雜草是全球農(nóng)業(yè)生產(chǎn)中面臨的主要問題,而稗草則是這其中危害比較嚴重的一種。研究表明,稗草可以導致約35%的水稻減產(chǎn)�；凶饔檬怯苫形镔|(zhì)釋放介導的作物與雜草相互作用的一個核心過程,這種化感物質(zhì)對相互作用的一種或另一種植物的生長造成不利的影響。近來,許多研究表明利用化感互作進行雜草防治可以降低雜草的危害,提升作物產(chǎn)量。然而目前對水稻與稗草之間的互作的分子機制知之甚少。尤其對許多關鍵化感物質(zhì)的生物合成基因組機制尚不清楚。本研究中我們利用不同時間點水稻與稗草單獨培養(yǎng)以及共培養(yǎng)的轉(zhuǎn)錄組學數(shù)據(jù),研究了水稻和稗草之間的化感互作。此外,我們分析鑒定了參與調(diào)控水稻與稗草化感互作過程中參與調(diào)控的基因簇和基因模塊。本研究主要發(fā)現(xiàn)如下:（1）通過轉(zhuǎn)錄組分析鑒定參與水稻-雜草互作的水稻化感基因我們使用水稻RNA-seq數(shù)據(jù)（單獨培養(yǎng)和與稗草共培）鑒定在3小時和3天兩個時間點調(diào)控水稻和稗草相互作用的基因及其功能�；诔蓪Ρ容^的方法,我們鑒定出3,453個上調(diào)和2,231個下調(diào)的差異表達基因（DEG）。值得注意的是,有393個基因是在所有時間節(jié)點都能被檢出,這些基因參與了不同的化感作用途徑�；虮倔w論（GO）結(jié)果表... 

【文章來源】：浙江大學浙江省 211工程院校 985工程院校 教育部直屬院校

【文章頁數(shù)】：150 頁

【學位級別】：博士

【文章目錄】：
DEDICATION
Acknowledgements
Abstract
摘要
Chapter1 Literature review
    1.1 Rice and paddy weeds
        1.1.1 Rice
        1.1.2 Barnyardgrass（Echinochloa crus-galli）
        1.1.3 Rice and barnyardgrass interaction
    1.2 Allelopathy and allelochemicals
        1.2.1 Mechanism of plant allelopathy
        1.2.2 Different type of allelopathy and allelochemicals
        1.2.3 Application of rice allelopathy
        1.2.4 Allelochemical application in weed management
        1.2.5 Genes/QTLs regulating the allelopathy
    1.3 Biosynthesis gene cluster（BGC）
        1.3.1 Biosynthesis gene cluster and allelochemicals
        1.3.2 Importance of biosynthesis gene cluster
    1.4 Co-expression network analysis
Chapter2 Transcriptomic profiling reveals rice allelochemical genes involving in the rice-barnyardgrass interaction
    2.1 Introduction
    2.2 Materials and Methods
        2.2.1 Plant materials and growth conditions
        2.2.2 RNA extraction,cDNA library construction and Illumina sequencing
        2.2.3 Data filtering,reads mapping and gene quantification
        2.2.4 Differentially expressed genes analysis and annotation
        2.2.5 Time-series expression profile
        2.2.6 Gene expression validation using quantitative real-time PCR（qRT-PCR）
    2.3 Results
        2.3.1 Summary of RNA-Seq data
        2.3.2 Identification of differentially expressed genes
        2.3.3 Gene Ontology（GO）and pathway enrichment analysis of DEGs
        2.3.4 Allelochemical responsible transcription factors
        2.3.5 Clustering of time-series expression profile by STEM
        2.3.6 Expression pattern of rice allelochemical genes
        2.3.7 Identification of allelochemical associated genes in rice
        2.3.8 qRT-PCR analysis results for RNA-Seq data validation
    2.4 Discussion
    2.5 Appendix
Chapter3 Identification of new biosynthetic gene clusters（BGCs）for allelopathy in rice and barnyardgrass genomes
    3.1 Introduction
    3.2 Materials and Methods
        3.2.1 Plant materials and growth conditions
        3.2.2 Analysis of RNA-seq data
        3.2.3 Metabolic pathway annotation and candidate BGCs prediction
        3.2.4 Gene cluster validation by co-pathway and co-expression analyses
        3.2.5 Co-expression network investigation
        3.2.6 Module hub gene and their enrichment analysis
        3.2.7 Orthologous gene identification
        3.2.8 Gene expression validation using quantitative real-time PCR（qRT-PCR）
    3.3 Results
        3.3.1 Transcriptomic profiling for allelopathic interaction between rice and barnyardgrass
        3.3.2 Identification of candidate biosynthetic gene clusters in rice and barnyardgrass
        3.3.3 Gene modules co-regulated with the DIMBOA and potential momilactone gene clusters in barnyardgrass
        3.3.4 New hub genes co-regulating with the two known diterpenoid gene clusters in rice
        3.3.5 Putative upstream genes of the DIMBOA and presumable momilactone BGCs in barnyardgrass
    3.4 Discussion
    3.5 Appendix
Chapter4 Major findings and future perspectives
    4.1 Major findings
    4.2 Future perspectives
References
List of publications


【參考文獻】：
期刊論文
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