跳到主要內容

臺灣博碩士論文加值系統

(100.28.132.102) 您好!臺灣時間:2024/06/21 23:32
字體大小: 字級放大   字級縮小   預設字形  
回查詢結果 :::

詳目顯示

我願授權國圖
: 
twitterline
研究生:馬欣瑜
研究生(外文):Hsin-Yu Ma
論文名稱:評估臺灣雜草稻收集系種子活力與其遺傳結構
論文名稱(外文):Evaluate seed vigour and related genetic architecture of weedy rice collected in Taiwan
指導教授:黃永芬
指導教授(外文):Yung-Fen Huang
口試委員:蔣永正吳東鴻許奕婷董致韡
口試委員(外文):Yeong-Jene ChiangDong-Hong WuYi-Ting HsuChih-Wei Tung
口試日期:2020-07-16
學位類別:碩士
校院名稱:國立臺灣大學
系所名稱:農藝學研究所
學門:農業科學學門
學類:一般農業學類
論文種類:學術論文
論文出版年:2020
畢業學年度:108
語文別:英文
論文頁數:83
中文關鍵詞:雜草稻種子活力全基因體關聯性分析
外文關鍵詞:Weedy riceSeed vigourGenome-wide association study
DOI:10.6342/NTU202003454
相關次數:
  • 被引用被引用:0
  • 點閱點閱:139
  • 評分評分:
  • 下載下載:0
  • 收藏至我的研究室書目清單書目收藏:0
近年來,雜草稻在世界各地的水稻生產區成為危害嚴重的雜草。臺灣的水稻生產即便使用慣以提高雜草管理效率的移植栽培系統,仍遭受雜草稻的入侵導致稻米產量以及品質降低。雜草稻與栽培稻同為Oryza sativa L. 卻帶有雜草化特性,如高度種子休眠性和種子落粒性,以及旺盛的種子活力。至今,關於雜草稻種子活力相關研究甚少,故本研究以250個收集自臺灣之雜草稻、地方品系以及常用秈稻與粳稻栽培品種,與數個野生稻及美國雜草稻作為材料,調查其種子活力特性以及與遺傳結構之關聯。本研究利用加速老化方法評估種子壽命以及簡易影像系統測量幼苗的中胚軸、芽長和根表面積,並進行全基因體關聯性分析。本研究鑑定21個與種子活力性狀具有關聯性的分子標誌,其中六個分子標誌位於已知基因的序列中,其功能與種子活力、中胚軸伸長、根系生長、低溫發芽和穀粒形態相關,日後需進一步研究釐清候選基因座的變異與種子活力的關係。本研究乃首次調查臺灣雜草稻收集系種子活力,並且利用全基因體關聯性分析探討 種子活力遺傳結構,這些結果將提供未來臺灣雜草稻遺傳育種研究做為參考。
Weedy rice (WR) is a major threat for rice production worldwide. In Taiwan, the infestation of WR is getting serious in recent years, despite of a transplanting system which is considered as an effective way for weed management. WR is a conspecific weed of cultivated rice (Oryza sativa L.) but it possesses weedy characters, such as variable seed dormancy, high seed shattering and good seed vigour. An effective weed management requires knowledge about the weed. However, little is known about the genetics of seed vigour in WR. Therefore, we aim to investigate genetic architecture of seed vigour traits on a panel of WR accessions. We use 250 rice accessions including WR collected in Taiwan and some in the USA, as well as wild rice and some cultivars. Seed longevity is characterized using artificial accelerate aging test. Mesocotyl length, shoot length and root surface areas are also measured. Genome-wide association study (GWAS) was further performed. Twenty-one seed vigour-related SNPs were identified. Six trait-marker associations were located in known genes, related to mesocotyl elongation, root growth, germination ability and grain size regulation. Validation should be conducted to confirm the actual allelic effect. This is the first study to evaluate seed vigour, as well as to conduct GWAS in WR collected in Taiwan. Together, these results provide information for further WR research.
口試委員審定書 i
致謝 ii
摘要 iii
Abstract iv
Table of contents v
List of tables vii
List of figures viii
List of abbreviation ix
1. Introduction 1
1.1. Weedy rice 1
1.2. Seed vigour 2
1.3. Genome-wide association studies of seed vigour 4
1.4. Weedy rice in Taiwan 4
1.5. Objective of the study 5
2. Materials and Methods 6
2.1. Plant materials 6
2.2. Genomic DNA extraction and genotyping 7
2.3. Evaluation of seed vigour 8
2.3.1. Seed longevity phenotyping 8
2.3.2. Seed longevity phenotyping-evaluation of 250 accessions 9
2.3.3. Mesocotyl, shoot and root phenotyping 10
2.3.4. Mesocotyl, shoot and root phenotyping-evaluation of 250 accessions 11
2.3.5. Grain size phenotyping 12
2.4. Statistical analysis and genome-wide association mapping 13
3. Results 14
3.1. Preliminary test 14
3.2. Evaluation of seed vigour traits 14
3.3. Genome-wide association studies and annotation 17
4. Discussion 19
4.1. Phenotyping method 19
4.2. Phenotypic analysis 21
4.3. GWAS and candidate gene analysis 23
5. Conclusion 26
References 28
Appendix 61
Akiyama K, Matsuzaki K, Hayashi H (2005) Plant sesquiterpenes induce hyphal branching in arbuscular mycorrhizal fungi. Nature 435:824-827
Borjas AH, De Leon TB, Subudhi PK (2015) Genetic analysis of germinating ability and seedling vigor under cold stress in US weedy rice. Euphytica 208:251-264
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
Burgos NR, Norman RJ, Gealy DR, Black H (2006) Competitive N uptake between rice and weedy rice. Field Crops Research 99:96-105
Cheng CY, Wu YC, Wu BG, Li CP, Gealy DR and Wu DH (2017) Morphological diversity study on Taiwan weedy red rice. Journal of the Agricutural Association of Taiwan 18:161-188
Choi J, Lee T, Cho J, Servante EK, Pucker B, Summers W, Bowden S, Rahimi M, An K, An G, Bouwmeester HJ, Wallington EJ, Oldroyd G, Paszkowski U (2020) The negative regulator SMAX1 controls mycorrhizal symbiosis and strigolactone biosynthesis in rice. Nature Communications 11:2114
Chung NJ (2010) Elongation habit of mesocotyls and coleoptiles in weedy rice with high emergence ability in direct-seeding on dry paddy fields. Crop and Pasture Science 61:911-917
Dai L, Song X, He B, Valverde BE, Qiang S (2017) Enhanced photosynthesis endows seedling growth vigour contributing to the competitive dominance of weedy rice over cultivated rice. Pest management science 73:1410-1420
Dang X, Thi TG, Dong G, Wang H, Edzesi WM, Hong D (2014) Genetic diversity and association mapping of seed vigor in rice (Oryza sativa L.). Planta 239:1309-1319
Delouche JC, Baskin CC (1973) Accelerated aging techniques for predicting the relative storability of seed lots. Seed Science Technology 1:427-52
Dilday RH, Mgonja MA, Amonsilpa SA, Collins FC, Wells BR (1990) Plant Height vs. Mesocotyl and Celeoptile Elongation in Rice: Linkage or Pleitropism? Crop science 30:815-818
Ellis RJ (1992) Seed and seedling vigour in relation to crop growth and yield. Plant growth regulation. 11:249-255
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
Feng F, Mei H, Fan P, Li Y, Xu X, Wei H, Yan M, Luo L (2017) Dynamic transcriptome and phytohormone profiling along the time of light exposure in the mesocotyl of rice seedling. Scientific reports 7:11961
Ferrero A (2003) Weedy rice, biological features and control. In: Weed Management for Developing Countries (ed. R LABRADA): 89-107 FAO, Rome, Italy
Franks SJ, Sekor MR, Davey S, Weis AE (2019) Artificial seed aging reveals the invisible fraction: Implications for evolution experiments using the resurrection approach. Evolutionary Ecology 33:811-824
Fujino K, Sekiguchi H, Matsuda Y, Sugimoto K, Ono K, Yano M (2008) Molecular identification of a major quantitative trait locus, qLTG-3-1, controlling low-temperature germinability in rice. Proceedings of the National Academy of Sciences 105:12623-12628
Galkovskyi T, Mileyko Y, Bucksch A, Moore B, Symonova O, Price CA, Topp CN, Iyer-Pascuzzi AS, Zurek PR, Fang S, Harer J, Benfey PN, Weitz JS (2012) GiA Roots: software for the high throughput analysis of plant root system architecture. BMC plant biology 12:116
Gibson KD, Foin TC, Hill JE (1999) The relative importance of root and shoot competition between water-seeded rice and Echinochloa phyllopogon. Weed research 39:181-190
Gomez-Roldan V, Fermas S, Brewer PB, Puech-Pages V, Dun EA, Pillot JP, Letisse F, Matusova R, Danoun S, Portais JC, Bouwmeester H, Becard G, Beveridge CA, Rameau C, Rochange SF (2008) Strigolactone inhibition of shoot branching. Nature 455:189-194
Goss WL, Brown E (1939) Buried Red Rice Seed 1. Agronomy Journal 31: 633-637
Huang CT (2019) Genome-wide association study reveals the genetic architecture of seed vigour in elite oat lines and landraces. Department of Agronomy. National Taiwan University. pp 1-84 (In Chinese)
Hang NT, Lin Q, Liu L, Liu X, Liu S, Wang W, Li L, He N, Liu Z, Jiang L, Wan J (2014) Mapping QTLs related to rice seed storability under natural and artificial aging storage conditions. Euphytica 203:673-681
Hu Z, Yamauchi T, Yang J, Jikumaru Y, Tsuchida-Mayama T, Ichikawa H, Takamure I, Nagamura Y, Tsutsumi N, Yamaguchi S, Kyozuka J, Nakazono M (2014) Strigolactone and cytokinin act antagonistically in regulating rice mesocotyl elongation in darkness. Plant Cell Physiol 55:30-41
Hu Z, Yan H, Yang J, Yamaguchi S, Maekawa M, Takamure I, Tsutsumi N, Kyozuka J, Nakazono M (2010) Strigolactones negatively regulate mesocotyl elongation in rice during germination and growth in darkness. Plant Cell Physiol 51:1136-1142
Imaizumi T (2018) Weedy rice represents an emerging threat to transplanted rice production systems in Japan. Weed Biology and Management 18:99-102
Jin J, Long W, Wang L, Liu X, Pan G, Xiang W, Li N, Li S (2018) QTL mapping of seed vigor of backcross inbred lines derived from Oryza longistaminata under artificial aging. Frontiers in Plant Science 9:1909
López‐Castañeda C, Richards RA, Farquhar GD, Williamson RE (1996) Seed and seedling characteristics contributing to variation in early vigor among temperate cereals. Crop Science 36:1257-1266
Lee HS, Sasaki K, Higashitani A, Ahn SN, Sato T (2012) Mapping and characterization of quantitative trait loci for mesocotyl elongation in rice (Oryza sativa L.). Rice 5:13
Lee JS, Velasco-Punzalan M, Pacleb M, Valdez R, Kretzschmar T, McNally KL, Ismail AM, Cruz PCS, Sackville Hamilton NR, Hay FR (2019) Variation in seed longevity among diverse Indica rice varieties. Annals of botany 124:447-460
Li H, Han Y, Cai Z (2003) Nitrogen mineralization in paddy soils of the Taihu Region of China under anaerobic conditions: dynamics and model fitting. Geoderma 115:161-175
Liang Q, Wang C, Ma D, Li L, Cui Z, Wang X, Qian Q, Cai B, Feng Y, Chen W (2016) Cortical microtubule disorganized related to an endogenous gibberellin increase plays an important role in rice mesocotyl elongation. Plant Biotechnology 33:59-69
Liu H, Zhan J, Li J, Lu X, Liu J, Wang Y, Zhao Q, Ye G (2019) Genome-wide association study (GWAS) for mesocotyl elongation in rice (Oryza sativa L.) under multiple culture conditions. Genes 11:49
Liu J, Chen J, Zheng X, Wu F, Lin Q, Heng Y, Tian P, Cheng Z, Yu X, Zhou K, Xin Z, Guo XP, Wang JL, Wang HY, Wan JM (2017) GW5 acts in the brassinosteroid signalling pathway to regulate grain width and weight in rice. Nature Plants 3:1-7
Loercher L (1966) Phytochrome changes correlated to mesocotyl inhibition in etiolated Avena seedlings. Plant physiology 41:932-936
Lu Q, Zhang M, Niu X, Wang C, Xu Q, Feng Y, Wang S, Yuan X, Yu H, Wang Y, Wei X (2016) Uncovering novel loci for mesocotyl elongation and shoot length in indica rice through genome-wide association mapping. Planta 243:645-657
Mahender A, Anandan A, Pradhan SK (2015) Early seedling vigour, an imperative trait for direct-seeded rice: an overview on physio-morphological parameters and molecular markers. Planta 241:1027-1050
Mao H, Sun S, Yao J, Wang C, Yu S, Xu C, Li X, Zhang Q (2010) Linking differential domain functions of the GS3 protein to natural variation of grain size in rice. Proceedings of the National Academy of Sciences 107:19579-19584
Mgonja M, Ladeinde TAO, Aken'Ova ME (1993) Genetic analysis of mesocotyl length and its relationship with other agronomic characters in rice (Oryza sativa L.). Euphytica 72:189-195
Miura K, Lin Y, Yano M, Nagamine T (2002) Mapping quantitative trait loci controlling seed longevity in rice (Oryza sativa L.). Theoretical and Applied Genetics 104:981-986
Nadir S, Xiong H-B, Zhu Q, Zhang X-L, Xu H-Y, Li J, Dongchen W, Henry D, Guo X-Q, Khan S, Suh H-S, Lee DS, Chen L-J (2017) Weedy rice in sustainable rice production. A review. Agronomy for Sustainable Development 37
Noldin JA, Chandler JM, McCauley GN (2006) Seed longevity of red rice ecotypes buried in soil. Planta Daninha 24:611-620
Ohno H, Banayo NPMC, Bueno CS, Kashiwagi J-i, Nakashima T, Corales AM, Garcia R, Sandhu N, Kumar A, Kato Y (2018) Longer mesocotyl contributes to quick seedling establishment, improved root anchorage, and early vigor of deep-sown rice. Field Crops Research 228:84-92
Olajumoke B, Juraimi AS, Uddin M, Husni MH, Alam M (2016) Competitive ability of cultivated rice against weedy rice biotypes: A review. Chilean journal of agricultural research 76:243-252
Pipatpongpinyo W, Korkmaz U, Wu H, Kena A, Ye H, Feng J, Gu XY (2020) Assembling seed dormancy genes into a system identified their effects on seedbank longevity in weedy rice. Heredity 124:135-145
Radford B, Henzell RG (1990) Temperature affects the mesocotyl and coleoptile length of grain sorghum genotypes. Australian Journal of Agricultural Research 41:79-87
Rao NK, Jackson MT (1996) Seed longevity of rice cultivars and strategies for their conservation in genebanks. Annals of Botany 77:251-260
Rebolledo MC, Dingkuhn M, Courtois B, Gibon Y, Clement-Vidal A, Cruz DF, Duitama J, Lorieux M, Luquet D (2015) Phenotypic and genetic dissection of component traits for early vigour in rice using plant growth modelling, sugar content analyses and association mapping. Journal of experimental botany 66:5555-5566
Redoña ED, Mackill DJ (1996) Genetic variation for seedling vigor traits in rice. Crop Science 36:285-290
Revelle WJ (2011) An overview of the psych package. Dep Psychol Northwest Uni 3:1-25
Saikrishna A, Dutta S, Subramanian V, Moses JA, Anandharamakrishnan C (2018) Ageing of rice: A review. Journal of Cereal Science 81:161-170
Sales MA, Burgos NR, Shivrain VK, Murphy B, Gbur EE (2011) Morphological and Physiological Responses of Weedy Red Rice (Oryza sativa L.) and Cultivated Rice (O. sativa) to N Supply. American Journal of Plant Sciences 02:569-577
Sano N, Rajjou L, North HM, Debeaujon I, Marion-Poll A, Seo M (2016) Staying Alive: Molecular Aspects of Seed Longevity. Plant Cell Physiology 57:660-674
Sasaki K, Takeuchi Y, Miura K, Yamaguchi T, Ando T, Ebitani T, Higashitani A, Yamaya T, Yano M, Sato T (2015) Fine mapping of a major quantitative trait locus, qLG-9, that controls seed longevity in rice (Oryza sativa L.). Theoretical and Applied Genetics 128:769-778
Schindelin J, Arganda-Carreras I, Frise E, Kaynig V, Longair M, Pietzsch T, Preibisch S, Rueden C, Saalfeld S, Schmid B, Tinevez JY, White DJ, Hartenstein V, Eliceiri K, Tomancak P, Cardona A (2012) Fiji: an open-source platform for biological-image analysis. Nature methods 9:676-682
Shrestha S, Stallworth S, Tseng TM (2018) Weedy Rice: competitive ability, evolution, and diversity. Integrated View of Population Genetics. IntechOpen
Simon A (2011) Relationship between coleoptile and mesocotyl elongation of upland rice (Oryza sativa L.) seedlings under submergence and soil-sand culture. African Journal of Agricultural Research 6: 6463-6472
Sweeney MT, Thomson MJ, Pfeil BE, 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
Wang F, Longkumer T, Catausan SC, Calumpang CLF, Tarun JA, Cattin-Ortola J, Ishizaki T, Pariasca Tanaka J, Rose T, Wissuwa M, Kretzschmar T (2018) Genome-wide association and gene validation studies for early root vigour to improve direct seeding of rice. Plant, Cell & Environment 41:2731-2743
Whan AP, Smith AB, Cavanagh CR, Ral JPF, Shaw LM, Howitt CA, Bischof L (2014) GrainScan: a low cost, fast method for grain size and colour measurements. Plant methods 10: 23
Wu DH, Gealy DR, Jia MH, Edwards JD, Lai MH, McClung AM (2020) Phylogenetic origin and dispersal pattern of Taiwan weedy rice. Pest Management Science 76:1639-1651
Wu J, Feng F, Lian X, Teng X, Wei H, Yu H, Xie W, Yan M, Fan P, Li Y, Ma X, Liu H, Yu S, Wang G, Zhou F, Luo L, Mei H (2015) Genome-wide association study (GWAS) of mesocotyl elongation based on re-sequencing approach in rice. BMC plant biology 15:218
Xia HB, Xia H, Ellstrand NC, Yang C, Lu BR (2011) Rapid evolutionary divergence and ecotypic diversification of germination behavior in weedy rice populations. New Phytologist 191:1119-1127
Xiong Q, Ma B, Lu X, Huang YH, He SJ, Yang C, Yin CC, Zhao H, Zhou Y, Zhang WK, Wang WS, Li ZK, Chen SY, Zhang JS (2017) Ethylene-inhibited jasmonic acid biosynthesis promotes mesocotyl/coleoptile elongation of etiolated rice seedlings. Plant Cell 29:1053-1072
Yoneyama K, Xie X, Sekimoto H, Takeuchi Y, Ogasawara S, Akiyama K, Hayashi H, Yoneyama K (2008) Strigolactones, host recognition signals for root parasitic plants and arbuscular mycorrhizal fungi, from Fabaceae plants. New Phytologist 179:484-494
You J, Zong W, Hu H, Li X, Xiao J, Xiong L (2014) A STRESS-RESPONSIVE NAC1-regulated protein phosphatase gene rice protein phosphatase18 modulates drought and oxidative stress tolerance through abscisic acid-independent reactive oxygen species scavenging in rice. Plant physiology 166:2100-2114
Zhan J, Lu X, Liu H, Zhao Q, Ye G (2019) Mesocotyl elongation, an essential trait for dry-seeded rice (Oryza sativa L.): a review of physiological and genetic basis. Planta 251:27
Zhao Y, Zhao W, Jiang C, Wang X, Xiong H, Todorovska EG, Yin Z, Chen Y, Wang X, Xie J, Pan Y, Rashid MAR, Zhang H, Li J, Li Z (2018) Genetic architecture and candidate genes for deep-sowing tolerance in rice revealed by non-syn GWAS. Frontiers in plant science 9:332
Zhou W, Chen F, Luo X, Dai Y, Yang Y, Zheng C, Yang W, Shu K (2020a) A matter of life and death: Molecular, physiological, and environmental regulation of seed longevity. Plant, Cell & Environment 43:293-302
Zhou Y, Zhou S, Wang L, Wu D, Cheng H, Du X, Mao D, Zhang C, Jiang X (2020b) miR164c and miR168a regulate seed vigor in rice. Journal of Integrative Plant Biology 62:470-486
Zhu C, Gore M, Buckler ES, Yu J (2008) Status and Prospects of Association Mapping in Plants. The Plant Genome 1:5-20
Ziska LH, Gealy DR, Burgos N, Caicedo AL, Gressel J, Lawton-Rauh AL, Avila LA, Theisen G, Norsworthy J, Ferrero A, Vidotto F, Johnson DE, Ferreira FG, Marchesan E, Menezes V, Cohn MA, Linscombe S, Carmona L, Tang R, Merotto A (2015) Weedy (Red) Rice: an emerging constraint to global rice production. In Advances in agronomy. Academic Press, pp 181-228
連結至畢業學校之論文網頁點我開啟連結
註: 此連結為研究生畢業學校所提供,不一定有電子全文可供下載,若連結有誤,請點選上方之〝勘誤回報〞功能,我們會盡快修正,謝謝!
QRCODE
 
 
 
 
 
                                                                                                                                                                                                                                                                                                                                                                                                               
第一頁 上一頁 下一頁 最後一頁 top