| 週次 |
授課內容 |
| 第1週 |
Week 1: Introduction (呂維茗)
An overview of genome biology (楊長賢)
Week 2: Plant genome organization
Week 3: Plant gene regulation
Structural Genomics (呂維茗)
Week 4: 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)
Week 5: 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)
Week 6 & 7: From phenotype to gene - Genetic map
7. “Polymorphic” molecular markers (RFLP, CAPS, RAPD, SCAR, AFLP, SSR, VNTR, SNP, dCAPS)
8. Construction of a coarse genetic map
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. Mapping by sequencing (QTL-seq, MutMap, Genotyping by sequencing (GBS))
14. Linkage between different maps
Week 8: New techniques used in genome project
15. Sanger’s dideoxy sequencing (first generation)
16. Next generation sequencing (NGS) (Pyrosequencing, Ion torrent, Solexa technology)
17. Third generation sequencing (SMRT- PacBio; Nonopore- Oxford)
18. Alternative strategies and technologies to help WGS (Optical mapping, Single-molecule next-generation mapping, 10X genomics)
19. Supporting techniques (QC of DNA/RNA, Removal of ribosomal RNA, Strand-specific library, DNA/RNA fragmentation, DNA/RNA fractionation
Week 9: Genomics and Postgenomics
20. Genome project (HGP, other genome project)
21. Terms (alternative splicing, gene density, molecular clock, homologous sequences, synteny, proteome)
22. Database resource (to browse, to search, or to obtain sequences using NCBI, TIGR, Addgene as examples)
23. Postgenomic era (ENCODE, SNP and TagSNP, Haplotype, GWAS, genotyping platforms)
Functional Genomics (呂維茗)
Week 10 & 11: 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 & datamining (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))
Week 12: 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)
Week 13: Student’s oral report
Proteomic studies in plants (童鈺棠)
Week 14: A guide to improve the proteome coverage
1. Approaches and challenges in crop plant proteomics
2. Innovative technologies used in quantitative plant proteomics
3. From cellular proteome to subcellular protein catalogs
Week 15: A powerful tool to study plant responses to biotic stress
4. Understanding the molecular mechanisms of the plant response to biotic stress through spatial proteomics
5. Recognizing post-translational modifications (PTMs) involved in plant defense
6. Comparative protein expression in response to biotic stress
Week 16: Quantitative proteomics in plants: Choices in abundance
7. Quantitation by mass spectrometry
8. In vivo isoyopic labeling
9. Stable isotopic labeling by amino acids in cell culture
10. 15N metabolic labeling
11. In vitro isotopic labeling of peptides
12. 18O-labeling during trypsin digest
Week 17: Challenges and prospects of plant proteomics
13. Biological questions and practical approaches
14. Developments and strategies in biological MS
15. Complementation of plant proteomics with other functional genomics tools
16. Development of proteomics resources for the plant research community
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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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