ST549: Introduction to QTL Analysis

ST549: AN APPLIED INTRODUCTION TO QTL MAPPING IN EXPERIMENTAL POPULATIONS

FALL Semester 2009

Class meets: Tuesday and Thursday
Time: 1:30-2:45pm
Place: REC 313
Professor: RW Doerge
Office Hours (MATH 522): Tuesday noon-1pm; Wednesday 3-4pm


Teaching Assistant (TA): Mr. Tilman Achberger
Office Hours: by appointment only
e-mail address: tachberg@stat.purdue.edu

***Please do not use or reproduce any of these lectures for the benefit of another class lecture, another University or business, or for the purpose of publication or profit.***


Course Description:

The detection of genes that control quantitative characters is a problem of great interest to many areas of research including bioinformatics, genomics , statistical genetics, computer science, mathematics, horticulture, biology, agronomy, genetics, and plant breeding. In this introductory applied course, basic experimental breeding designs (e.g., backcross, F2, and RI) will be used to investigate estimation of recombination fractions or genetic distances between molecular markers and/or quantitative trait loci (QTL). Standard genetic mapping techniques will be presented for the purpose of estimating genetic maps and employing current software for map building. Both simulated and real data will be used to demonstrate the map building process.

Once a genetic map is in place, this structure is used to search for associations with quantitative traits, and then to locate regions in the genome known as quantitative trait loci (QTL). QTL-Cartographer will be introduced and utilized throughout this course for the purpose of understanding how the algorithms are designed and employed for proper QTL mapping. Mapping methodologies such as single marker QTL mapping, interval mapping, and composite interval mapping will be covered in detail. In addition, resampling techniques (i.e., bootstrapping, permutations) will be presented as methods for estimating critical values used to declare significant QTL.

This is a graduate level interdisciplinary course that requires minimal computer experience, lower levels of statistical training (STAT 503 or 511, and/or STAT 512), and biology/genetics and a maximal level of motivation. All students who are interested in genomics and/or bioinformatics are encouraged to come learn about QTL mapping. Students who have real data as part of their research program are especially encouraged to participate. If you are a postdoc., staff, or faculty member I would appreciate it if you would ask me about sitting in so that we can both understand your goals. While lectures are interesting the real learning moments come through the projects, homeworks, and discussions.


  • Syllabus (Fall 2009).

  • Cartographer manual in PDF format
  • Link to current QTL-Cartographer man pages.

    Weekly Lectures (Fall 2009)


    Week 1:
  • Lecture 1 (August 25, 2009)
  • Lecture 2 (August 27, 2009)

  • Homework 1 (due September 3, 2009; at the start of class)

    Week 2:
  • No lecture on Tuesday, September 1, 2009. Please use the room and this time slot to organize into project/homework groups.
  • Lecture 3 (September 3, 2009)
  • up to slide 18 and intro to QTL-Cartographer

  • No homework this week...

    Week 3:
  • Finish lecture 3 from September 3rd (September 8, 2009)
  • Lecture 4 (September 8, 2009)
  • Lecture 5: In class demo of QTL Cartographer data simulation (September 10, 2009)

  • Homework 2 (due September 17, 2009; at the start of class)

    Week 4:
  • Lecture 6 (September 15, 2009)
  • Facts about Y
  • Lecture 7 (September 17, 2009)

  • Homework 3 (due September 24, 2009; at the start of class)

    Week 5:
  • Lecture 7-2 (September 22, 2009)
  • Lecture 8 (September 24, 2009)

  • No homework this week...

    Week 6:
  • Lecture 9 (September 29, 2009)
  • Please bring a calculator to class on September 29 and October 1, 2009

  • Please read in preparation for Lecture 9 and 10:
  • R.W. Doerge (Journal of Quantitative Trait Loci. Volume 2. Article 6. 1996). "Constructing genetic maps by rapid chain delineation".

  • Mik Black's 1999 Survial Guide to STAT 525, but adaptable to STAT 549: you are not alone in your thoughts about RWD's class structure.... :)

    Test 1: in class, closed notes, Tuesday; October 20, 2009 (1:30-2:45pm)

    The test is closed book, closed notes, and no practice exams will be distributed prior to exam.
    The test will be one hour (you will have the entire 1 hour and 15 min.).
    Please bring a simple calculator (i.e., it adds, subtracts, multiplies, and divides.). Thank you.


  • Lecture 10 (October 1, 2009)
  • Champoux et al. 1995 TAG
  • Subset of Champoux et al. data
  • Mapmaker *.maps file

  • Project One (Due: November 10, 2009)
  • Homework 4 (due October 8, 2009; at the start of class)

    Week 7:
  • Lecture 11 (October 6, 2009)

  • Reference paper with data set and analysis we covered in class:
  • R.W. Doerge, Z-B. Zeng and B.S. Weir. 1997. Statistical Science. 12(3):195-219.
  • Horvat, S. and Medrano, J. F. (1995). Interval mapping of high growth (hg), a major locus that increases weight gain in mice. Genetics 139:1737-1748.
  • Horvat and Medrano data file (*.raw).
  • Horvat and Medrano ".maps" file require to translate a MAPMAKER formated data set. Rmaps uses the input file *.maps; Rcross uses the input file *.raw

  • Went over class handout for QTL-Cartographer example; reviewed Emap for rice data; blackboard explanation of segregation distortion test for one marker (October 8, 2009)

    Week 8:
  • Fall Break: no class October 13, 2009
  • Lecture 12a (October 15, 2009)

    Week 9:
  • Test 1: in class, closed notes, Tuesday; October 20, 2009 (1:30-2:45pm)
    The test is closed book, closed notes, and no practice exams will be distributed prior to exam.
    The test will be one hour (you will have the entire 1 hour and 15 min.).
    Please bring a simple calculator (i.e., it adds, subtracts, multiplies, and divides.). Thank you.


    Week 10:
  • Lecture 12b (October 22, 2009)
  • Lecture 13 (October 22, 2009)
  • Homework 5 (due October 29, 2009; at the start of class)

    Week 11:
  • We went over the answers to the test (October 27, 2009)
  • Lecture 14 (read on your own)
  • No Class. RWD sick. Please work on your projects that are due November 10, 2009

    Week 12:
  • Due to poor performance on test, there will be a review of all course material up to this point in the semester. No notes will be distributed.
  • Lecture 15 (November 5, 2009)
  • We also worked through the rice example with Zmapqtl (model 3, interval mapping).

    Week 13:
  • Homework 6 (due November 19, 2009; at the start of class)
  • Data file for homework 6
  • Data file for homework 6


  • Lecture 16 (November 10, 2009)
    Please read (available via e-Journals, Purdue University): Lander and Botstein. 1989. Mapping Mendelian Factors Underlying Quantitative Traits Using RFLP Linkage Maps. Genetics 121:185-199.

  • Lecture 17 (November 12, 2009)
    Please read (available via e-Journals, Purdue University): Churchill and Doerge. 1994. Empirical threshold values for quantitative trait mapping. Genetics. 138:963-971.

    Week 14:
  • Lecture 18 (November 17, 2009)
  • Lecture 19 (November 17, 2009)
  • Lecture 20 (November 19, 2009)

  • EAE reference (Teuscher et al. 1999)
  • EAE maps file
  • EAE raw file

  • Homework 7 (due December 1, 2009; at the start of class)
  • maps file
  • raw file

    Week 15:
  • No class. Read on your own: Lecture 21 (November 24, 2009)
  • RW Doerge. 2002. Mapping and Analysis of Quantitative Trait Loci in Experimental Populations. Nature Genetics Reviews
  • No class. November 26, 2009