, H. (2013). Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv preprint arXiv:1303.3997. Li, H., and Durbin, R. (2010). Fast and accurate long-read alignment with Burrows–Wheeler transform. Bioinformatics 26, 589-595. Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., and Durbin, R. (2009). The sequence alignment/map format and SAMtools. Bioinformatics 25, 2078-2079. Li, J.-Y., Wang, J., and Zeigler, R.S. (2014). The 3,000 rice genomes project: new opportunities and challenges for future rice research. Gigascience 3, 2047-2217X-2043-2048. Li, L.-F., Li, Y.-L., Jia, Y., Caicedo, A.L., and Olsen, K.M. (2017). Signatures of adaptation in the weedy rice genome. Nature genetics 49, 811-814. Li, P.J. (2002). Preliminary interpretations of the 15 recently uncovered Sinkang manuscripts. Taiwan Historical Research 9, 1-68. Lin, H., Ashikari, M., Yamanouchi, U., Sasaki, T., and Yano, M. (2002). Identification and characterization of a quantitative trait locus, Hd9, controlling heading date in rice. Breeding Science 52, 35-41. Lin, S., Sasaki, T., and Yano, M. (1998). Mapping quantitative trait loci controlling seed dormancy and heading date in rice, Oryza sativa L., using backcross inbred lines. Theoretical and Applied Genetics 96, 997-1003. Lin, Z., Griffith, M.E., Li, X., Zhu, Z., Tan, L., Fu, Y., Zhang, W., Wang, X., Xie, D., and Sun, C. (2007). Origin of seed shattering in rice (Oryza sativa L.). Planta 226, 11-20. Liu, C., Song, G., Zhou, Y., Qu, X., Guo, Z., Liu, Z., Jiang, D., and Yang, D. (2015). OsPRR37 and Ghd7 are the major genes for general combining ability of DTH, PH and SPP in rice. Scientific Reports 5, 1-11. Liu, C., Zheng, S., Gui, J., Fu, C., Yu, H., Song, D., Shen, J., Qin, P., Liu, X., Han, B., Yang, Y., and Li, L. (2018). Shortened basal internodes encodes a gibberellin 2-oxidase and contributes to lodging resistance in rice. Mol Plant 11, 288-299. Luan, W., Chen, H., Fu, Y., Si, H., Peng, W., Song, S., Liu, W., Hu, G., Sun, Z., and Xie, D. (2009). The effect of the crosstalk between photoperiod and temperature on the heading-date in rice. PLoS One 4. Luo, J., Liu, H., Zhou, T., Gu, B., Huang, X., Shangguan, Y., Zhu, J., Li, Y., Zhao, Y., Wang, Y., Zhao, Q., Wang, A., Wang, Z., Sang, T., Wang, Z., and Han, B. (2013). An-1 encodes a basic helix-loop-helix protein that regulates awn development, grain size, and grain number in rice. Plant Cell 25, 3360-3376. Mackill, D.J., and Rutger, J. (1979). The inheritance of induced-mutant semidwarfing genes in rice. Journal of Heredity 70, 335-341. Mansueto, L., Fuentes, R.R., Borja, F.N., Detras, J., Abriol-Santos, J.M., Chebotarov, D., Sanciangco, M., Palis, K., Copetti, D., and Poliakov, A. (2017). Rice SNP-seek database update: new SNPs, indels, and queries. Nucleic acids research 45, D1075-D1081. Matsuo, T., and Hoshikawa, K. (1993). Science of the rice plant. (Food and Agriculture Policy Research Center Tokyo). McKenna, A., Hanna, M., Banks, E., Sivachenko, A., Cibulskis, K., Kernytsky, A., Garimella, K., Altshuler, D., Gabriel, S., Daly, M., and DePristo, M.A. (2010). The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data. Genome Research 20, 1297-1303. McLaren, C.G., Bruskiewich, R.M., Portugal, A.M., and Cosico, A.B. (2005). The International Rice Information System. A platform for meta-analysis of rice crop data. Plant Physiology 139, 637-642. Merrey, D.J., Mondal, M.K., Hoanh, C.T., Humphreys, E., and Dao, N. (2018). Agricultural Development and Sustainable Intensification (Routledge. Meyer, R.S., and Purugganan, M.D. (2013). Evolution of crop species: genetics of domestication and diversification. Nature Reviews Genetics 14, 840. Nagano, H., Onishi, K., Ogasawara, M., Horiuchi, Y., and Sano, Y. (2005). Genealogy of the “Green Revolution” gene in rice. Genes Genetic Systems 80, 351-356. Neeraja, C.N., Vemireddy, L.R., Malathi, S., and Siddiq, E.A. (2009). Identification of alternate dwarfing gene sources to widely used Dee-Gee-Woo-Gen allele of sd1 gene by molecular and biochemical assays in rice (Oryza sativa L.). Electronic Journal of Biotechnology, 12.3, 7-8. Ohyanagi, H., Tanaka, T., Sakai, H., Shigemoto, Y., Yamaguchi, K., Habara, T., Fujii, Y., Antonio, B.A., Nagamura, Y., and Imanishi, T. (2006). The Rice Annotation Project Database (RAP-DB): hub for Oryza sativa ssp. japonica genome information. Nucleic Acids Research 34, D741-D744. Oka, H. (1958). Intervarietal variation and classification of cultivated rice. Ind. J. Genet. Plant Breed. 18, 79-89. Olsen, K.M., and Wendel, J.F. (2013). Crop plants as models for understanding plant adaptation and diversification. Frontiers in plant science 4, 290. Ookawa, T., and Ishihara, K. (1992). Varietal difference of physical characteristics of the culm related to lodging resistance in paddy rice. Japanese Journal of Crop Science 61, 419-425. Ortiz, E. (2019). vcf2phylip v2. 0: convert a VCF matrix into several matrix formats for phylogenetic analysis. URL https://doi. org/10.5281/zenodo 2540861. Panesar, P.S., and Kaur, S. (2016). Rice: Types and Composition. In Encyclopedia of Food and Health, pp. 646-652. Parfitt, J., Barthel, M., and Macnaughton, S. (2010). Food waste within food supply chains: quantification and potential for change to 2050. Philosophical Transactions of the Royal Society B: Biological Sciences 365, 3065-3081. Pawley, A. (2002). The Austronesian dispersal: Languages, technologies, people. In Examining the farming/language dispersal hypothesis (McDonald Institute for Archaeological Research. Poplin, R., Ruano-Rubio, V., DePristo, M.A., Fennell, T.J., Carneiro, M.O., Van der Auwera, G.A., Kling, D.E., Gauthier, L.D., Levy-Moonshine, A., and Roazen, D. (2018). Scaling accurate genetic variant discovery to tens of thousands of samples. BioRxiv, 201178. Prathepha, P. (2009). The fragrance (fgr) gene in natural populations of wild rice (Oryza rufipogon Griff.). Genetic Resources and Crop Evolution 56, 13-18. Purugganan, M.D. (2019). Evolutionary Insights into the Nature of Plant Domestication. Current Biology 29, R705-R714. Purugganan, M.D., and Fuller, D.Q. (2009). The nature of selection during plant domestication. Nature 457, 843-848. Qiu, J., Zhu, J., Fu, F., Ye, C.-Y., Wang, W., Mao, L., Lin, Z., Chen, L., Zhang, H., and Guo, L. (2014). Genome re-sequencing suggested a weedy rice origin from domesticated indica-japonica hybridization: a case study from southern China. Planta 240, 1353-1363. Qiu, J., Zhou, Y., Mao, L., Ye, C., Wang, W., Zhang, J., Yu, Y., Fu, F., Wang, Y., and Qian, F. (2017). Genomic variation associated with local adaptation of weedy rice during de-domestication. Nature Communications 8, 1-12. R Core Team. (2013). R: A language and environment for statistical computing. Reagon, M., Thurber, C.S., Gross, B.L., Olsen, K.M., Jia, Y., and Caicedo, A.L. (2010). Genomic patterns of nucleotide diversity in divergent populations of US weedy rice. BMC Evolutionary Biology 10, 180. Rice Annotation Project. (2007). The rice annotation project database (RAP-DB): 2008 update. Nucleic Acids Research 36, D1028-D1033. Rindos, D. (2013). The origins of agriculture: an evolutionary perspective. (Academic Press). Robinson, J.T., Thorvaldsdóttir, H., Wenger, A.M., Zehir, A., and Mesirov, J.P. (2017). Variant review with the integrative genomics viewer. Cancer Research 77, e31-e34. Robinson, J.T., Thorvaldsdóttir, H., Winckler, W., Guttman, M., Lander, E.S., Getz, G., and Mesirov, J.P. (2011). Integrative genomics viewer. Nature Biotechnology 29, 24-26. Robson, F., Costa, M.M.R., Hepworth, S.R., Vizir, I., Pin˜ eiro, M., Reeves, P.H., Putterill, J., and Coupland, G. (2001). Functional importance of conserved domains in the flowering‐time gene CONSTANS demonstrated by analysis of mutant alleles and transgenic plants. The Plant Journal 28, 619-631. Rozas, J., Ferrer-Mata, A., Sánchez-DelBarrio, J.C., Guirao-Rico, S., Librado, P., Ramos-Onsins, S.E., and Sánchez-Gracia, A. (2017). DnaSP 6: DNA sequence polymorphism analysis of large data sets. Molecular Biology and Evolution 34, 3299-3302. Sagart, L., Jacques, G., Lai, Y., Ryder, R.J., Thouzeau, V., Greenhill, S.J., and List, J.-M. (2019). Dated language phylogenies shed light on the ancestry of Sino-Tibetan. Proceedings of the National Academy of Sciences 116, 10317-10322. Sagart, L., Hsu, T.F., Tsai, Y.C., Wu, C.C., Huang, L.T., Chen, Y.C., Chen, Y.F., Tseng, Y.C., Lin, H.Y., and Hsing, Y.C. (2018). A northern Chinese origin of Austronesian agriculture: new evidence on traditional Formosan cereals. Rice (N Y) 11, 57. Saitou, N., and Nei, M. (1987). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406-425. Sakai, H., Lee, S.S., Tanaka, T., Numa, H., Kim, J., Kawahara, Y., Wakimoto, H., Yang, C.-c., Iwamoto, M., and Abe, T. (2013). Rice Annotation Project Database (RAP-DB): an integrative and interactive database for rice genomics. Plant and Cell Physiology 54, e6-e6. Sakai, H., Kanamori, H., Arai-Kichise, Y., Shibata-Hatta, M., Ebana, K., Oono, Y., Kurita, K., Fujisawa, H., Katagiri, S., Mukai, Y., Hamada, M., Itoh, T., Matsumoto, T., Katayose, Y., Wakasa, K., Yano, M., and Wu, J. (2014). Construction of pseudomolecule sequences of the aus rice cultivar Kasalath for comparative genomics of Asian cultivated rice. DNA Res 21, 397-405. Sasaki, A., Ashikari, M., Ueguchi-Tanaka, M., Itoh, H., Nishimura, A., Swapan, D., Ishiyama, K., Saito, T., Kobayashi, M., and Khush, G.S. (2002). A mutant gibberellin-synthesis gene in rice. Nature 416, 701-702. Saunders, R. (1985). Rice bran: composition and potential food uses. Food Reviews International 1, 465-495. Schatz, M.C., Maron, L.G., Stein, J.C., Wences, A.H., Gurtowski, J., Biggers, E., Lee, H., Kramer, M., Antoniou, E., and Ghiban, E. (2014). Whole genome de novo assemblies of three divergent strains of rice, Oryza sativa, document novel gene space of aus and indica. Genome Biology 15, 1-16. Schiere, J., and Ibrahim, M. (1989). Feeding of urea-ammonia treated rice straw. (Centre for Agricultural Publications and Documentation). Seck, P.A., Diagne, A., Mohanty, S., and Wopereis, M.C. (2012). Crops that feed the world 7: Rice. Food Security 4, 7-24. Shrestha, R., Gómez-Ariza, J., Brambilla, V., and Fornara, F. (2014). Molecular control of seasonal flowering in rice, arabidopsis and temperate cereals. Annals of Botany 114, 1445-1458. Song, B.K., Chuah, T.S., Tam, S.M., and Olsen, K.M. (2014). Malaysian weedy rice shows its true stripes: wild Oryza and elite rice cultivars shape agricultural weed evolution in Southeast Asia. Molecular Ecology 23, 5003-5017. Spielmeyer, W., Ellis, M.H., and Chandler, P.M. (2002). Semidwarf (sd-1),“green revolution” rice, contains a defective gibberellin 20-oxidase gene. Proceedings of the National Academy of Sciences 99, 9043-9048. Stein, J.C., Yu, Y., Copetti, D., Zwickl, D.J., Zhang, L., Zhang, C., Chougule, K., Gao, D., Iwata, A., Goicoechea, J.L., Wei, S., Wang, J., Liao, Y., Wang, M., Jacquemin, J., Becker, C., Kudrna, D., Zhang, J., Londono, C.E.M., Song, X., Lee, S., Sanchez, P., Zuccolo, A., Ammiraju, J.S.S., Talag, J., Danowitz, A., Rivera, L.F., Gschwend, A.R., Noutsos, C., Wu, C.C., Kao, S.M., Zeng, J.W., Wei, F.J., Zhao, Q., Feng, Q., El Baidouri, M., Carpentier, M.C., Lasserre, E., Cooke, R., Rosa Farias, D.D., da Maia, L.C., Dos Santos, R.S., Nyberg, K.G., McNally, K.L., Mauleon, R., Alexandrov, N., Schmutz, J., Flowers, D., Fan, C., Weigel, D., Jena, K.K., Wicker, T., Chen, M., Han, B., Henry, R., Hsing, Y.C., Kurata, N., de Oliveira, A.C., Panaud, O., Jackson, S.A., Machado, C.A., Sanderson, M.J., Long, M., Ware, D., and Wing, R.A. (2018). Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza. Nat Genet 50, 285-296. Sun, J., Qian, Q., Ma, D.R., Xu, Z.J., Liu, D., Du, H.B., and Chen, W.F. (2013). Introgression and selection shaping the genome and adaptive loci of weedy rice in northern China. New Phytologist 197, 290-299. Sun, J., Ma, D., Tang, L., Zhao, M., Zhang, G., Wang, W., Song, J., Li, X., Liu, Z., and Zhang, W. (2019). Population genomic analysis and de novo assembly reveal the origin of weedy rice as an evolutionary game. Molecular Plant 12, 632-647. Sweeney, M., and McCouch, S. (2007). The Complex History of the Domestication of Rice. Annals of Botany 100, 951-957. Sweeney, M.T., Thomson, M.J., Pfeil, B.E., and McCouch, S. (2006). Caught red-handed: Rc encodes a basic helix-loop-helix protein conditioning red pericarp in rice. The Plant Cell 18, 283-294. Sweeney, M.T., Thomson, M.J., Cho, Y.G., Park, Y.J., Williamson, S.H., Bustamante, C.D., and McCouch, S.R. (2007). Global dissemination of a single mutation conferring white pericarp in rice. PLoS Genet 3……… | |
| dc.identifier.uri | http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/81944 | - |
| dc.description.abstract | "亞洲稻米（Oryza sativa）由馴化地傳播至南亞、東亞以及東南亞對於社會及文化造成巨大影響，水稻的馴化及在地適應均提供極好的模型以研究水稻的傳播以及生長。突變導致形態和生理性狀改變，而後經人為的選拔、遷徙擴散後，導致適合不同環境的外表型。藉由抽穗期基因 (Heading date 1, HD1) 的序列訊息以研究不同地區的序列變化與水稻開花性狀的關聯性。前人研究中已有許多著重於基因單倍型 (haplotype)。本篇研究中通過基因體序列分析，發現另外3種新的基因單倍型。藉由抽穗期功能性基因單倍型的分析，發現人為選拔出喪失功能的基因單倍型分布於亞熱帶及熱帶地區。其中一些基因單倍型僅在局部地區發現，然而，包含地方品系及現在栽培稻，全世界超過三分之一的稻米品系中皆發現第7及第13型基因單倍型。藉由親緣關係、基因單倍型網狀以及選擇壓力等分析，我們證實這兩種基因單倍型可能首先發生於東南亞島嶼地區，隨後滲入至附近其他地區的地方品系中。同時經比較野生稻序列數據後，我們建議這些喪失功能的基因單倍型發生於農田系統中，而非來自於野生稻。 距今60年前，著名的半矮化且高產的水稻品系IR8被育成及推廣，被稱為造成「綠色奇蹟」的亞洲水稻品系。根據遺傳分析得知，這個關鍵的性狀是由位於第一條染色體上喪失功能的半矮性基因 (semi-dwarf 1, SD1) 所引起。前人研究中發現核苷酸的缺失或單一核苷酸多態性導致吉貝素氧化酶 (GA20 oxidase 2)的缺陷。在本篇研究中進行三千個稻米品系基因體序列 (3K RGP) 分析，發現更多的突變類型也可能導致半矮性基因功能喪失。儘管稉稻與秈稻均帶有半矮性基因突變，相較於所有現代秈稻品系，只有少數現代稉稻品系使用突變的等位基因。我們建議此具有383 鹼基對缺失的第7型半矮性等位基因至少500年前首次出現於中國南方的農田中，隨後由漢人遷移到台灣。而傳播至台灣的品系可能為低腳烏尖及新竹矮腳尖。 本篇研究利用全基因體重測序數據重建台灣與相鄰區域之稻米地方品系之親緣以及傳播關係。相較於相鄰地區的稻米，由台灣原住民地區栽種的稻米品系其親緣及族群關係較為複雜。台灣的稉稻分別與東南亞、中南半島、日本、韓國以及中國的稉稻群集。這一發現闡明台灣的稉稻與鄰近地區間存在密切的遺傳關係。此外，五千年前抵達台灣的稉稻應屬於溫帶型稉稻，秈稻較晚抵達台灣。隨後我們針對抽穗期基因及半矮性基因進行基因單倍型網狀分析，發現稻米的傳播與在地適應有關。本篇研究揭示台灣原住民種植的傳統地方品系稻米與周邊地區的關係，並將聯繫此關聯與稉稻在北亞、南亞、東南亞的傳播。當重建稻米馴化後傳播歷史後，我們將持續關注氣候變遷、人類遷徙活動以及在地適應導致水稻多樣性。" | zh_TW |
| dc.description.provenance | Made available in DSpace on 2022-11-25T03:07:10Z (GMT). No. of bitstreams: 1 U0001-3008202110525300.pdf: 65036472 bytes, checksum: ee07d902a77abd968e76bc28dd355e09 (MD5) Previous issue date: 2021 | en |
| dc.description.tableofcontents | "口試委員審定書 I 謝詞 II 中文摘要 III ABSTRACT V CHAPTER 1: INTRODUCTION 1 1.1 THE IMPORTANCE OF RICE 1 1.2 CLASSIFICATION OF RICE 1 1.3 RICE REFERENCE GENOME SEQUENCES 3 1.4 MANY RE-SEQUENCING PROJECTS ARE AVAILABLE 4 1.5 DOMESTICATION OF ASIAN RICE 6 1.6 ADAPTATION OF ASIAN RICE 8 1.7 THE EARLY RICE CULTIVATION IN TAIWAN 11 1.8 AUSTRONESIAN PREHISTORY IN SOUTHEAST ASIA 12 1.9 BRIEFING OF THE STUDY 14 CHAPTER 2: STUDIES OF RICE HD1 HAPLOTYPES WORLDWIDE REVEAL ADAPTATION OF FLOWERING TIME TO DIFFERENT ENVIRONMENTS 15 2.1 ABSTRACT 15 2.2 INTRODUCTION 17 2.3 MATERIALS AND METHODS 20 2.3.1 Classification of Hd1 haplotypes and DNA sequence analyses 20 2.3.2 Estimation of diversity of different Hd1 haplotypes 22 2.4 RESULTS 23 2.4.1 Many LOF haplotypes are present in rice accessions 23 2.4.2 Many accessions have types 7 or 13 LOF hd1, as revealed by the 3K genome data 25 2.4.3 The 1.9-kb insertion in type 19 is a small retrotransposon 26 2.4.4 Other haplotypes occurred in local regions 26 2.4.5 LOF haplotypes also found in Chinese weedy rice accessions and an African wild rice accession 27 2.4.6 Phylogenetic and haplotype network analyses of types 7 and 13 28 2.5 DISCUSSION 30 2.5.1 Hd1 was suggested to be the main allele associated with adaptation of rice plants to tropical regions 31 2.5.2 Several Hd1 haplotypes were limited to small regions and some were widely spread 32 2.5.3 Some weedy rice or wild rice accessions also contained LOF hd1 33 2.5.4 LOF hd1 mutations occurred in agro 34 2.5.5 A 36-bp deletion in the first ORF of Nipponbare genome 35 2.5.6 Introgressions and human activities played important roles for rice diversification/adaptation as revealed by the Hd1 gene region 36 2.6 CONCLUSIONS 37 2.7 TABLES AND FIGURES 38 2.8 SUPPLEMENTARY TABLES AND FIGURES 45 CHAPTER 3: STUDIES OF RICE SD1 HAPLOTYPES IN THE 3K DATASET REVEAL THE IMPORTANT DOMAINS OF THE ENZYME GA20 OXIDASE 58 3.1 ABSTRACT 58 3.2 INTRODUCTION 60 3.3 MATERIALS AND METHODS 62 3.3.1 Classification of sd1 haplotypes and DNA sequence analysis 62 3.3.2 Estimation of diversity of different sd1 haplotypes 63 3.4 RESULTS 63 3.4.1 Many sd1 haplotypes are present in rice accessions 63 3.4.2 The origins of sd1 haplotypes 66 3.4.3 Alignment and missense mutations indicate the important domain for GA20 oxidase 71 3.5 DISCUSSION 71 3.5.1 Detailed analysis of GR/EQ/ER types in the 3K population 72 3.5.2 Tajima D indicated no selective sweep of most sd1 mutations 73 3.5.3 Many indica modern varieties have sd1 functional nucleotide polymorphisms 73 3.6 CONCLUSIONS 74 3.7 TABLES AND FIGURES 76 3.8 SUPPLEMENTARY TABLES AND FIGURES 82 CHAPTER 4: PRELIMINARY STUDIES ON THE RELATIONSHIP OF TAIWAN RICE ACCESSIONS WITH ADJACENT REGIONS 104 4.1 INTRODUCTION 105 4.2 MATERIALS AND METHOD 106 4.2.1 Sequencing data 106 4.2.2 Sequence alignment and genotype calling 107 4.2.3 Phylogenetic analyses 108 4.2.4 PCA, admixture, and haplotype network analysis 109 4.2.5 Phenotypic and passport data 110 4.3 RESULTS 110 4.3.1 Sequence and geographic structure of rice genomic diversity 110 4.3.2 Allele network analysis of the 4 domestication genes: PROG1, Sh4, Bh4, and An-2/LABA1 116 4.3.3 Allele network analysis of the 2 adaptation genes: Hd1 and SD1 117 4.4 DISCUSSION 121 4.5 TABLES AND FIGURE 125 4.6 SUPPLEMENTARY TABLES AND FIGURE 137 CHAPTER 5: CONCLUSIONS 150 REFERENCES 152 APPENDIX 165 " | |
| dc.language.iso | en | |
| dc.subject | 半矮性 | zh_TW |
| dc.subject | 抽穗期基因 | zh_TW |
| dc.subject | 單一核苷酸多型性 | zh_TW |
| dc.subject | 序列的插入與刪除 | zh_TW |
| dc.subject | 在地適應 | zh_TW |
| dc.subject | 馴化 | zh_TW |
| dc.subject | Indels | en |
| dc.subject | adaptation | en |
| dc.subject | domestication | en |
| dc.subject | heading date | en |
| dc.subject | semi-dwarf | en |
| dc.subject | SNPs | en |
| dc.title | 利用比較基因體學探討水稻之在地適應關係 | zh_TW |
| dc.title | "Comparative genomics analyses of cultivated, primitive, and wild rice –focusing on adaptation" | en |
| dc.date.schoolyear | 109-2 | |
| dc.description.degree | 博士 | |
| dc.contributor.author-orcid | 0000-0002-5495-9095 | |
| dc.contributor.coadvisor | 吳克強(Keqiang Wu) | |
| dc.contributor.oralexamcommittee | 李承叡(Hsin-Tsai Liu),董致韡(Chih-Yang Tseng),鍾國芳,伊藤剛 | |
| dc.subject.keyword | 馴化,在地適應,抽穗期基因,半矮性,單一核苷酸多型性,序列的插入與刪除, | zh_TW |
| dc.subject.keyword | adaptation,domestication,heading date,semi-dwarf,SNPs,Indels, | en |
| dc.relation.page | 180 | |
| dc.identifier.doi | 10.6342/NTU202102838 | |
| dc.rights.note | 同意授權(全球公開) | |
| dc.date.accepted | 2021-08-31 | |
| dc.contributor.author-college | 生命科學院 | zh_TW |
| dc.contributor.author-dept | 植物科學研究所 | zh_TW |
| dc.date.embargo-lift | 2023-08-30 | - |
| 顯示於系所單位： | 植物科學研究所 | |
文件中的檔案：
| 檔案 | 大小 | 格式 | |
|---|---|---|---|
| U0001-3008202110525300.pdf | 63.51 MB | Adobe PDF | 檢視/開啟 |
系統中的文件，除了特別指名其著作權條款之外，均受到著作權保護，並且保留所有的權利。