水稻与稗草化感互作相关基因及基因簇鉴定

发布时间：2021-03-04 02:46

　　杂草是全球农业生产中面临的主要问题,而稗草则是这其中危害比较严重的一种。研究表明,稗草可以导致约35%的水稻减产。化感作用是由化感物质释放介导的作物与杂草相互作用的一个核心过程,这种化感物质对相互作用的一种或另一种植物的生长造成不利的影响。近来,许多研究表明利用化感互作进行杂草防治可以降低杂草的危害,提升作物产量。然而目前对水稻与稗草之间的互作的分子机制知之甚少。尤其对许多关键化感物质的生物合成基因组机制尚不清楚。本研究中我们利用不同时间点水稻与稗草单独培养以及共培养的转录组学数据,研究了水稻和稗草之间的化感互作。此外,我们分析鉴定了参与调控水稻与稗草化感互作过程中参与调控的基因簇和基因模块。本研究主要发现如下:（1）通过转录组分析鉴定参与水稻-杂草互作的水稻化感基因我们使用水稻RNA-seq数据（单独培养和与稗草共培）鉴定在3小时和3天两个时间点调控水稻和稗草相互作用的基因及其功能。基于成对比较的方法,我们鉴定出3,453个上调和2,231个下调的差异表达基因（DEG）。值得注意的是,有393个基因是在所有时间节点都能被检出,这些基因参与了不同的化感作用途径。基因本体论（GO）结果表... 

【文章来源】：浙江大学浙江省 211工程院校 985工程院校 教育部直属院校

【文章页数】：150 页

【学位级别】：博士

【文章目录】：
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


【参考文献】：
期刊论文
[1]Allelopathy:Potential Role to Achieve New Milestones in Rice Cultivation[J]. M.K.AMB,A.S.AHLUWALIA.  Rice Science. 2016(04)
[2]中国粮食安全和水稻生产[J]. 章秀福,王丹英,方福平,曾衍坤,廖西元.  农业现代化研究. 2005(02)
[3]水稻化感品种根分泌物中非酚酸类化感物质的鉴定与抑草活性[J]. 孔垂华,徐效华,梁文举,周勇军,胡飞.  生态学报. 2004(07)
[4]Genetic analysis of rice allelopathy[J]. ZENG Dali1, QIAN Qian1, TENG Sheng1, DONG Guojun1, H. Fujimoto2, Kunihifo Yasufumi2 & ZHU Lihuang3 1. Key Lab for Rice Biology, Ministry of Agriculture, Institute of China National Rice Research, Hangzhou 310006, China; 2. Japan International Research Center for Agriculture Science, Tsukuba 305-8686, Japan; 3. Institute of Genetics, Chinese Academy of Sciences, Beijing 100101, China.  Chinese Science Bulletin. 2003(03)
[5]Using specific secondary metabolites as markers to evaluate allelopathic potentials of rice varieties and individual plants[J]. KONG Chuihua, XU Xiaohua, HU Fei, CHEN Xionghui, LING Bing & TAN ZhongwenInstitute of Tropical and Subtropical Ecology, South China Agricultural University, Guangzhou 510642, China;National Key Lab of Organo-elemental Chemistry in Nankai University, Tianj.  Chinese Science Bulletin. 2002(10)
[6]水稻化感作用及其生理生化特性的研究[J]. 林文雄,何华勤,郭玉春,梁义元,陈芳育.  应用生态学报. 2001(06)



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