Advanced Plant Genetics

Structural Genomics, PS480

Course Syllabus Page

This year (fall, 2005) I am introducing a new course, Structural Genomics. This is a class oriented around practical lab exercises, and it's important that you be exposed to more computational tools. Initially, we will do the Steptoe/Morex mapping and QTL experiment. This will be presented along with lectures on genome organization and germplasm diversity. The second experimental component of the project will involve exploration of several genetic marker technologies. As we work from linkage analysis to marker technologies, we will begin to explore the growing DNA sequence databases. The third experimental unit will be centered on positional cloning. Laboratory exercises were designed to introduce current techniques and approaches, and to let the student explore a relatively broad array of research topics, within a reasonably controlled environment. I believe that a firm foundation in the history of any field is necessary in order to avoid making mistakes that were already made years or decades previous. I've found a superb collection of classical papers in genetics, and hope each of you becomes familiar with these remarkable manuscripts.

Each student will be expected to read the papers for each lecture before the lecture, and be prepared for discussion. Each student will also be required to complete and present one major writing project. This year you will write a USDA competitive grant proposal. I will be gone for about a week's worth of lectures, but have arranged for guest lecturers.

Grading

The lab reports (three reports) will each account for 10% of the total grade. The grant proposal will account for 20%. The midterm will be valued at 20%, and the final at 30%. While no formal points will be given for in-class discussion participation, be assured that I will notice and that classroom discussion (or its absence) will impact the rigor of the exams. We have at least one off-campus student taking the course. The off campus student(s) will be expected to participate in the Steptoe/Morex experiment, and the in-silico laboratory exercises. The off-campus student(s) will be assigned an additional major reading assignment (I have several fine books to read, ranging from Sturtevant's 'history of genetics' to Diamond's Guns, Germs and Steel), will write a paper discussing the book, and will be prepared to lead a classroom discussion on the work at the end of the semester. For the nervous on-campus student, this could provide a way to pick up 10% of the grade as a substitute for another assignment.

Course syllabus: Structural Genomics, PSPP 480

Aug 30. Overview: How do we know which genes are important?

Sept. 1. Heritability, additivity, heterosis and non-additive gene action

Lab 1: Let’s go to the field and see a mapping population. Initiation to QTL analysis.

Sept. 6. Linkage analysis- using 2 point and 3 point analyses to construct a linkage map.

Sept. 8. Quantitative Analysis Tools

Lab 2. Linkage map construction- Mapmaker and JoinMap

Sept. 13. Epistasis

Sept. 15. Alternative routes to chromosomal location of genes

Lab 3. More mapmaker

Sept. 20. Synteny and its counterpart, Diversity

Sept. 22. Maps and more maps