Skip navigation

DSpace

機構典藏 DSpace 系統致力於保存各式數位資料(如:文字、圖片、PDF)並使其易於取用。

點此認識 DSpace
DSpace logo
English
中文
  • 瀏覽論文
    • 校院系所
    • 出版年
    • 作者
    • 標題
    • 關鍵字
  • 搜尋 TDR
  • 授權 Q&A
    • 我的頁面
    • 接受 E-mail 通知
    • 編輯個人資料
  1. NTU Theses and Dissertations Repository
  2. 生物資源暨農學院
  3. 農藝學系
請用此 Handle URI 來引用此文件: http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/20043
完整後設資料紀錄
DC 欄位值語言
dc.contributor.advisor董致韡(Chih-Wei Tung)
dc.contributor.authorChia-Hui Chouen
dc.contributor.author周家卉zh_TW
dc.date.accessioned2021-06-08T02:39:12Z-
dc.date.copyright2020-11-13
dc.date.issued2020
dc.date.submitted2020-10-27
dc.identifier.citationAbrouk, M., Stritt, C., Müller, T., Keller, B., Roulin, A. C., Krattinger, S. G. (2018). High-throughput genotyping of the spelt gene pool reveals patterns of agricultural history in Europe. BioRxiv, 481424. https://doi.org/10.1101/481424
Ain, Q., Rasheed, A., Anwar, A., Mahmood, T., Mahmood, T., Imtiaz, M., He, Z., Xia, X., Quraishi, U. M. (2015). Genome-wide association for grain yield under rainfed conditions in historical wheat cultivars from Pakistan. Frontiers in Plant Science, 6. https://doi.org/10.3389/fpls.2015.00743
Alexander, D. H., Novembre, J., Lange, K. (2009). Fast model-based estimation of ancestry in unrelated individuals. Genome Research, 19(9), 1655–1664. https://doi.org/10.1101/gr.094052.109
Alqudah, A. M., Haile, J. K., Alomari, D. Z., Pozniak, C. J., Kobiljski, B., Börner, A. (2020). Genome-wide and SNP network analyses reveal genetic control of spikelet sterility and yield-related traits in wheat. Scientific Reports, 10(1), 2098. https://doi.org/10.1038/s41598-020-59004-4
Alvarez Prado, S., Sanchez, I., Cabrera-Bosquet, L., Grau, A., Welcker, C., Tardieu, F., Hilgert, N. (2019). To clean or not to clean phenotypic datasets for outlier plants in genetic analyses? Journal of Experimental Botany, 70(15), 3693–3698. https://doi.org/10.1093/jxb/erz191
Baidouri, M. E., Murat, F., Veyssiere, M., Molinier, M., Flores, R., Burlot, L., Alaux, M., Quesneville, H., Pont, C., Salse, J. (2017). Reconciling the evolutionary origin of bread wheat (Triticum aestivum). New Phytologist, 213(3), 1477–1486. https://doi.org/10.1111/nph.14113
Bellucci, A., Torp, A. M., Bruun, S., Magid, J., Andersen, S. B., Rasmussen, S. K. (2015). Association mapping in Scandinavian winter wheat for yield, plant height, and traits important for second-generation bioethanol production. Frontiers in Plant Science, 6. https://doi.org/10.3389/fpls.2015.01046
Bewley, J. (Ed.). (1985). Seeds: Physiology of Development and Germination. Springer US. https://doi.org/10.1007/978-1-4615-1747-4
Bhatta, M., Shamanin, V., Shepelev, S., Baenziger, P. S., Pozherukova, V., Pototskaya, I., Morgounov, A. (2019). Marker-trait associations for enhancing agronomic performance, disease resistance, and grain quality in synthetic and bread Wheat accessions in Western Siberia. G3: Genes, Genomes, Genetics, 9(12), 4209–4222. https://doi.org/10.1534/g3.119.400811
Bradbury, P. J., Zhang, Z., Kroon, D. E., Casstevens, T. M., Ramdoss, Y., Buckler, E. S. (2007). TASSEL: Software for association mapping of complex traits in diverse samples. Bioinformatics, 23(19), 2633–2635. https://doi.org/10.1093/bioinformatics/btm308
Canvin, D. T., Mcvetty, P. B. E. (1976). Hybrid grass-clump dwarfness in wheat: Physiology and genetics. Euphytica, 25(1), 471–483. https://doi.org/10.1007/BF00041581
Cao, L., Hayashi, K., Tokui, M., Mori, M., Miura, H., Onishi, K. (2016). Detection of QTLs for traits associated with pre-harvest sprouting resistance in bread wheat (Triticum aestivum L.). Breeding Science, 66(2), 260–270. https://doi.org/10.1270/jsbbs.66.260
Chafin, T. K., Martin, B. T., Mussmann, S. M., Douglas, M. R., Douglas, M. E. (2018). FRAGMATIC: In silico locus prediction and its utility in optimizing ddRADseq projects. Conservation Genetics Resources, 10(3), 325–328. https://doi.org/10.1007/s12686-017-0814-1
Cheng, B., Gao, X., Cao, N., Ding, Y., Gao, Y., Chen, T., Xin, Z., Zhang, L. (2020). Genome-wide association analysis of stripe rust resistance loci in wheat accessions from southwestern China. Journal of Applied Genetics, 61(1), 37–50. https://doi.org/10.1007/s13353-019-00533-8
Cheng, H., Liu, J., Wen, J., Nie, X., Xu, L., Chen, N., Li, Z., Wang, Q., Zheng, Z., Li, M., Cui, L., Liu, Z., Bian, J., Wang, Z., Xu, S., Yang, Q., Appels, R., Han, D., Song, W., … Jiang, Y. (2019). Frequent intra- and inter-species introgression shapes the landscape of genetic variation in bread wheat. Genome Biology, 20(1), 136. https://doi.org/10.1186/s13059-019-1744-x
Dong, H., Wang, R., Yuan, Y., Anderson, J., Pumphrey, M., Zhang, Z., Chen, J. (2018). Evaluation of the potential for genomic selection to improve spring wheat resistance to Fusarium head blight in the Pacific Northwest. Frontiers in Plant Science, 9. https://doi.org/10.3389/fpls.2018.00911
Dvorak, J., Akhunov, E. D. (2005). Tempos of gene locus deletions and duplications and their relationship to recombination rate during diploid and polyploid evolution in the Aegilops-Triticum alliance. Genetics, 171(1), 323–332. https://doi.org/10.1534/genetics.105.041632
Dvorak, J., Deal, K. R., Luo, M.-C., You, F. M., von Borstel, K., Dehghani, H. (2012). The origin of spelt and free-threshing hexaploid wheat. Journal of Heredity, 103(3), 426–441. https://doi.org/10.1093/jhered/esr152
Eid, J., Fehr, A., Gray, J., Luong, K., Lyle, J., Otto, G., Peluso, P., Rank, D., Baybayan, P., Bettman, B., Bibillo, A., Bjornson, K., Chaudhuri, B., Christians, F., Cicero, R., Clark, S., Dalal, R., Dewinter, A., Dixon, J., … Turner, S. (2009). Real-time DNA sequencing from single polymerase molecules. Science (New York, N.Y.), 323(5910), 133–138. https://doi.org/10.1126/science.1162986
Ellis, M. H., Rebetzke, G. J., Azanza, F., Richards, R. A., Spielmeyer, W. (2005). Molecular mapping of gibberellin-responsive dwarfing genes in bread wheat. Theoretical and Applied Genetics, 111(3), 423–430. https://doi.org/10.1007/s00122-005-2008-6
Elshire, R. J., Glaubitz, J. C., Sun, Q., Poland, J. A., Kawamoto, K., Buckler, E. S., Mitchell, S. E. (2011). A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS ONE, 6(5), e19379. https://doi.org/10.1371/journal.pone.0019379
Ester, M., Kriegel, H.-P., Sander, J., Xu, X. (1996). A density-based algorithm for discovering clusters in large spatial databases with noise. Proceedings of the Second International Conference on Knowledge Discovery and Data Mining, 226–231.
Flint-Garcia, S. A., Thornsberry, J. M., Buckler, E. S. (2003). Structure of linkage disequilibrium in plants. Annual Review of Plant Biology, 54, 357–374. https://doi.org/10.1146/annurev.arplant.54.031902.134907
Food and Agriculture Organization of the United Nations. (2020a). FAOSTAT statistics database, Crops. FAOSTAT. http://www.fao.org/faostat/en/#data/QC
Food and Agriculture Organization of the United Nations. (2020b). FAOSTAT statistics database, New Food Balances. FAOSTAT. http://www.fao.org/faostat/en/#data/FBS
Gao, F., Wen, W., Liu, J., Rasheed, A., Yin, G., Xia, X., Wu, X., He, Z. (2015). Genome-wide linkage mapping of QTL for yield components, plant height and yield-related physiological traits in the Chinese wheat cross Zhou 8425B/Chinese Spring. Frontiers in Plant Science, 6. https://doi.org/10.3389/fpls.2015.01099
Gerjets, T., Scholefield, D., Foulkes, M. J., Lenton, J. R., Holdsworth, M. J. (2010). An analysis of dormancy, ABA responsiveness, after-ripening and pre-harvest sprouting in hexaploid wheat (Triticum aestivum L.) caryopses. Journal of Experimental Botany, 61(2), 597–607. https://doi.org/10.1093/jxb/erp329
Glaubitz, J. C., Casstevens, T. M., Lu, F., Harriman, J., Elshire, R. J., Sun, Q., Buckler, E. S. (2014). TASSEL-GBS: A high capacity genotyping by sequencing analysis pipeline. PLoS ONE, 9(2), e90346. https://doi.org/10.1371/journal.pone.0090346
Guedira, M., Xiong, M., Hao, Y. F., Johnson, J., Harrison, S., Marshall, D., Brown-Guedira, G. (2016). Heading date QTL in winter wheat (Triticum aestivum L.) coincide with major developmental genes VERNALIZATION1 and PHOTOPERIOD1. PLOS ONE, 11(5), e0154242. https://doi.org/10.1371/journal.pone.0154242
He, F., Pasam, R., Shi, F., Kant, S., Keeble-Gagnere, G., Kay, P., Forrest, K., Fritz, A., Hucl, P., Wiebe, K., Knox, R., Cuthbert, R., Pozniak, C., Akhunova, A., Morrell, P. L., Davies, J. P., Webb, S. R., Spangenberg, G., Hayes, B., … Akhunov, E. (2019). Exome sequencing highlights the role of wild-relative introgression in shaping the adaptive landscape of the wheat genome. Nature Genetics, 51(5), 896–904. https://doi.org/10.1038/s41588-019-0382-2
Hill, W. G., Weir, B. S. (1988). Variances and covariances of squared linkage disequilibria in finite populations. Theoretical Population Biology, 33(1), 54–78. https://doi.org/10.1016/0040-5809(88)90004-4
Huang, S., Sirikhachornkit, A., Su, X., Faris, J., Gill, B., Haselkorn, R., Gornicki, P. (2002). Genes encoding plastid acetyl-CoA carboxylase and 3-phosphoglycerate kinase of the Triticum/Aegilops complex and the evolutionary history of polyploid wheat. Proceedings of the National Academy of Sciences, 99(12), 8133–8138. https://doi.org/10.1073/pnas.072223799
IWGSC, Rudi Appels, Ute Baumann, Hikmet Budak, Isabelle Caugant, Jan Dvorak, Kellye Eversole, Mingcheng Luo, Etienne Paux, Sébastien Praud. (2020, January 22). The International Wheat Genome Sequencing Consortium [Poster]. The Plant and Animal Genome XXVIII Conference, San Diego, CA, USA.
Jamil, M., Ali, A., Gul, A., Ghafoor, A., Napar, A. A., Ibrahim, A. M. H., Naveed, N. H., Yasin, N. A., Mujeeb-Kazi, A. (2019). Genome-wide association studies of seven agronomic traits under two sowing conditions in bread wheat. BMC Plant Biology, 19(1), 149. https://doi.org/10.1186/s12870-019-1754-6
Juliana, P., Poland, J., Huerta-Espino, J., Shrestha, S., Crossa, J., Crespo-Herrera, L., Toledo, F. H., Govindan, V., Mondal, S., Kumar, U., Bhavani, S., Singh, P. K., Randhawa, M. S., He, X., Guzman, C., Dreisigacker, S., Rouse, M. N., Jin, Y., Pérez-Rodríguez, P., … Singh, R. P. (2019). Improving grain yield, stress resilience and quality of bread wheat using large-scale genomics. Nature Genetics, 51(10), 1530–1539. https://doi.org/10.1038/s41588-019-0496-6
Khalid, M., Afzal, F., Gul, A., Amir, R., Subhani, A., Ahmed, Z., Mahmood, Z., Xia, X., Rasheed, A., He, Z. (2019). Molecular characterization of 87 functional genes in wheat diversity panel and their association with phenotypes under well-watered and water-limited conditions. Frontiers in Plant Science, 10. https://doi.org/10.3389/fpls.2019.00717
Kidane, Y. G., Gesesse, C. A., Hailemariam, B. N., Desta, E. A., Mengistu, D. K., Fadda, C., Pè, M. E., Dell’Acqua, M. (2019). A large nested association mapping population for breeding and quantitative trait locus mapping in Ethiopian durum wheat. Plant Biotechnology Journal, 17(7), 1380–1393. https://doi.org/10.1111/pbi.13062
Li, F., Wen, W., Liu, J., Zhang, Y., Cao, S., He, Z., Rasheed, A., Jin, H., Zhang, C., Yan, J., Zhang, P., Wan, Y., Xia, X. (2019). Genetic architecture of grain yield in bread wheat based on genome-wide association studies. BMC Plant Biology, 19(1), 168. https://doi.org/10.1186/s12870-019-1781-3
Li, H., Durbin, R. (2010). Fast and accurate long-read alignment with Burrows–Wheeler transform. Bioinformatics, 26(5), 589–595. https://doi.org/10.1093/bioinformatics/btp698
Li, L.-F., Liu, B., Olsen, K. M., Wendel, J. F. (2015a). A re-evaluation of the homoploid hybrid origin of Aegilops tauschii, the donor of the wheat D-subgenome. New Phytologist, 208(1), 4–8. https://doi.org/10.1111/nph.13294
Li, L.-F., Liu, B., Olsen, K. M., Wendel, J. F. (2015b). Multiple rounds of ancient and recent hybridizations have occurred within the Aegilops–Triticum complex. New Phytologist, 208(1), 11–12. https://doi.org/10.1111/nph.13563
Lin, Y., Liu, S., Liu, Y., Liu, Y., Chen, G., Xu, J., Deng, M., Jiang, Q., Wei, Y., Lu, Y., Zheng, Y., Lin, Y., Liu, S., Liu, Y., Liu, Y., Chen, G., Xu, J., Deng, M., Jiang, Q., … Zheng, Y. (2017). Genome-wide association study of pre-harvest sprouting resistance in Chinese wheat founder parents. Genetics and Molecular Biology, 40(3), 620–629. https://doi.org/10.1590/1678-4685-gmb-2016-0207
Liu, G., Xu, S., Ni, Z., Xie, C., Qin, D., Li, J., Lu, L., Zhang, J., Peng, H., Sun, Q. (2011). Molecular dissection of plant height QTLs using recombinant inbred lines from hybrids between common wheat (Triticum aestivum L.) and spelt wheat (Triticum spelta L.). Chinese Science Bulletin, 56(18), 1897. https://doi.org/10.1007/s11434-011-4506-z
Liu, J., He, Z., Wu, L., Bai, B., Wen, W., Xie, C., Xia, X. (2015). Genome-wide linkage mapping of QTL for adult-plant resistance to stripe rust in a Chinese wheat population Linmai 2 × Zhong 892. PLOS ONE, 10(12), e0145462. https://doi.org/10.1371/journal.pone.0145462
Liu, J., Xu, Z., Fan, X., Zhou, Q., Cao, J., Wang, F., Ji, G., Yang, L., Feng, B., Wang, T. (2018). A genome-wide association study of wheat spike related traits in China. Frontiers in Plant Science, 9. https://doi.org/10.3389/fpls.2018.01584
Mangini, G., Nigro, D., Margiotta, B., De Vita, P., Gadaleta, A., Simeone, R., Blanco, A. (2018). Exploring SNP diversity in wheat landraces germplasm and setting of a molecular barcode for fingerprinting. Cereal Research Communications, 46(3), 377–387. https://doi.org/10.1556/0806.46.2018.033
Martinez, S. A., Godoy, J., Huang, M., Zhang, Z., Carter, A. H., Garland Campbell, K. A., Steber, C. M. (2018). Genome-wide association mapping for tolerance to preharvest sprouting and low falling numbers in wheat. Frontiers in Plant Science, 9. https://doi.org/10.3389/fpls.2018.00141
Mcfadden, E. S., Sears, E. R. (1946). The origin of Triticum spelta and its free-threshing hexaploid relatives. Journal of Heredity, 37(3), 81–89. https://doi.org/10.1093/oxfordjournals.jhered.a105590
Meirmans, P. G. (2020). genodive version 3.0: Easy-to-use software for the analysis of genetic data of diploids and polyploids. Molecular Ecology Resources, n/a(n/a). https://doi.org/10.1111/1755-0998.13145
Molero, G., Joynson, R., Pinera‐Chavez, F. J., Gardiner, L.-J., Rivera‐Amado, C., Hall, A., Reynolds, M. P. (2019). Elucidating the genetic basis of biomass accumulation and radiation use efficiency in spring wheat and its role in yield potential. Plant Biotechnology Journal, 17(7), 1276–1288. https://doi.org/10.1111/pbi.13052
Moore, K. (1969). The genetical control of the grass-dwarf phenotype in Triticum aestivum L. Euphytica, 18(2), 190–203. https://doi.org/10.1007/BF00035691
Moore, K., Cubitt, I. R. (1979). Physiological studies on grass-dwarf selection lines in wheat (Triticum aestivum L.). Euphytica, 28(3), 769–778. https://doi.org/10.1007/BF00038948
Müller, T., Schierscher-Viret, B., Fossati, D., Brabant, C., Schori, A., Keller, B., Krattinger, S. G. (2018). Unlocking the diversity of genebanks: Whole-genome marker analysis of Swiss bread wheat and spelt. Theoretical and Applied Genetics, 131(2), 407–416. https://doi.org/10.1007/s00122-017-3010-5
Muqaddasi, Q. H., Brassac, J., Börner, A., Pillen, K., Röder, M. S. (2017). Genetic architecture of anther extrusion in spring and winter wheat. Frontiers in Plant Science, 8. https://doi.org/10.3389/fpls.2017.00754
Nishida, H., Yoshida, T., Kawakami, K., Fujita, M., Long, B., Akashi, Y., Laurie, D. A., Kato, K. (2013). Structural variation in the 5′ upstream region of photoperiod-insensitive alleles Ppd-A1a and Ppd-B1a identified in hexaploid wheat (Triticum aestivum L.), and their effect on heading time. Molecular Breeding, 31(1), 27–37. https://doi.org/10.1007/s11032-012-9765-0
Peng, J. H., Sun, D., Nevo, E. (2011). Domestication evolution, genetics and genomics in wheat. Molecular Breeding, 28(3), 281–301. https://doi.org/10.1007/s11032-011-9608-4
Peng, J., Richards, D. E., Hartley, N. M., Murphy, G. P., Devos, K. M., Flintham, J. E., Beales, J., Fish, L. J., Worland, A. J., Pelica, F., Sudhakar, D., Christou, P., Snape, J. W., Gale, M. D., Harberd, N. P. (1999). ‘Green revolution’ genes encode mutant gibberellin response modulators. Nature, 400(6741), 256–261. https://doi.org/10.1038/22307
Purcell, S., Neale, B., Todd-Brown, K., Thomas, L., Ferreira, M. A. R., Bender, D., Maller, J., Sklar, P., de Bakker, P. I. W., Daly, M. J., Sham, P. C. (2007). PLINK: A tool set for whole-genome association and population-based linkage analyses. The American Journal of Human Genetics, 81(3), 559–575. https://doi.org/10.1086/519795
Qaseem, M. F., Qureshi, R., Muqaddasi, Q. H., Shaheen, H., Kousar, R., Röder, M. S. (2018). Genome-wide association mapping in bread wheat subjected to independent and combined high temperature and drought stress. PLOS ONE, 13(6), e0199121. https://doi.org/10.1371/journal.pone.0199121
Rahimi, Y., Bihamta, M. R., Taleei, A., Alipour, H., Ingvarsson, P. K. (2019). Genome-wide association study of agronomic traits in bread wheat reveals novel putative alleles for future breeding programs. BMC Plant Biology, 19(1), 541. https://doi.org/10.1186/s12870-019-2165-4
Ramírez-González, R. H., Borrill, P., Lang, D., Harrington, S. A., Brinton, J., Venturini, L., Davey, M., Jacobs, J., Ex, F. van, Pasha, A., Khedikar, Y., Robinson, S. J., Cory, A. T., Florio, T., Concia, L., Juery, C., Schoonbeek, H., Steuernagel, B., Xiang, D., … Uauy, C. (2018). The transcriptional landscape of polyploid wheat. Science, 361(6403). https://doi.org/10.1126/science.aar6089
Ray, D. K., Mueller, N. D., West, P. C., Foley, J. A. (2013). Yield trends are insufficient to double global crop production by 2050. PLOS ONE, 8(6), e66428. https://doi.org/10.1371/journal.pone.0066428
Remington, D. L., Thornsberry, J. M., Matsuoka, Y., Wilson, L. M., Whitt, S. R., Doebley, J., Kresovich, S., Goodman, M. M., Buckler, E. S. (2001). Structure of linkage disequilibrium and phenotypic associations in the maize genome. Proceedings of the National Academy of Sciences, 98(20), 11479–11484. https://doi.org/10.1073/pnas.201394398
Shewry, P. R., Hey, S. J. (2015). The contribution of wheat to human diet and health. Food and Energy Security, 4(3), 178–202. https://doi.org/10.1002/fes3.64
Shorinola, O., Bird, N., Simmonds, J., Berry, S., Henriksson, T., Jack, P., Werner, P., Gerjets, T., Scholefield, D., Balcárková, B., Valárik, M., Holdsworth, M. J., Flintham, J., Uauy, C. (2016). The wheat Phs-A1 pre-harvest sprouting resistance locus delays the rate of seed dormancy loss and maps 0.3 cM distal to the PM19 genes in UK germplasm. Journal of Experimental Botany, 67(14), 4169–4178. https://doi.org/10.1093/jxb/erw194
Simon, A. (2020). FastQC A Quality Control tool for High Throughput Sequence Data. https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
Sukumaran, S., Dreisigacker, S., Lopes, M., Chavez, P., Reynolds, M. P. (2015). Genome-wide association study for grain yield and related traits in an elite spring wheat population grown in temperate irrigated environments. Theoretical and Applied Genetics, 128(2), 353–363. https://doi.org/10.1007/s00122-014-2435-3
Sun, C., Zhang, F., Yan, X., Zhang, X., Dong, Z., Cui, D., Chen, F. (2017). Genome-wide association study for 13 agronomic traits reveals distribution of superior alleles in bread wheat from the Yellow and Huai Valley of China. Plant Biotechnology Journal, 15(8), 953–969. https://doi.org/10.1111/pbi.12690
Taranto, F., D’Agostino, N., Rodriguez, M., Pavan, S., Minervini, A. P., Pecchioni, N., Papa, R., De Vita, P. (2020). Whole genome scan reveals molecular signatures of divergence and selection related to important traits in durum wheat germplasm. Frontiers in Genetics, 11. https://doi.org/10.3389/fgene.2020.00217
The International Wheat Genome Sequencing Consortium (IWGSC). (2019). IWGSC RefSeq v2.0 assembly. https://wheat-urgi.versailles.inra.fr/Seq-Repository/Assemblies
The International Wheat Genome Sequencing Consortium (IWGSC), Appels, R., Eversole, K., Stein, N., Feuillet, C., Keller, B., Rogers, J., Pozniak, C. J., Choulet, F., Distelfeld, A., Poland, J., Ronen, G., Sharpe, A. G., Barad, O., Baruch, K., Keeble-Gagnère, G., Mascher, M., Ben-Zvi, G., Josselin, A.-A., … Wang, L. (2018). Shifting the limits in wheat research and breeding using a fully annotated reference genome. Science, 361(6403), eaar7191. https://doi.org/10.1126/science.aar7191
Thind, A. K., Wicker, T., Müller, T., Ackermann, P. M., Steuernagel, B., Wulff, B. B. H., Spannagl, M., Twardziok, S. O., Felder, M., Lux, T., Mayer, K. F. X., Keller, B., Krattinger, S. G., International Wheat Genome Sequencing Consortium. (2018). Chromosome-scale comparative sequence analysis unravels molecular mechanisms of genome dynamics between two wheat cultivars. Genome Biology, 19(1), 104. https://doi.org/10.1186/s13059-018-1477-2
Tinker, N. A., Chao, S., Lazo, G. R., Oliver, R. E., Huang, Y.-F., Poland, J. A., Jellen, E. N., Maughan, P. J., Kilian, A., Jackson, E. W. (2014). A SNP genotyping array for hexaploid oat. The Plant Genome, 7(3), plantgenome2014.03.0010. https://doi.org/10.3835/plantgenome2014.03.0010
United Nations, Department of Economic and Social Affairs, Population Division. (2019). World Population Prospects 2019 - Volume II: Demographic Profiles. UN. https://doi.org/10.18356/7707d011-en
Usda, Agricultural Research Service, National Plant Germplasm System. 2020. Germplasm Resources Information Network (grin-Taxonomy). (2020). https://npgsweb.ars-grin.gov/gringlobal/search.aspx
Vos, P. G., Paulo, M. J., Voorrips, R. E., Visser, R. G. F., van Eck, H. J., van Eeuwijk, F. A. (2017). Evaluation of LD decay and various LD-decay estimators in simulated and SNP-array data of tetraploid potato. TAG. Theoretical and Applied Genetics. Theoretische Und Angewandte Genetik, 130(1), 123–135. https://doi.org/10.1007/s00122-016-2798-8
Wang, S., Wong, D., Forrest, K., Allen, A., Chao, S., Huang, B. E., Maccaferri, M., Salvi, S., Milner, S. G., Cattivelli, L., Mastrangelo, A. M., Whan, A., Stephen, S., Barker, G., Wieseke, R., Plieske, J., Lillemo, M., Mather, D., Appels, R., … Akhunov, E. (2014). Characterization of polyploid wheat genomic diversity using a high-density 90 000 single nucleotide polymorphism array. Plant Biotechnology Journal, 12(6), 787–796. https://doi.org/10.1111/pbi.12183
Wang, S., Xu, S., Chao, S., Sun, Q., Liu, S., Xia, G. (2019). A genome-wide association study of highly heritable agronomic traits in durum wheat. Frontiers in Plant Science, 10. https://doi.org/10.3389/fpls.2019.00919
Ward, B. P., Brown-Guedira, G., Kolb, F. L., Sanford, D. A. V., Tyagi, P., Sneller, C. H., Griffey, C. A. (2019). Genome-wide association studies for yield-related traits in soft red winter wheat grown in Virginia. PLOS ONE, 14(2), e0208217. https://doi.org/10.1371/journal.pone.0208217
Wen, W., He, Z., Gao, F., Liu, J., Jin, H., Zhai, S., Qu, Y., Xia, X. (2017). A high-density consensus map of common wheat integrating four mapping populations scanned by the 90K SNP array. Frontiers in Plant Science, 8. https://doi.org/10.3389/fpls.2017.01389
Wheat and Barley Legacy for Breeding Improvement (WHEALBI) consortium, Pont, C., Leroy, T., Seidel, M., Tondelli, A., Duchemin, W., Armisen, D., Lang, D., Bustos-Korts, D., Goué, N., Balfourier, F., Molnár-Láng, M., Lage, J., Kilian, B., Özkan, H., Waite, D., Dyer, S., Letellier, T., Alaux, M., … Salse, J. (2019). Tracing the ancestry of modern bread wheats. Nature Genetics, 51(5), 905–911. https://doi.org/10.1038/s41588-019-0393-z
Wicker, T., Matthews, D. E., Keller, B. (2002). TREP: A database for Triticeae repetitive elements. Trends in Plant Science, 7(12), 561–562. https://doi.org/10.1016/S1360-1385(02)02372-5
Würschum, T., Leiser, W. L., Longin, C. F. H. (2017). Molecular genetic characterization and association mapping in spelt wheat. Plant Breeding, 136(2), 214–223. https://doi.org/10.1111/pbr.12462
Xu, Y., Li, P., Yang, Z., Xu, C. (2017). Genetic mapping of quantitative trait loci in crops. The Crop Journal, 5(2), 175–184. https://doi.org/10.1016/j.cj.2016.06.003
Yan, L., Loukoianov, A., Tranquilli, G., Helguera, M., Fahima, T., Dubcovsky, J. (2003). Positional cloning of the wheat vernalization gene VRN1. Proceedings of the National Academy of Sciences, 100(10), 6263–6268. https://doi.org/10.1073/pnas.0937399100
Yu, M., Mao, S.-L., Chen, G.-Y., Pu, Z.-E., Wei, Y.-M., Zheng, Y.-L. (2014). QTLs for uppermost internode and spike length in two wheat RIL populations and their affect upon plant height at an individual QTL level. Euphytica, 200(1), 95–108. https://doi.org/10.1007/s10681-014-1156-7
Zhai, S., He, Z., Wen, W., Jin, H., Liu, J., Zhang, Y., Liu, Z., Xia, X. (2016). Genome-wide linkage mapping of flour color-related traits and polyphenol oxidase activity in common wheat. Theoretical and Applied Genetics, 129(2), 377–394. https://doi.org/10.1007/s00122-015-2634-6
Zhou, Y., Tang, H., Cheng, M.-P., Dankwa, K. O., Chen, Z.-X., Li, Z.-Y., Gao, S., Liu, Y.-X., Jiang, Q.-T., Lan, X.-J., Pu, Z.-E., Wei, Y.-M., Zheng, Y.-L., Hickey, L. T., Wang, J.-R. (2017). Genome-wide association study for pre-harvest sprouting resistance in a large germplasm collection of Chinese wheat landraces. Frontiers in Plant Science, 8. https://doi.org/10.3389/fpls.2017.00401
Zhu, Y., Wang, S., Wei, W., Xie, H., Liu, K., Zhang, C., Wu, Z., Jiang, H., Cao, J., Zhao, L., Lu, J., Zhang, H., Chang, C., Xia, X., Xiao, S., Ma, C. (2019). Genome-wide association study of pre-harvest sprouting tolerance using a 90K SNP array in common wheat (Triticum aestivum L.). Theoretical and Applied Genetics, 132(11), 2947–2963. https://doi.org/10.1007/s00122-019-03398-x
行政院農業委員會農糧署統計室。(2020)。台灣糧食統計要覽。 http://210.69.71.166/Pxweb2007/Dialog/Saveshow.asp
dc.identifier.urihttp://tdr.lib.ntu.edu.tw/jspui/handle/123456789/20043-
dc.description.abstract臺灣本土栽種小麥品種主要為已育成超過三十年的台中選2號,在近年氣候變遷及市場需求改變下,亟需新品種以因應現今頻繁發生的極端天氣現象以及多元的加工用途。然而臺灣目前對小麥的育種投入及遺傳研究較為缺乏,因此本研究針對臺中區農業改良場所引種之小麥種原進行遺傳分析及外表型評估,並進一步探勘與重要農藝性狀緊密連鎖的分子標誌。
此種原族群包含39個四倍體杜蘭小麥(Triticum turgidum ssp. durum),60個六倍體斯佩耳特小麥(T. aestivum ssp. spelta),以及765個六倍體麵包小麥(T. aestivum ssp. aestivum)。首先我們利用小麥90K單核苷酸多型性之微陣列晶片進行基因型分型,經過次要等位基因頻率與缺值率的篩選後,將基因型資料用於探勘族群結構與評估親緣關係。主成分分析的結果偵測到三個明顯分群,可分別對應杜蘭小麥、斯佩耳特小麥,以及麵包小麥,另有一些個體則是散布於不同分群之間,我們進一步探勘麵包小麥的族群結構並發現其族群結構與品系的起源有關;而祖源分析與親緣關係樹的結果亦與主成分分析的結果相互呼應。
另外我們也從種原當中分別挑選211及132個麵包小麥品系,於兩次實驗中調查其抽穗期、株高、穗長,以及穗上發芽耐受性等重要農藝性狀,並結合基因型資料進行全基因體關聯性分析,在不同染色體片段上偵測到許多與性狀顯著相關的分子標誌。其中,部分分子標誌則是位於前人研究所偵測到的數量性狀基因座或是已知基因附近,例如利用抽穗期性狀在染色體5A上所偵測到的訊號與Vrn-A1基因位於鄰近區域。
本研究探勘與性狀顯著相關的分子標誌將可應用於未來分子標誌輔助選種,以進一步提升小麥的品質與產量。
zh_TW
dc.description.abstractThe most widely grown wheat variety in Taiwan is “Taichung Sel. 2”, which was released over three decades ago. Climate change and shifting market demand have led to the urgent need for new varieties that are tolerant of extreme weather events and suitable for versatile end uses. However, the breeding resources and genetic studies in wheat are limited in Taiwan. Therefore, the objective of the study was to characterize the population structure of an introduced wheat germplasm and identify SNP markers associated with agronomic traits.
An introduced wheat diversity panel from the Taichung District Agricultural Research and Extension Station, including 39 durum wheat (Triticum turgidum ssp. durum), 60 spelt wheat (T. aestivum ssp. spelta), and 765 bread wheat accessions (T. aestivum ssp. aestivum), was genotyped using 90K single nucleotide polymorphism (SNP) array. After filtering for minor allele frequency and missing rate, the genotypic data were used to characterize the population structure. The results from principal component analysis revealed three distinct clusters which corresponded to durum wheat, spelt wheat, and bread wheat, while some individuals were admixed among groups, in concordance with the results of ancestry analysis and the phylogenetic trees. We further found that the population structure of bread wheat group was related to the origin of accessions.
Two subsets containing 211 and 132 varieties were evaluated for traits such as plant height, days to heading, spike length and resistance to preharvest sprouting. Phenotypic data together with genotypic data were used for genome-wide association studies (GWAS) to identify markers significantly associated with quantitative trait loci (QTL) underlying these traits. Significant markers were detected across the wheat genome. We also found SNPs adjacent to known QTL and cloned genes controlling the traits we investigated. For example, a cluster of SNPs on chromosome 5A was located near the Vrn-A1 gene for days to heading.
Our study provides valuable information that could be used in marker-assisted selection for improving wheat yield and quality.
en
dc.description.provenanceMade available in DSpace on 2021-06-08T02:39:12Z (GMT). No. of bitstreams: 1
U0001-2710202011131600.pdf: 19599490 bytes, checksum: b66ced2ce8d038329081e59b9f469482 (MD5)
Previous issue date: 2020
en
dc.description.tableofcontents誌謝 I
摘要 II
Abstract III
Table of Content V
Index of Figures VII
Index of Tables X
Introduction 1
Materials and Methods 5
Plant material and SNP array hybridization 5
Assign physical position of iSelect 90K SNP markers 5
Genotyping of wheat accessions using Illumina iSelect 90K SNP arrays 6
Principal component analysis (PCA) and phylogenetic tree 7
Model-based clustering analysis and genetic diversity index 7
Genotyping-by-sequencing (GBS) and SNP calling 8
Linkage disequilibrium (LD) analysis 8
Phenotypic evaluation 9
Genome-wide association studies 10
Kompetitive Allele-Specific PCR (KASP) assay 11
Results 12
Physical position of Illumina iSelect wheat 90K markers 12
SNP clustering and SNP genotyping of a wheat diversity panel 14
Genotyping-by-sequencing (GBS) 16
Population structure of wheat species 17
Linkage disequilibrium of wheat species 20
GWAS to identify loci associated with agronomic traits 21
1. Phenotypic variation 21
2. Marker-trait association identified in E1 experiment 22
3. Marker-trait association identified in E2 experiment 24
KASP assay 25
Discussion 28
Resolving physical positions of 90K markers in updated IWGSC RefSeq v2.0 28
SNP clustering, genotype calling, and validation of 90K markers 28
Population structure of the diversity panel and bread wheat accessions 30
Linkage disequilibrium in wheat species 31
Phenotypic variation of a diverse wheat panel 32
Marker-trait associations for agronomic traits 34
Reference 36
Figures 51
Tables 81
dc.language.isoen
dc.title探勘小麥引種種原之族群結構及全基因體關聯性分析zh_TW
dc.titleCharacterization of the Population Structure and Genome-Wide Association Study of Introduced Wheat Germplasmen
dc.typeThesis
dc.date.schoolyear109-1
dc.description.degree碩士
dc.contributor.oralexamcommittee陳凱儀(Kai-Yi Chen),黃永芬(Yung-Fen Huang),林耀正(Yao-Cheng Lin)
dc.subject.keyword小麥,小麥 90K 晶片,族群結構,全基因體關聯性分析,株高,穗長,抽穗期,zh_TW
dc.subject.keywordWheat,Wheat 90K SNP array,Population structure,Genome-wide association study (GWAS),Plant height,Spike length,Days to heading,en
dc.relation.page93
dc.identifier.doi10.6342/NTU202004309
dc.rights.note未授權
dc.date.accepted2020-10-28
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

文件中的檔案:
檔案 大小格式 
U0001-2710202011131600.pdf
  目前未授權公開取用
19.14 MBAdobe PDF
顯示文件簡單紀錄


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。

社群連結
聯絡資訊
10617臺北市大安區羅斯福路四段1號
No.1 Sec.4, Roosevelt Rd., Taipei, Taiwan, R.O.C. 106
Tel: (02)33662353
Email: ntuetds@ntu.edu.tw
意見箱
相關連結
館藏目錄
國內圖書館整合查詢 MetaCat
臺大學術典藏 NTU Scholars
臺大圖書館數位典藏館
本站聲明
© NTU Library All Rights Reserved