SCSC, GENE, MEPS and BIOT 654: Analysis of Complex Genomes (Lec) Spring 2018

Transcription

1 SCSC, GENE, MEPS and BIOT 654: Analysis of Complex Genomes (Lec) 1. Instructor: Spring 2018 Name: Professor Dr. Hongbin Zhang Office: 427A Heep Center Office Phone: Office hours: 9:00 am 11:00 am, Fridays, by appointment or at any time by Course Description: Changes that will have effects comparable to those of the Industrial Revolution and the Computer-based Revolution are now beginning. The next great era, a genomics revolution, is in an early phase" (Science, Vol. 279 p2019, 1998). This course is to teach the principles, methodology and applications of genome technologies widely used in analysis of complex genomes in modern genomics, genetics, molecular biology and molecular breeding, from the basic to the state-of-the-art ones. Emphasis will be given to those widely used for DNA marker technology, genetic mapping, gene/qtl mapping, genome-wide association study (GWAS), genome physical mapping, large-scale genome analysis, high-molecular weight recombinant DNA technology, gene and QTL cloning (forward genetics approach), genome and transcriptome sequencing, gene expression profiling and analysis, gene functional analysis (reverse genetics approach), and molecular breeding (marker-assisted selection, MAS; genomic selection, GS; gene or genome editing; gene-based breeding, GBB). Contents: Lecture 1 - Course introduction: Modern Genomics and Genome Technologies: Status, Opportunities, Challenges and Perspectives Lecture 2 - DNA marker technology: RFLP, STS, RAPD, AFLP, SSR and SNP (RAD-seq): MAS, GS and GBB Lecture 3 - Genetic mapping I: Linkage map construction Lecture 4 - Genetic mapping II: Trait, QTL and gene genome-wide association study (GWAS) Lecture 5 - Gene tagging with DNA markers: Bulked Segregant Analysis (BSA) Lecture 6 - DNA Cloning - Recombinant DNA I: Megabase-sized DNA Analysis Lecture 7 - DNA cloning - Recombinant DNA II Phage, Fosmid, BAC, TAC, BIBAC, Lecture 8 - BAC applications I: Plant BIBAC and TAC transformation, targeted marker development, and genome analysis Lecture 9 - BAC applications II: Map-based cloning, chromosome walking, gene fishing, and gene golfing Lecture 10 - Physical mapping: PFGE, FISH, RH, clone-based (fingerprinting and next-gen seq) and optical Lecture 11 - Genome sequencing: Sanger and next-generation high-throughput sequencing, RNA-seq and RAD-seq Lecture 12 - Gene expression profiling and RNA alternative splicing: Northern, Microarray, SAGE, RNA-seq and RT-qPCR Lecture 13 - Others tools for functional genomics: sirna, mirna, RNAi, gene overexpression, TILLING, mutagenesis and gene or genome editing At the end of the course, the following goals will be expected to reach: Page 1 of 5

2 To understand the principles of major genome technologies and methods widely used in modern genomics research; To have knowledge and concepts in uses of the genome technologies and methods in modern genomics, molecular biology and plant/animal breeding; and To be able to design a research project in genomics, molecular biology and molecular breeding using the genome technologies and methods. 3. Course Prerequisite: GENE 603, equivalent, or instructor approval. 4. Course Level: Graduate students having majors in life sciences, including plants, animals, human, insects, and microbes. 5. Teaching Materials: There is no textbook recommended for this course; however, relevant reading materials will be provided before each lecture. 6. Credits: This is a 3-credit hour course, meeting on Tuesdays and Thursdays, from 11:10 12:25 PM. 7. Grading: Midterm 40% Final 60% 100% Exams will be taken at home (1 week) or in class room (2 hours each exam). Grading standard: A, 90%; B, %; C, %; failure, <60%. 8. Americans with Disabilities Act (ADA) Policy Statement: The Americans with Disabilities Act (ADA) is a federal antidiscrimination statute that provides comprehensive civil rights protection for persons with disabilities. Among other things, this legislation requires that all students with disabilities be guaranteed a learning environment that provide for reasonable accommodation of their disabilities. If you believe you have a disability requiring an accommodation, please contact the Department of Student Life, Services for Students with Disabilities in Cain Hall, Rm. B118, or call Academic Integrity Statement and Policy: An Aggie does not lie, cheat or steal, or tolerant those who do. Page 2 of 5

3 10. Course Schedule: Lecture Date Time Class Room 1.1 Course introduction: Modern 01/19 (F) 1:00 4:00 PM HPCT 224 Genomics and Genome Technologies: (please note the time and location) Status, Opportunities, Challenges and Perspectives 2.1 DNA marker technology: 01/23 (T) 11:10 12:25 PM HPCT 123X 2.2 DNA marker technology: 01/25 (R) 11:10 12:25 PM HPCT 123X 2.3 DNA marker technology: 01/30 (T) 11:10 12:25 PM HPCT 123X 3.1 Genetic mapping I: Map development 02/01 (R) 11:10 12:25 PM HPCT 123X 3.2 Genetic mapping I: Map development 02/06 (T) 11:10 12:25 PM HPCT 123X 4.1 Genetic mapping II: Trait, QTL, gene 02/08 (R) 11:10 12:25 PM HPCT 123X 4.2 Genetic mapping II: Trait, QTL, gene 02/13 (T) 11:10 12:25 PM HPCT 123X 4.3 Genetic mapping II: Trait, QTL, gene 02/15 (R) 11:10 12:25 PM HPCT 123X 5.1 Gene tagging: Bulked Segregant 02/20 (T) 11:10 12:25 PM HPCT 123X Analysis (BSA) 6.1 DNA Cloning - Recombinant DNA I: 02/22 (R) 11:10 12:25 PM HPCT 123X Megabase-sized DNA Analysis 7.1 DNA cloning - Recombinant DNA II 02/27 (T) 11:10 12:25 PM HPCT 123X Page 3 of 5

4 Schedule (continued) Lecture Date Hours Class Room 7.2 DNA cloning - Recombinant DNA II: 03/01 (R) 11:10 12:25 PM HPCT 123X 7.3 DNA cloning - Recombinant DNA II: 03/06 (T) 11:10 12:25 PM HPCT 123X 8.1 BAC applications I: Plant BIBAC and 03/08 (R) 11:10 12:25 PM HPCT 123X TAC transformation, targeted marker development, and genome analysis Spring Break, 03/12 03/16 MIDTERM EXAM 03/20 (T) 9.1 BAC applications II: Map-based cloning, 03/20 (T) 11:10 12:25 PM HPCT 123X chromosome walking, gene fishing, and gene golfing (forward genetics approach) 9.2 BAC applications II: Map-based cloning, 03/22 (R) 11:10 12:25 PM HPCT 123X chromosome walking, gene fishing, and gene golfing (forward genetics approach) MIDTERM EXAM DUE 03/27 (T) 10.1 Physical mapping: PFGE, FISH, RH, 03/27 (T) 11:10 12:25 PM HPCT 123X clone-based (fingerprinting and next-gen seq) and optical 10.2 Physical mapping: PFGE, FISH, RH, 03/29 (R) 11:10 12:25 PM HPCT 123X clone-based (fingerprinting and next-gen seq) and optical 11.1 Genome sequencing: Sanger and next- 04/03 (T) 11:10 12:25 PM HPCT 123X generation high-throughput sequencing, 11.2 Genome sequencing: Sanger and next- 04/05 (R) 11:10 12:25 PM HPCT 123X Generation high-throughput sequencing, 11.3 Genome sequencing: Sanger and next- 04/10 (T) 11:10 12:25 PM HPCT 123X Generation high-throughput sequencing, Page 4 of 5

5 Schedule (continued) Lecture Date Hours Class Room 11.4 Genome sequencing: Sanger and next- 04/12 (R) 11:10 12:25 PM HPCT 123X generation high-throughput sequencing, 12.1 Gene expression profiling and RNA 04/17 (T) 11:10 12:25 PM HPCT 123X alternative splicing: Northern, Microarray, SAGE, RNA-seq and RT-qPCR 12.2 Gene expression profiling and RNA 04/19 (R) 11:10 12:25 PM HPCT 123X alternative splicing: Northern, Microarray, SAGE, RNA-seq and RT-qPCR 13.1 Others tools for functional genomics: sirna, 04/24 (T) 11:10 12:25 PM HPCT 123X 13.2 Others tools for functional genomics: sirna, 04/26 (R) 11:10 12:25 PM HPCT 123X FINAL EXAM 05/01 (T) 13.3 Others tools for functional genomics: sirna, 05/01 (T) 11:10 12:25 PM HPCT 123X FINAL EXAM DUE 05/07 (M) 5:00 PM Page 5 of 5