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研究生(外文):Hsin-Yu Ma
論文名稱(外文):Evaluate seed vigour and related genetic architecture of weedy rice collected in Taiwan
指導教授(外文):Yung-Fen Huang
口試委員(外文):Yeong-Jene ChiangDong-Hong WuYi-Ting HsuChih-Wei Tung
外文關鍵詞:Weedy riceSeed vigourGenome-wide association study
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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
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