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http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/1299完整後設資料紀錄
| DC 欄位 | 值 | 語言 |
|---|---|---|
| dc.contributor.advisor | 黃永芬(Yung-Fen Huang) | |
| dc.contributor.author | Tzu-Han Weng | en |
| dc.contributor.author | 翁子涵 | zh_TW |
| dc.date.accessioned | 2021-05-12T09:35:50Z | - |
| dc.date.available | 2020-01-01 | |
| dc.date.available | 2021-05-12T09:35:50Z | - |
| dc.date.copyright | 2018-03-05 | |
| dc.date.issued | 2018 | |
| dc.date.submitted | 2018-02-06 | |
| dc.identifier.citation | 李長沛 (2010) 野生稻Oryza nivara、Oryza officinalis、Oryza australiensis基因導入與育種上之利用。博士論文，國立中興大學，臺中市
Andrews S (2010) FastQC : a quality control tool for high throughput sequence data. http://www.bioinformatics.babraham.ac.uk/projects/fastqc/. Accessed 11 April 2016 Athwal D, Pathak M, Bacalangco E, Pura C (1971) Genetics of resistance to brown planthoppers and green leafhoppers in Oryza sativa L. Crop Sci 11:747-750 Baird NA, Etter PD, Atwood TS, Currey MC, Shiver AL, Lewis ZA, Selker EU, Cresko WA, Johnson EA (2008) Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLoS One 3:e3376 Barbazuk WB, Emrich SJ, Chen HD, Li L, Schnable PS (2007) SNP discovery via 454 transcriptome sequencing. Plant J 51:910-918 Barman SR, Gowda M, Venu RC, Chattoo BB (2004) Identification of a major blast resistance gene in the rice cultivar ‘Tetep’. Plant Breed 123:300-302 Berruyer R, Adreit H, Milazzo J, Gaillard S, Berger A, Dioh W, Lebrun M-H, Tharreau D (2003) Identification and fine mapping of Pi33, the rice resistance gene corresponding to the Magnaporthe grisea avirulence gene ACE1. Theor Appl Genet 107:1139-1147 Bhasin H, Bhatia D, Raghuvanshi S, Lore JS, Sahi GK, Kaur B, Vikal Y, Singh K (2012) New PCR-based sequence-tagged site marker for bacterial blight resistance gene Xa38 of rice. Mol Breed 30:607-611 Blair MW, Garris AJ, Iyer AS, Chapman B, Kresovich S, McCouch SR (2003) High resolution genetic mapping and candidate gene identification at the xa5 locus for bacterial blight resistance in rice (Oryza sativa L.). Theor Appl Genet 107:62-73 Bouharmont J (1961) Embryo culture of rice on sterile medium. Euphytica 10:283-293 Bradbury PJ, Zhang Z, Kroon DE, Casstevens TM, Ramdoss Y, Buckler ES (2007) TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics 23:2633-2635 Brar DS, Dalmacio R, Elloran R, Aggarwal R, G.S. K (1996) Gene transfer and molecular characterization of introgression from wild Oryza species into rice Third International Rice Genetics Symposium, IRRI, Manila (Philippines), 3:477–486 Brar DS, Khush GS (1997) Alien introgression in rice. Plant Mol Biol 35:35–47 Broman KW, Wu H, Sen Ś, Churchill GA (2003) R/qtl: QTL mapping in experimental crosses. Bioinformatics 19:889-890 Brozynska M, Furtado A, Henry RJ (2016) Genomics of crop wild relatives: expanding the gene pool for crop improvement. Plant Biotechnol J 14:1070-1085 Busungu C, Taura S, Sakagami J-I, Ichitani K (2016) Identification and linkage analysis of a new rice bacterial blight resistance gene from XM14, a mutant line from IR24. Breed Sci 66:636-645 Cai Hwahm (1998) Mapping QTLs for heading behavior using RI population derived from a cross between wild and cultivated rice strains. Rice Genet Newsl 15:144-146 Catchen J, Hohenlohe PA, Bassham S, Amores A, Cresko WA (2013) Stacks: an analysis tool set for population genomics. Mol Ecol 22:3124-3140 Catchen JM, Amores A, Hohenlohe P, Cresko W, Postlethwait JH (2011) Stacks: building and genotyping Loci de novo from short-read sequences. G3:Genes- Genomes-Genetics (Bethesda) 1:171-182 Causse MA, Fulton TM, Cho YG, Ahn SN, Chunwongse J, Wu K, Xiao J, Yu Z, Ronald PC, Harrington SE (1994) Saturated molecular map of the rice genome based on an interspecific backcross population. Genetics 138:1251-1274 Che K, Zhan Q, Xing Q, Wang Z, Jin D, He D, Wang B (2003) Tagging and mapping of rice sheath blight resistant gene. Theor Appl Genet 106:293-297 Cheema KK, Grewal NK, Vikal Y, Sharma R, Lore JS, Das A, Bhatia D, Mahajan R, Gupta V, Bharaj TS, Singh K (2008) A novel bacterial blight resistance gene from Oryza nivara mapped to 38 kb region on chromosome 4L and transferred to Oryza sativa L. Genet Res (Camb) 90:397-407 Chen A-L, Liu C-Y, Chen C-H, Wang J-F, Liao Y-C, Chang C-H, Tsai M-H, Hwu K-K, Chen K-Y (2014) Reassessment of QTLs for late blight resistance in the tomato accession L3708 using a restriction site associated DNA (RAD) linkage map and highly aggressive isolates of phytophthora infestans. PLoS One 9:e96417 Chen H, Boutros PC (2011) VennDiagram: a package for the generation of highly-customizable Venn and Euler diagrams in R. BMC Bioinformatics 12:35 Chen S, Liu X, Zeng L, Ouyang D, Yang J, Zhu X (2011) Genetic analysis and molecular mapping of a novel recessive gene xa34(t) for resistance against Xanthomonas oryzae pv. oryzae. Theor Appl Genet 122:1331-1338 Chen XW, Li SG, Xu JC, Zhai WX, Ling ZZ, Ma BT, Wang YP, Wang WM, Cao G, Ma YQ, Shang JJ, Zhao XF, Zhou KD, Zhu LH (2004) Identification of two blast resistance genes in a rice variety, Digu. J Phytopathol 152:77-85 Choi SC, Lee S, Kim S-R, Lee Y-S, Liu C, Cao X, An G (2014) Trithorax group protein Oryza sativa trithorax1 controls flowering time in rice via interaction with early heading date3. Plant Physiol 164:1326-1337 Churchill GA, Doerge RW (1994) Empirical threshold values for quantitative trait mapping. Genetics 138:963-971 Dempewolf H, Eastwood RJ, Guarino L, Khoury CK, Müller JV, Toll J (2014) Adapting agriculture to climate change: A global initiative to collect, conserve, and use crop wild relatives. Agroecology and Sustainable Food Systems 38:369-377 Dong NV, Subudhi PK, Luong PN, Quang VD, Quy TD, Zheng HG, Wang B, Nguyen HT (2000) Molecular mapping of a rice gene conditioning thermosensitive genic male sterility using AFLP, RFLP and SSR techniques. Theor Appl Genet 100:727-734 Edwards D, Batley J (2010) Plant genome sequencing: applications for crop improvement. Plant Biotechnol J 8:2-9 Egan AN, Schlueter J, Spooner DM (2012) Applications of next-generation sequencing in plant biology. Bot Soc Am 99:175-185 Eizenga G, Lee F, Rutger J (2002) Screening Oryza species plants for rice sheath blight resistance. Plant Dis 86:808-812 Elshire RJ, Glaubitz JC, Sun Q, Poland JA, Kawamoto K, Buckler ES, Mitchell SE (2011) A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS One 6:e19379 Fan C, Xing Y, Mao H, Lu T, Han B, Xu C, Li X, Zhang Q (2006) GS3, a major QTL for grain length and weight and minor QTL for grain width and thickness in rice, encodes a putative transmembrane protein. Theor Appl Genet 112:1164-1171 Feng F, Xu X, Du X, Tong H, Luo L, Mei H (2012) Assessment of drought resistance among wild rice accessions using a protocol based on single-tiller propagation and PVC-tube cultivation. Aust J Crop Sci 6:1204-1211 Fukuoka S, Okuno K (2001) QTL analysis and mapping of pi21, a recessive gene for field resistance to rice blast in Japanese upland rice. Theor Appl Genet 103:185-190 Fukuta Y, Yanoria MJT, Mercado-Escueta D, Ebron LA, Fujita Y, Araki E, Khush GS (2004) Quantitative Trait Loci (QTL) reactions to rice blast isolates from Japan and the Philippines. Proceedings of the 3rd International Rice Blast Conference. Springer Netherlands, Dordrecht, pp 113-121 Glaubitz JC, Casstevens TM, Lu F, Harriman J, Elshire RJ, Sun Q, Buckler ES (2014) TASSEL-GBS: a high capacity genotyping by sequencing analysis pipeline. PLoS One 9:e90346 Godfray HCJ, Beddington JR, Crute IR, Haddad L, Lawrence D, Muir JF, Pretty J, Robinson S, Thomas SM, Toulmin C (2010) Food security: the challenge of feeding 9 billion people. Science 327:812-818 Goto I (1988) Genetic studies on resistance of rice plant to blast fungus. (VII). Blast resistance genes of Kuroka. Jpn J Phytopathol 54:460-465 Hajjar R, Hodgkin T (2007) The use of wild relatives in crop improvement: a survey of developments over the last 20 years. Euphytica 156:1-13 Hayashi K, Yoshida H, Ashikawa I (2006) Development of PCR-based allele-specific and InDel marker sets for nine rice blast resistance genes. Theor Appl Genet 113:251-260 He Q, Li D, Zhu Y, Tan M, Zhang D, Lin X (2006) Fine Mapping of Xa2, a bacterial blight resistance gene in rice. Mol Breed 17:1-6 Henry RJ (2014) Genomics strategies for germplasm characterization and the development of climate resilient crops. Crop Breeding: Bioinformatics and Preparing for Climate Change. CRC Press, pp 3-10 Henry RJ, Nevo E (2014) Exploring natural selection to guide breeding for agriculture. Plant Biotechnol J 12:655-662 Hirabayashi H, Kaji R, Okamoto M, Ogawa T, Brar DS, Angeles ER, Khush GS (2003) Mapping QTLs for brown planthopper (BPH) resistance introgressed from O. officinalis in rice. In: Khush GS, Brar DS, Hardy B (eds) Advances in rice genetics. International Rice Research Institute, Manila, pp 268–270 Hittalmani S, Huang N, Courtois B, Venuprasad R, Shashidhar H, Zhuang J, Zheng K, Liu G, Wang G, Sidhu J (2003) Identification of QTL for growth-and grain yield-related traits in rice across nine locations of Asia. Theor Appl Genet 107:679-690 Hoisington D, Khairallah M, Reeves T, Ribaut J-M, Skovmand B, Taba S, Warburton M (1999) Plant genetic resources: what can they contribute towards increased crop productivity? PNAS 96:5937–5943 Huang D, Qiu Y, Zhang Y, Huang F, Meng J, Wei S, Li R, Chen B (2013) Fine mapping and characterization of BPH27, a brown planthopper resistance gene from wild rice (Oryza rufipogon Griff.). Theor Appl Genet 126:219-229 Huang Z, He G, Shu L, Li X, Zhang Q (2001) Identification and mapping of two brown planthopper resistance genes in rice. Theor Appl Genet 102:929-934 Ikeda R, Khush G, Tabien R (1990) A new resistance gene to bacterial blight derived from O. longistaminata. Jpn J Breed 40:280-281 International Rice Genome Sequencing Project (IRGSP) (2005) The map-based sequence of the rice genome. Nature 436:793–800 Ishimaru T, Hirabayashi H, Ida M, Takai T, San-Oh YA, Yoshinaga S, Ando I, Ogawa T, Kondo M (2010) A genetic resource for early-morning flowering trait of wild rice Oryza officinalis to mitigate high temperature-induced spikelet sterility at anthesis. Ann Bot 106:515-520 Iwata N (1996) Registration of new gene symbols. Rice Genet Newsl 13:12-18 Jena K, Khush G (1984) Embryo rescue of interspecific hybrids and its scope in rice improvement. Rice Genet Newsl 1:133-134 Jena KK, Khush GS (1990) Introgression of genes from Oryza officinalis Well ex Watt to cultivated rice, O. sativa L. Theor Appl Genet 80:737-745 Jia L, Yan W, Zhu C, Agrama HA, Jackson A, Yeater K, Li X, Huang B, Hu B, McClung A, Wu D (2012) Allelic analysis of sheath blight resistance with association mapping in rice. PLoS One 7:e32703 Jiao Y, Wang Y, Xue D, Wang J, Yan M, Liu G, Dong G, Zeng D, Lu Z, Zhu X (2010) Regulation of OsSPL14 by OsmiR156 defines ideal plant architecture in rice. Nat Genet 42:541-544 Kao C-H, Zeng Z-B, Teasdale RD (1999) Multiple interval mapping for quantitative trait loci. Genetics 152:1203-1216 Karmakar S, Molla KA, Chanda PK, Sarkar SN, Datta SK, Datta K (2016) Green tissue-specific co-expression of chitinase and oxalateoxidase 4 genes in rice for enhanced resistance against sheath blight. Planta 243:115-130 Kearsey MJ, Hyne V (1994) QTL analysis: a simple ‘marker-regression’ approach. Theor Appl Genet 89:698-702 Khan MH, Dar ZA, Dar SA (2015) Breeding Strategies for Improving Rice Yield—A Review. Agric Sci 6:467-478 Khush GS (2000) Rice germplasm enhancement at IRRI. Phillipp J Crop Sci 25:45-51 Khush GS, Ling KC (1974) Inheritance of resistance to grassy stunt virus and its vector in rice. J Hered 65:134 - 136 Lakshmanan P, Velusamy R (1991) Resistance to sheath rot (ShR) of breeding lines derived from Oryza officinalis. Int Rice Res Newsl 16:8-9 Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 9:357-359 Li C, Zhou A, Sang T (2006) Genetic analysis of rice domestication syndrome with the wild annual species, Oryza nivara. New phytologist 170:185-194 Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25:1754-1760 Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R (2009) The sequence alignment/map format and SAMtools. Bioinformatics 25:2078-2079 Li Y, Fan C, Xing Y, Jiang Y, Luo L, Sun L, Shao D, Xu C, Li X, Xiao J (2011) Natural variation in GS5 plays an important role in regulating grain size and yield in rice. Nat Genet 43:1266-1269 Li Z, Pinson S, Marchetti M, Stansel J, Park W (1995) Characterization of quantitative trait loci (QTLs) in cultivated rice contributing to field resistance to sheath blight (Rhizoctonia solani). Theor Appl Genet 91:382-388 Ling KC, Aguiero VM, S.H.Lee. (1970) Mass screening method for testing resistance to grassy stunt disease of rice. Plant Dis Reptr 56:565-569 Liu R, Zhang H, Chen Z, Shahid M, Fu X, Liu X (2015) Drought-tolerant rice germplasm developed from an Oryza officinalis transformation-competent artificial chromosome clone. Genet Mol Res 14:13667-13678 Liu X, Yang Q, Lin F, Hua L, Wang C, Wang L, Pan Q (2007) Identification and fine mapping of Pi39(t), a major gene conferring the broad-spectrum resistance to Magnaporthe oryzae. Mol Genet Genomics 278:403-410 Liu XQ, Wang L, Chen S, Lin F, Pan QH (2005) Genetic and physical mapping of Pi36(t), a novel rice blast resistance gene located on rice chromosome 8. Mol Genet Genomics 274:394-401 Lu F, Lipka AE, Glaubitz J, Elshire R, Cherney JH, Casler MD, Buckler ES, Costich DE (2013) Switchgrass genomic diversity, ploidy, and evolution: Novel Insights from a Network-Based SNP Discovery Protocol. PLoS Genet 9:e1003215 Malik N, Dwivedi N, Singh AK, Parida SK, Agarwal P, Thakur JK, Tyagi AK (2016) An integrated genomic strategy delineates candidate mediator genes regulating grain size and weight in rice. Sci Rep 6:23253 Maxted N, Kell S (2009) Establishment of a global network for the in situ conservation of crop wild relatives: Status and Needs. Background Study Paper No. 39. Commission on Genetic Resources for Food and Agriculture, FAO, Rome, Italy. 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 S-N (2007) Through the genetic bottleneck: O. rufipogon as a source of trait-enhancing alleles for O. sativa. Euphytica 154:317-339 Miah G, Rafii M, Ismail M, Puteh A, Rahim H, Asfaliza R, Latif M (2013) Blast resistance in rice: a review of conventional breeding to molecular approaches. Mol Biol Rep 40:2369-2388 Minakuchi K, Kameoka H, Yasuno N, Umehara M, Luo L, Kobayashi K, Hanada A, Ueno K, Asami T, Yamaguchi S (2010) FINE CULM1 (FC1) works downstream of strigolactones to inhibit the outgrowth of axillary buds in rice. Plant Cell Physiol 51:1127-1135 Miura K, Yamamoto E, Morinaka Y, Takashi T, Kitano H, Matsuoka M, Ashikari M (2008) The hybrid breakdown 1(t) locus induces interspecific hybrid breakdown between rice Oryza sativa cv. Koshihikari and its wild relative O. nivara. Breed Sci 58:99 - 105 Moncada P, Martínez CP, Borrero J, Chatel M, Gauch Jr H, Guimaraes E, Tohme J, McCouch SR (2001) Quantitative trait loci for yield and yield components in an Oryza sativa×Oryza rufipogon BC2F2 population evaluated in an upland environment. Theor Appl Genet 102:41-52 Multani D, Khush G, Delos Reyes B, Brar D (2003) Alien genes introgression and development of monosomic alien addition lines from Oryza latifolia Desv. to rice, Oryza sativa L. Theor Appl Genet 107:395-405 Naz AA, Arifuzzaman M, Muzammil S, Pillen K, Léon J (2014) Wild barley introgression lines revealed novel QTL alleles for root and related shoot traits in the cultivated barley (Hordeum vulgare L.). BMC Genetics 15:107 Nevo E, Chen G (2010) Drought and salt tolerances in wild relatives for wheat and barley improvement. Plant Cell Environ 33:670-685 Nguyen Q-N, Lee Y-S, Cho L-H, Jeong H-J, An G, Jung K-H (2015) Genome-wide identification and analysis of Catharanthus roseus RLK1-like kinases in rice. Planta 241:603-613 Ni D-H, Li J, Duan Y-B, Yang Y-C, Wei P-C, Xu R-F, Li C-R, Liang D-D, Li H, Song F-S, Ni J-L, Li L, Yang J-B (2014) Identification and utilization of cleistogamy gene cl7(t) in rice (Oryza sativa L.). J Exp Bot 65:2107-2117 Nweke F (2004) New challenges in thecassava transformation in nigeria and ghana, environment and production technology division discussion paper. International Food Policy Research Institute, Washington, DC Pan X, Zou J, Chen Z, Lu J, Yu H, Li H, Wang Z, Pan X, Rush M, Zhu L (1999) Tagging major quantitative trait loci for sheath blight resistance in a rice variety, Jasmine 85. Chin Sci Bull 44:1783-1789 Peterson BK, Weber JN, Kay EH, Fisher HS, Hoekstra HE (2012) Double digest RADseq: an inexpensive method for de novo SNP discovery and genotyping in model and non-model species. PLoS One 7:e37135 Pinson SR, Capdevielle FM, Oard JH (2005) Confirming QTLs and finding additional loci conditioning sheath blight resistance in rice using recombinant inbred lines. Crop Sci 45:503-510 Poland JA, Brown PJ, Sorrells ME, Jannink JL (2012) Development of high-density genetic maps for barley and wheat using a novel two-enzyme genotyping-by-sequencing approach. PLoS One 7:e32253 Prescott-Allen C, Prescott-Allen R (1987) The first resource: wild species in the North American economy. Brittonia, 39:427 Qi X, Li M-W, Xie M, Liu X, Ni M, Shao G, Song C, Kay-Yuen Yim A, Tao Y, Wong F-L, Isobe S, Wong C-F, Wong K-S, Xu C, Li C, Wang Y, Guan R, Sun F, Fan G, Xiao Z, Zhou F, Phang T-H, Liu X, Tong S-W, Chan T-F, Yiu S-M, Tabata S, Wang J, Xu X, Lam H-M (2014) Identification of a novel salt tolerance gene in wild soybean by whole-genome sequencing. Nat Commun 5:4340 Qiu Y, Guo J, Jing S, Zhu L, He G (2010) High-resolution mapping of the brown planthopper resistance gene Bph6 in rice and characterizing its resistance in the 9311 and Nipponbare near isogenic backgrounds. Theor Appl Genet 121:1601-1611 Qiu Y, Guo J, Jing S, Zhu L, He G (2012) Development and characterization of japonica rice lines carrying the brown planthopper-resistance genes BPH12 and BPH6. Theor Appl Genet 124:485-494 R Core Team (2017) R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. http://www.R-project.org/. Accessed 28 September 2017 Rahman ML, Jiang W, Chu SH, Qiao Y, Ham T-H, Woo M-O, Lee J, Khanam MS, Chin J-H, Jeung J-U, Brar DS, Jena KK, Koh H-J (2009) High-resolution mapping of two rice brown planthopper resistance genes, Bph20(t) and Bph21(t), originating from Oryza minuta. Theor Appl Genet 119:1237-1246 Ren J, Gao F, Wu X, Lu X, Zeng L, Lv J, Su X, Luo H, Ren G (2016) Bph32, a novel gene encoding an unknown SCR domain-containing protein, confers resistance against the brown planthopper in rice. Sci Rep 6 :37645 Rick CM, Chetelat RT (1995) Utilization of related wild species for tomato improvement, First International Symposium on Solanacea for Fresh Market. Acta Hortic 412:21–38 Sallaud C, Lorieux M, Roumen E, Tharreau D, Berruyer R, Svestasrani P, Garsmeur O, Ghesquiere A, Notteghem JL (2003) Identification of five new blast resistance genes in the highly blast-resistant rice variety IR64 using a QTL mapping strategy. Theor Appl Genet 106:794-803 Sanchez PL, Wing RA, Brar DS (2013) The wild relatives of rice: genomes and genomics. In: Zhang Q, Wing RA (eds) Genetics and genomics of rice. Plant genetics and genomics. Springer, New York, pp 9–26 Sanger F, Nicklen S, Coulson AR (1977) DNA sequencing with chain-terminating inhibitors. PNAS 74:5463-5467 Sasaki A, Ashikari M, Ueguchi-Tanaka M, Itoh H, Nishimura A, Swapan D, Ishiyama K, Saito T, Kobayashi M, Khush GS (2002) Green revolution: a mutant gibberellin-synthesis gene in rice. Nature 416:701-702 Septiningsih EM, Prasetiyono J, Lubis E, Tai TH, Tjubaryat T, Moeljopawiro S, McCouch SR (2003) 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 107:1419-1432 Shang XL, Xie RR, Tian H, Wang QL, Guo FQ (2016) Putative zeatin O‐glucosyltransferase OscZOG1 regulates root and shoot development and formation of agronomic traits in rice. J Integr Plant Biol 58:627-641 Sharma A, McClung AM, Pinson SR, Kepiro JL, Shank AR, Tabien RE, Fjellstrom R (2009) Genetic mapping of sheath blight resistance QTLs within tropical rice cultivars. Crop Sci 49:256-264 Sharma TR, Rai AK, Gupta SK, Vijayan J, Devanna BN, Ray S (2012) Rice blast management through host-plant resistance: retrospect and prospects. Agric Res 1:37-52 Shi Y, Liu X, Li R, Gao Y, Xu Z, Zhang B, Zhou Y (2014) Retention of OsNMD3 in the cytoplasm disturbs protein synthesis efficiency and affects plant development in rice. J Exp Bot 65:3055-3069 Sonah H, Bastien M, Iquira E, Tardivel A, Légaré G, Boyle B, Normandeau É, Laroche J, Larose S, Jean M, Belzile F (2013) An improved genotyping by sequencing (GBS) Approach offering increased versatility and efficiency of SNP discovery and genotyping. PLoS One 8:e54603 Spindel J, Wright M, Chen C, Cobb J, Gage J, Harrington S, Lorieux M, Ahmadi N, McCouch S (2013) Bridging the genotyping gap: using genotyping by sequencing (GBS) to add high-density SNP markers and new value to traditional bi-parental mapping and breeding populations. Theor Appl Genet 126:2699-2716 Sui Z, Wang T, Li H, Zhang M, Li Y, Xu R, Xing G, Ni Z, Xin M (2016) Overexpression of peptide-encoding OsCEP6.1 Results in pleiotropic effects on growth in rice (O. sativa). Front Plant Sci 7:228 Sun L, Su C, Wang C, Zhai H, Wan J (2005) Mapping of a major resistance gene to the brown planthopper in the rice cultivar Rathu Heenati. Breed Sci 55:391-396 Tai APK, Martin MV, Heald CL (2014) Threat to future global food security from climate change and ozone air pollution. Nat Clim Chang 4:817-821 Takita T (1996) A new dominant gene for brown planthopper resistance found in an improved Japanese rice strain. Breed Sci 46:211 Tanksley SD, McCouch SR (1997) Seed banks and molecular maps: unlocking genetic potential from the wild. Science 277:1063-1066 Tan G-X, Ren X, Weng Q-M, Shi Z-Y, Zhu L-L, He G-C (2004) Mapping of a new resistance gene to bacterial blight in rice line introgressed from Oryza officinalis. Acta Genetica Sinica 31:724-729 Taylor J, Butler D, Taylor MJ (2015) Package ‘ASMap’. Linkage map construction using the MSTmap Algorithm R Package. https://CRAN.R-project.org/package=ASMap. Accessed 5 October 2017 Thomson MJ, Tai TH, McClung AM, Lai X-H, Hinga ME, Lobos KB, Xu Y, Martinez CP, 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 Torkamaneh D, Laroche J, Bastien M, Abed A, Belzile F (2017) Fast-GBS: a new pipeline for the efficient and highly accurate calling of SNPs from genotyping-by-sequencing data. BMC Bioinformatics 18:5 Van Tassell CP, Smith TP, Matukumalli LK, Taylor JF, Schnabel RD, Lawley CT, Haudenschild CD, Moore SS, Warren WC, Sonstegard TS (2008) SNP discovery and allele frequency estimation by deep sequencing of reduced representation libraries. Nat Methods 5:247-252 Vavilov NI (1926) Studies on the Origin of Cultivated Plants. Bull Appl Bot Genet Plant Breed USSR 16:1-248 Voorrips RE (2002) MapChart: Software for the graphical presentation of linkage maps and QTLs. J Hered 93:77-78 Wang C, Wen G, Lin X, Liu X, Zhang D (2009) Identification and fine mapping of the new bacterial blight resistance gene, Xa31(t), in rice. Eur J Plant Pathol 123:235-240 Wang L, Sun S, Jin J, Fu D, Yang X, Weng X, Xu C, Li X, Xiao J, Zhang Q (2015a) Coordinated regulation of vegetative and reproductive branching in rice. PNAS 112:15504-15509 Wang Y, Xiong G, Hu J, Jiang L, Yu H, Xu J, Fang Y, Zeng L, Xu E, Xu J (2015b) Copy number variation at the GL7 locus contributes to grain size diversity in rice. Nat Genet 47:944-948 Wang S, Wu K, Yuan Q, Liu X, Liu Z, Lin X, Zeng R, Zhu H, Dong G, Qian Q (2012) Control of grain size, shape and quality by OsSPL16 in rice. Nat Genet 44:950-954 Wang Y-S, Pi L-Y, Chen X, Chakrabarty PK, Jiang J, De Leon AL, Liu G-Z, Li L, Benny U, Oard J, Ronald PC, Song W-Y (2006) Rice XA21 Binding Protein 3 is a ubiquitin ligase required for full Xa21-Mediated disease resistance. The Plant Cell 18:3635-3646 Win KT, Kubo T, Miyazaki Y, Doi K, Yamagata Y, Yoshimura A (2009) Identification of two loci causing F1 pollen sterility in inter- and intraspecific crosses of rice. Breed Sci 59:411-418 Wu J, Mizuno H, Hayashi‐Tsugane M, Ito Y, Chiden Y, Fujisawa M, Katagiri S, Saji S, Yoshiki S, Karasawa W, Yoshihara R, Hayashi A, Kobayashi H, Ito K, Hamada M, Okamoto M, Ikeno M, Ichikawa Y, Katayose Y, Yano M, Matsumoto T, Sasaki T (2003) Physical maps and recombination frequency of six rice chromosomes. Plant J 36:720-730 Xiao N, Wu Y, Pan C, Yu L, Chen Y, Liu G, Li Y, Zhang X, Wang Z, Dai Z, Liang C, Li A (2017) Improving of rice blast resistances in Japonica by pyramiding major R genes. Front Plant Sci 7:1-10 Xie XW, Mei-Rong X, Jin-Ping Z, Yong S, Ling-Hua Z, Jian-Long X, Yong-Li Z, Zhi-Kang L (2008) Genetic background and environmental effects on QTLs for sheath blight resistance revealed by reciprocal introgression lines in rice. Acta Agronomica Sinica 34:1885-1893 Yamamoto T, Nagasaki H, Yonemaru J-i, Ebana K, Nakajima M, Shibaya T, Yano M (2010) Fine definition of the pedigree haplotypes of closely related rice cultivars by means of genome-wide discovery of single-nucleotide polymorphisms. BMC genomics 11:267 Yang H, Ren X, Weng Q, Zhu L, He G (2002) Molecular mapping and genetic analysis of a rice brown planthopper (Nilaparvata lugens Stal) resistance gene. Hereditas 136:39-43 Yang H, You A, Yang Z, Zhang F, He R, Zhu L, He G (2004) High-resolution genetic mapping at the Bph15 locus for brown planthopper resistance in rice (Oryza sativa L.). Theor Appl Genet 110:182-191 Yang L, Li RB, Li YR, Huang FK, Chen YZ, Huang SS, Huang LF, Liu C, Ma ZF, Huang DH, Jiang JJ (2011) Genetic mapping of bph20(t) and bph21(t) loci conferring brown planthopper resistance to Nilaparvata lugens Stal in rice (Oryza sativa L.). Euphytica 183:161-171 Yao M, Chen S (2009) The impact evaluation of climate change on the growth and yield of rice (in Chinese with English abstract). Crop, Environment and Bioinformatics 6:141-156 Zhang B, Xu M, Bian S, Hou L, Tang D, Li Y, Gu M, Cheng Z, Yu H (2015) Global identification of genes specific for rice meiosis. PLoS One 10:e0137399 Zhou G, Zhang Q, Zhang X-q, Tan C, Li C (2015) Construction of high-density genetic map in barley through restriction-site associated DNA sequencing. PLoS One 10:e0133161 Zhu XY, QY. Yang, JY. Lei, C. Wang, J. Ling, Z. (2004) Differentiation ability of monogenic lines to Magnaporthe grisea in indica rice (in Chinese with English abstract). Acta Phytopathol Sin 34:361–368 | |
| dc.identifier.uri | http://tdr.lib.ntu.edu.tw/handle/123456789/1299 | - |
| dc.description.abstract | 稻米 (Oryza sativa L.) 為世界上重要的糧食作物，現今育種策略造成稻米之遺傳背景窄化及遺傳脆弱性等問題，使用野生近緣種 (crop wild relatives) 作為雜交親本被視為解決方法之一。本研究利用兩組野生稻導入系統，分別為導入野生稻O. nivara基因體的AA族群及導入野生稻O. officinalis基因體的AC族群，以限制酶切位連結核酸定序技術 (restriction site-associated DNA sequencing, RAD-seq) 建立定序庫，採用Illumina-Hiseq 2500次世代核酸定序平台完成定序後，以Stacks及TASSEL兩種程式進行單一核苷酸多型性 (SNP, single nucleotide polymorphism) 辨識。AA族群共獲得3,428個缺值率小於10%且具有多型性之分子標誌，加上前人使用之157個簡單重覆序列 (Simple sequence repeat, SSR) 分子標誌，經篩選後共以2,489個分子標誌建立總長1,743.3 cM之連鎖圖譜，並以多重區間定位法 (multiple interval mapping, MIM)，針對基本農藝性狀、產量相關性狀、穗與穀粒性狀及抗病表現等性狀進行數量性狀基因座 (quantitative trait loci, QTL) 定位，共定位到178個QTL，平均外表型解釋度為12.1% (介於2.21%至35.7%之間)。AC族群獲得4,601個缺值率小於10%且具有多型性之SNP分子標誌，以單一分子標誌迴歸法 (single marker regression) 定位54個QTL，平均外表型解釋度為10.3% (介於0.2%至52.4%之間)。在千粒重、每穗粒數、穗重、稻熱病抗性、褐飛蝨抗性、紋枯病抗性等許多性狀中皆有發現來自野生稻之有利對偶基因存在，配合搜尋前人文獻後佐證QTL鄰近位置有相關基因存在，且發現未出現於文獻中的QTL，可供進一步研究。 | zh_TW |
| dc.description.abstract | Rice (Oryza sativa L.) is one of the most important staple food crop in the world. Breeding strategies for rice nowadays often lead to problems such as narrow genetic background and genetic vulnerability. Using crop wild relatives (CWR) as crossing parents is viewed as one solution to these problems. In this study, two populations of introgression lines, AA and AC, which were generated using O. nivara and O. officinalis as donor parents, respectively, were used. Restriction site-associated DNA sequencing (RAD-seq) libraries were constructed and sequenced using Illumina-Hiseq 2500. Stacks and TASSEL were used for single nucleotide polymorphism (SNP) calling. In AA population, 3,428 SNPs with missing rate less than 10% were discovered. Along with 157 simple sequence repeat (SSR) markers from previous study, after marker filtering, we used a total of 2,489 markers to construct a linkage map spanning 1,743.3 cM. Multiple interval mapping (MIM) was used for mapping quantitative trait loci (QTL) for agronomic traits, yield-related traits and resistance to different pests and diseases. One hundred and seventy-eight QTL, each explained on average 12.1% phenotypic variance (ranging from 2.21 to 35.7%), were identified in AA population. In AC population, 4,601 SNPs with missing rate less than r 10% were discovered and analyzed using single marker regression. Fifty-four QTL, each explained on average 10.3% phenotypic variance (ranging from 0.2% to 52.4%), were identified. Favorable alleles from wild rice were found for several traits such as thousand grain weight, panicle weight, blast resistance and brown plant hopper resistance, etc. Some QTL were confirmed through previous studies, while others have not been reported yet, which may serve as targets for further studies. | en |
| dc.description.provenance | Made available in DSpace on 2021-05-12T09:35:50Z (GMT). No. of bitstreams: 1 ntu-107-R03621122-1.pdf: 2906759 bytes, checksum: cf07f2610c6886d21d470d5b3e660048 (MD5) Previous issue date: 2018 | en |
| dc.description.tableofcontents | 口試委員審定書 i
致謝 ii 摘要 iii Abstract iv 目錄 v 表目錄 vii 圖目錄 viii 第一章、 前言 1 一、 野生近緣種於育種之運用 1 二、 野生稻於稻米育種之運用 2 三、 高通量分子標誌的原理及應用 5 四、 研究目的 7 第二章、 材料與方法 8 一、 試驗材料 8 二、 農藝性狀調查 9 三、 葉片DNA萃取與定量 9 四、 RAD-seq定序庫製備 10 五、 RAD-seq資料分析及基因型資料整理 12 六、 連鎖圖譜建立 16 七、 數量性狀基因座分析 17 第三章、 結果 18 一、 外表型資料 18 二、 RAD-seq序列資料分析與比較 21 三、 連鎖圖譜 22 四、 數量性狀基因座 23 第四章、 討論 28 一、 序列資料分析流程 28 二、 連鎖圖譜與物理圖譜之比較 29 三、 性狀之遺傳結構 30 第五章、 結論與未來展望 35 參考文獻 70 附錄 83 | |
| dc.language.iso | zh-TW | |
| dc.subject | 限制?切位連結核酸定序技術 | zh_TW |
| dc.subject | 數量性狀基因座 | zh_TW |
| dc.subject | 野生近緣種 | zh_TW |
| dc.subject | 稻米 (Oryza sativa L.) | zh_TW |
| dc.subject | restriction site-associated DNA sequencing (RAD-seq) | en |
| dc.subject | quantitative trait loci (QTL) | en |
| dc.subject | crop wild relatives | en |
| dc.subject | rice (Oryza sativa L.) | en |
| dc.title | 利用限制酶切位連結核酸定序技術探討野生稻導入系統之基因體多型性 | zh_TW |
| dc.title | Genomic characterization of wild rice introgression lines using restriction site-associated DNA sequencing | en |
| dc.type | Thesis | |
| dc.date.schoolyear | 106-1 | |
| dc.description.degree | 碩士 | |
| dc.contributor.oralexamcommittee | 李長沛(Charng-Pei Li),陳凱儀(Kai-Yi Chen),董致韡(Chih-Wei Tung) | |
| dc.subject.keyword | 稻米 (Oryza sativa L.),野生近緣種,限制?切位連結核酸定序技術,數量性狀基因座, | zh_TW |
| dc.subject.keyword | rice (Oryza sativa L.),crop wild relatives,restriction site-associated DNA sequencing (RAD-seq),quantitative trait loci (QTL), | en |
| dc.relation.page | 89 | |
| dc.identifier.doi | 10.6342/NTU201800044 | |
| dc.rights.note | 同意授權(全球公開) | |
| dc.date.accepted | 2018-02-07 | |
| dc.contributor.author-college | 生物資源暨農學院 | zh_TW |
| dc.contributor.author-dept | 農藝學研究所 | zh_TW |
| 顯示於系所單位： | 農藝學系 | |
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