- Spring 2024
- Location: Animal Science A128
- Time: 9:00-9:50am (MWF)
- Prerequisites: STAT-801A or equivalent, or permission of the instructor(s).
Texts and Reading Materials
Required textbook
- Falconer & Mackay, Introduction to Quantitative Genetics
Free Online Materials
- Graham Coop, Population Genetics notes
- Basic R: Quick online reference for data input, basic statistics, and plots.
- STHDA: Statistical tools for high-throughput data analysis.
Schedule Spring 2024
The HTML slides will likely be posted on Sunday pm for the next week. The slides are subject to change before the class.
Week 1: Allele and Genotype Frequencies (Ch1)
- 01-22 (M): Introduction [HTML]
- 01-24 (W): Hardy-Weinberg Equilibrium [HTML]
- 01-26 (F): Linkage Disequilibrium [HTML]
Week 2: Changes of Allele Frequency (Ch2 & Ch3)
- 01-29 (M): Migration, Mutation, and Selection [HTML]
- HW1 assignment in Canvas on Monday (Due Friday morning)
- 01-31 (W): Effectiveness of Selection [HTML]
- 02-02 (F): Genetic Drift [HTML]
- HW1 Due today at 9AM!
Week 3: Small Populations — Simplified Conditions (Ch3 & Ch4)
- 02-05 (M): Inbreeding [HTML]
- 02-07 (W): Effective Population Size [HTML]
- 02-09 (F): Heterozygosity [HTML]
Week 4: Population Structure and Neutrality test (Notes in Canvas)
Week 5: Neutrality Test (Notes in Canvas)
- 02-19 (M): Neutral theory [HTML]
- HW2 assigned in Canvas!
- 02-21 (W): Detecting natural selection [HTML]
- 02-23 (F): Journal article review [HTML]
- HW2 Due today!
- Journal article assigned for peer review (due in two weeks)
Week 6: Pedigreed Population and Close Inbreeding (Ch5)
- 02-26 (M): Pedigreed population [HTML]
- 02-28 (W): Coancestry [HTML]
- 03-01 (F): Relationship matrix [HTML]
- Watch recorded video in Canvas
Week 7: Statistical Foundations for Continuous Variation (Ch6 and Notes in Canvas)
- 03-04 (M): Statistical foundations of quantitative genetics [HTML]
- 03-06 (W): Continuous Variation [HTML]
- 03-08 (F): Journal Review Discussion [HTML]
- Peer review due
Week 8: No class
- Enjoy Spring Break!
Week 9: Population values and means (Ch7)
- 03/18 (M): Average effect of an allele [HTML]
- 03/20 (W): Breeding value, dominance, and interaction [HTML]
- 03/22 (F): Exam II (take home)
Week 10: Genetic components of variance (Ch8)
- 03/25 (M): Breeding value interpretation [HTML].
- Exam II (Due today)
- 03/27 (W): Variance partitioning [HTML]
- 03/29 (F): Heritability and Repeatability [HTML]
- HW3 assigned in Canvas!
Week 11: Heritability and resemblance between relatives (Ch9)
- 04/01 (M): Resemblance between relatives [HTML]
- 04/03 (W): Genetic and environmental covariance [HTML]
- No in-person class, watch recorded video in Canvas
- 04/05 (F): Estimation of heritability [HTML]
- HW3 Due today!
Week 12: Heritability estimation (Ch10 & Ch11)
- 04/08 (M): Precision of estimation [HTML]
- 04/10 (W): Examples for h2 estimation [HTML]
- 04/12 (F): The breeder’s equation [HTML]
- HW4 assigned in Canvas!
Week 13: Predicting response to selection and interpretation (Ch11 & Ch12)
- 04/15 (M): Variability in response [HTML]
- 04/17 (W): Asymmetry of responses [HTML]
- 04/19 (F): Long-term results [HTML]
- HW4 due today and Exam III (take-home)
Week 14: Heterosis and correlated traits (Ch14 & Ch19)
- 04/22 (M): Inbreeding depression and heterosis [HTML]
- 04/24 (W): Correlated responses to selection [HTML]
- 04/26 (F): Correlated traits: Index selection [HTML]
- HW5 assigned in Canvas!
Week 15: Quantitative trait loci (QTL) and GWAS (Ch21)
- 04/29 (M): QTL: Single-marker analysis [HTML]
- No in-person class, watch recorded video in Canvas
- 05/01 (W): QTL: Interval Mapping [HTML]
- 05/03 (F): QTL and GWAS [HTML]
- HW5 due today
Week 16: Genome-wide association study (Reading Materials in Canvas)
- 05/06 (M): GWAS [HTML]
- 05/08 (W): GWAS wrap up and Q&A
- 05/10 (F): Final exam (take-home)