| 週次 |
授課內容 |
| 第1週 |
2/18: Introduction (呂維茗)
An overview of genome biology (楊長賢)
2/25: Plant genome organization
3/4: Plant gene regulation
Student’s oral report (時間另訂，約在6/10)
Structural Genomics (呂維茗)
3/11: Structure of the eukaryotic genome- Cytogenetic map
1. Single sequence DNA (Promoters, CpG island, 5-methylcytosine, Bisulfite sequencing)
2. Intermediate repeat DNA (Retrotransposon, DNA transposon, Tandem repeat gene arrays)
3. Highly repetitive DNA (Satellite, Minisatellite, Microsatellite/SSR)
4. Techniques for cytogenetic study (Chromosomal banding, Chromosomal FISH)
3/18: How to sequence a genome? Physical map
5. Whole genome shotgun (WGS) approach (N50 & L50)
6. Clone-by-clone approach (“Landmark” molecular markers- STS & EST, Vectors, Strategies for clone-contig constructions, Physical gaps)
3/25: From phenotype to gene - Genetic map (4/1: 放假)
7. “Polymorphic” molecular markers (RFLP, CAP, RAPD, AFLP, SCAR, SSR, INDEL, SNP, dCAP)
8. Coarse mapping
9. Fine mapping
10. Map-based gene cloning
11. Molecular Breeding (Marker-Assisted Selection, MAS)
12. Mapping population (NIL, RIL, Bulked segregant analysis (BSA))
13. Linkage between different maps
4/8: New techniques used in genome project
14. Sanger’s dideoxy sequencing (first generation)
15. Next generation sequencing (NGS) (Pyrosequencing, Ion torrent, Solexa technology)
16. Third generation sequencing (SMRT- PacBio; Nonopore- Oxford)
17. Alternative strategies and technologies to help WGS (Optical mapping, Single-molecule next-generation mapping, 10X genomics)
18. Supporting techniques (QC of DNA/RNA, Removal of ribosomal RNA, Strand-specific library, DNA/RNA fragmentation, DNA/RNA fractionation
4/15: Genomics and Postgenomics
19. Genome project (HGP, other genome project)
20. Terms (alternative splicing, molecular clock, homologous sequences, synteny, proteome)
21. Database resource (to browse, to search, or to obtain sequences using NCBI, TIGR, Addgene as examples)
22. Postgenomic era (ENCODE, SNP, MAF, Haplotype, Tag SNP, GWAS, genotyping platforms, T2T)
Functional Genomics (呂維茗)
4/22 & 4/29: Gene expression- mRNA profiling
1. Microarray (Spotted array, Agilent, Affymetrix, Nimblegen; Single base extension (SBE), ChIP-chip, exome sequencing, array Comparative Genomic Hybridization (aCGH))
2. RNA-seq & data mining (mapping, DEseq2 and DEGSeq, Pricipal Componene Analysis (PCA), GO enrichiment analysis, K means clustering, etc.)
3. Real-time PCR (quantitative PCR (qPCR), TaqMan, SYBR)
4. Digital PCR (droplet digital PCR (ddPCR))
5. To view gene expression data (Genevestigator, the bioanalytical resource for plant biology (BAR))
5/6: Reverse genetics
6. Transgenic analysis (activation-tagging, tagged-mutation, RNA interference; tail-PCR, Plasmid rescue, Inverse-PCR)
7. Tilling and random mutation
8. New strategy for plant knock-out (TALEN, CRISPR/Cas9)
Functional Assays and CRISPR/Cas9 Applications in Plant Genomics (黃纓雯)
5/13: Gene Functional Assays in Plants: Gene Silencing and Overexpression
Part 1: Gene Knockdown through RNAi and Other Silencing Methods
• Mechanisms of RNA interference (RNAi) in plants
• Alternative silencing technologies (e.g., VIGS, amiRNA)
• Experimental design and troubleshooting
Part 2: Strategies for Gene Overexpression in Plants
• Vector design and promoter selection
• Methods to achieve effective overexpression
• Case studies and data analysis techniques
5/20: CRISPR/Cas9 Fundamentals for Plant Genome Editing
Part 1: CRISPR/Cas9 – From Bacterial Immunity to Genome Editing
• Historical background and discovery
• Basic mechanism of CRISPR/Cas9 system
• Key components and their functions
Part 2: Designing CRISPR/Cas9 Experiments in Plants
• Guide RNA design and target site selection
• Delivery methods in plant cells
• Off-target analysis and validation strategies
5/27: CRISPR/Cas9 in Precision Breeding: Applications and Case Studies
• Real-world examples of CRISPR/Cas9 in precision breeding
• Integration of functional assays with genome editing
• Regulatory and ethical issues in genome editing
• Overcoming technical and biological challenges
6/3: Student-Driven Experiment Design Workshop
• Students select a target gene from a plant of interest
• Choose an approach: gene silencing, gene overexpression, or CRISPR/Cas9 design
• Develop an experimental plan including rationale, method, and expected outcomes
• Students present their design proposals
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| 第3週 |
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| 第4週 |
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| 第5週 |
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| 第6週 |
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| 第7週 |
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| 第8週 |
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| 第9週 |
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| 第10週 |
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| 第11週 |
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| 第12週 |
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| 第13週 |
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| 第14週 |
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| 第15週 |
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| 第16週 |
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| 第17週 |
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| 第18週 |
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