發(fā)布時間：2024-02-03 18:27

　　水稻(Oryza sativa L.)對全球數(shù)十億人的生活至關(guān)重要。因為環(huán)境因素多種多樣,包括可能限制水稻產(chǎn)量的生物和非生物逆境脅迫,使得大米的生產(chǎn)一直面臨挑戰(zhàn)。深入探究與水稻抗逆性狀密切相關(guān)的基因?qū)λ居N實踐具有重要的指導(dǎo)意義。應(yīng)用不同測序技術(shù)產(chǎn)生的大量作物基因組DNA序列信息讓研究人員能夠從中識別出大量的分子遺傳標記,并將這些標記用于分析作物的遺傳性狀和品種改良。新一代測序技術(shù)正在加快基因組測序的速度,同時大量的基因組測序產(chǎn)生了海量數(shù)據(jù),這為數(shù)據(jù)管理分析帶來巨大的挑戰(zhàn)。此外,基因組重測序序列分析流程中的各種工具具有參數(shù)設(shè)置與使用復(fù)雜的特點,使研究人員,尤其是非生物信息學(xué)專業(yè)人員,在生物大數(shù)據(jù)前面臨諸多困難。為了實現(xiàn)作物基因組重測序數(shù)據(jù)的流程化管理與分析,本文首先設(shè)計了全新的作物基因組重測序數(shù)據(jù)分析與基因組變異挖掘技術(shù)平臺;然后應(yīng)用該平臺技術(shù),從對不同逆境脅迫具有不同抗性能力的水稻品種中檢測出SNP(Single Nucleotide Polymorphism)及其基因,并構(gòu)建了一個水稻抗逆脅迫SNPs數(shù)據(jù)庫;最后,在廣泛收集抗稻瘟病水稻品種及其基因組重測序數(shù)據(jù)的基礎(chǔ)上,應(yīng)用上述平...

【文章頁數(shù)】：166 頁

【學(xué)位級別】：博士

【文章目錄】：
摘要
ABSTRACT
1 Introduction
    1.1 Rice importance and challenges
    1.2 Breeding technologies
    1.3 Rice NGS
    1.4 Study aims and objectives
2 LITERATURE REVIEW
    2.1 Next Generation Sequencing technology
        2.1.1 Next-generation sequencing
        2.1.2 DNA and RNA data analysis
        2.1.3 Analysis pipelines for the NGS data
    2.2 Next Generation Sequencing technology applications in plants
        2.2.1 Techniques for SNP identification in plants
        2.2.2 The applications of SNPs in plants
        2.2.3 Plant comparative transcriptomics
3 Rice Genomic Variant Analysis platform
    3.1 Introduction
    3.2 Materials and Methods
        3.2.1 Data collection
        3.2.2 Implementation
        3.2.3 NGS Snakemake workflow
        3.2.4 Equipment
    3.3 Results
        3.3.1 Running genomic variant analysis pipeline
        3.3.2 Output Files
    3.4 Discussion
        3.4.1 The necessity of developing a new genomic variant analysis pipeline
        3.4.2 Rice genomic variant analysis pipeline features
    3.5 Conclusion
4 Rice Stress-Resistant SNP database
    4.1 Introduction
    4.2 Materials and Methods
        4.2.1 Data collection and organization
        4.2.2 SNP Calling and Annotation
        4.2.3 Identification of Stress-Resistant SNPs in Rice
        4.2.4 Database Design and Web-Application Architecture
    4.3 Results and Discussion
        4.3.1 Database Content
        4.3.2 Phenotype Data
        4.3.3 SNP Data
        4.3.4 Biotic Stress-Resistant SNPs
        4.3.5 Abiotic Stress-Resistant SNPs
        4.3.6 Web Interface
    4.4 Conclusion
5 Genome-wide identification of blast resistant SNPs and genes in rice(Oryza sativa L.)
    5.1 Introduction
    5.2 Materials and Methods
        5.2.1 Data Collection
        5.2.2 Detection of Variant in different rice varieties
        5.2.3 Functional classification of SNPs
        5.2.4 Identification of blast-resistant candidate SNPs from blast resistant rice varieties
        5.2.5 Identification of blast-responsive genes in rice using RNA-seq data
        5.2.6 Assessment of deleterious SNPs
        5.2.7 Detailed annotation of identified blast-resistant candidate genes
    5.3 Results
        5.3.1 Genome assembly of different rice varieties
        5.3.2 Variant detection from the different rice variety genomes
        5.3.3 Classification of the blast-resistant candidate SNPs
        5.3.4 Identification of blast-resistant candidate genes in rice
        5.3.5 GO enrichment analysis of blast-resistant candidate genes
        5.3.6 Analysis on the expression of blast-resistant candidate genes in rice under the infection of blast fungus
        5.3.7 In-silico prediction of deleterious ns SNPs in the blast-resistant candidate genes
        5.3.8 Prediction of the impact of deleterious ns SNPs on the function and structure of the blast-resistant candidate genes
    5.4 Discussion
        5.4.1 Mining of blast-resistant candidate ns SNPs and genes in rice
        5.4.2 Analysis on the function and expression of blast-resistant candidate genes
        5.4.3 Analysis of the impact of blast-resistant candidate ns SNPs on their target genes
    5.5 Conclusion
Appendix
    A-1 List of Abiotic and Biotic stress responsive rice varieties
    A-2 Snakemake workflow
    A-3 List of Abiotic and Biotic Resistant Genes in rice
    A-4 List of ns SNPs in up-regulated genes predicted as deleterious using SIFT and Poly Phen-2 SNP prediction tools
    A-5 Differential expression fold change of genes associated with the deleterious nsSNPs
    A-6 Functional annotation of up-regulated genes having deleterious ns SNPs
References
Published Papers and other Academic Achievements during the Program
Acknowledgements



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