Course Description
The methods, design, and implementation of genome-wide association studies (GWAS) to map genetic loci in crop plants. We will discuss the theory and history of genome-wide association, parameters that affect its power and accuracy, and practical considerations for carrying it out.
Athena Title
Genome-wide Association Plants
Prerequisite
PBGG(CRSS)(HORT)(PBIO) 8871 or PBGG(CRSS)(HORT)(PBIO) 8872 or PBGG(CRSS)(HORT) 8874 or permission of department
Pre or Corequisite
PBGG(CRSS)(HORT)(PBIO) 8871 or PBGG(CRSS)(HORT)(PBIO) 8872 or PBGG(CRSS)(HORT) 8874 or permission of department
Semester Course Offered
Offered spring
Grading System
A - F (Traditional)
Course Objectives
The objective will be for students to learn methods, design, and implementation of genome-wide association studies to map genetic loci in crop plants. Learning objectives: 1. Understand the theory behind genome-wide association and how to design a GWAS experiment with plants. 2. Know the various parameters that can influence the power and resolution of GWAS and how the experimenter can adjust them. 3. Be able to perform GWAS using both generalized and mixed linear models, including the use of covariates population.
Topical Outline
Background on association analysis and GWAS Considerations of a GWAS experiment Population size Trait architecture Genotyping density and linkage disequilibrium decay GWAS algorithms & components Generalized linear models Mixed linear models Population structure and kinship GWAS variants (logistical regression, NAM/MAGIC populations, etc.) Software for GWAS analysis
Syllabus