Oregon State University

PBG620 series


Molecular Markers & Marker-Trait Association
PBG 620, 621, 622 Fall 2016

Course Description

The objective of this course is to familiarize students with historic, current, and emerging methods in plant molecular marker discovery, genetic mapping, and marker-trait association.  The student will be introduced to molecular marker platforms, the analysis of marker data, QTL mapping, and genome-wide association studies.  Upon completion of this course, the student will be able to generate, analyze, and interpret molecular marker and marker-trait association data.


Dr. Kelly Vining: 4123 Agriculture and Life Sciences Bldg.



Lecture: Monday & Wednesday, 11:00-11:50 AM, Ag. and Life Sci. Bldg. Rm 4000

Lab: Friday, 11:00-11:50 AM, Cordley Bldg. Rm 4056

Final Exam*: TBD

     *Instructor may elect not to hold a final exam.

Where to find course information:

  • Course website: All course materials except journal articles, grades, and discussion.


The course is divided into three modules, each of which covers a different topic. Lecture and lab expectations are the same for all modules. After lectures, students are expected to understand 1) selection of appropriate methods and software for common plant breeding projects, 2) the basic concepts of the functions of those methods/software, and 3) basic quality control and troubleshooting with the output of those methods/software. In Friday labs, students will be expected to successfully load data and perform key analytic and graphing operations using popular software, but they are not required to become independently proficient in any software.


Module I. PBG/MCB 620 - DNA Fingerprinting

This section provides an introduction to molecular marker types and techniques. Historic marker types will be included, to facilitate the understanding of older literature. Current marker technologies based on next-generation sequencing and genomics will be emphasized, along with resources to explore sequence data to identify candidate genes for traits of interest. Finally, we will cover methods for using marker data to quantitatively assess germplasm relationships.

Module II. PBG/MCB 621 - Genetic Mapping

This section will introduce students to concepts and software for linkage mapping, creating actual genetic maps and interpreting the relationships between different maps of the same and related species, and other techniques for estimating gene/locus/polymorphism positions.

Module III. PBG/MCB 622 - Marker-Trait Association

This section covers bi-parental QTL mapping and the options for combining data over environments to detect general QTL as well as environment-specific QTL. The use of genome-wide association studies to detect QTL will be compared to the bi-parental approach and various strategies to correct such analyses for underlying population structure will be explored. Finally, the synthesis of such information into successful marker-assisted selection strategies, and genomic selection will be discussed.

Contact Info

Copyright ©  2017 Oregon State University