• Spring 2020 Syllabus
  • Location: Plant Sciences Hall (room 272)
  • Time: Tuesday and Thursday 9:00-10:15 am
  • Office Hour: Thursday 10:15-11:00 am (except the first Thursday of the month)
  • Prerequisites:
    • AGRO 815A, 815B, and 815D,
    • AGRO/ANSCI-931,
    • and STAT-802 or equivalent,
    • or permission of the instructor.

Suggested textbooks and Reading Materials

  • Hahn, M. 2019. Molecular population genetics. Oxford.
  • Bernardo, R. 2020. Breeding for quantitative traits in plants. 3rd Ed. Stemma Press.
  • Lynch, M. and B. Walsh. 1998. Vol. 1: Genetics and analysis of quantitative traits. Sinauer, MA

R and statistics resources


Schedule 2020

Week 1: Introduction and Overview

  • 01-14 (Tue): [Lecture] Introduction about crop improvement
    • [Canvas materials]
  • 01-16 (Thu): [Guest Lecture/Lab] A basic tutorial on HCC

Part I. Population Genomics: Crop Domestication and Implications for Plant Breeding

Week 2: Experimental design for selection scan

  • 01-21 (Tue): [Lecture] Experimental design and basci popgen terminology
    • [Canvas materials]
  • 01-23 (Thu): [Lab] Research project management

Week 3: Next-generation sequencing and diversity measurement

  • 01-28 (Tue): [Lecture] Next-generation sequencing and diversity measurement
    • [Hahn 2019, Chapter 4]
    • [Canvas materials] and [HTML]
  • 01-30 (Thu): [Lab] Command line and Slurm job submission

Week 4: Population differentiation

Week 5: Scan for direct selection

  • 02-11 (Tue): [Lecture] Direct selection
    • [Hahn 2019, Chapter 7]
    • [Canvas materials] and [HTML]
  • 02-13 (Thu): [Lab] Visualize theta Fst results

Week 6: Linked selection

  • 02-18 (Tue): [Lecture] Linked selection
    • [Hahn 2019, Chapter 8]
    • [Canvas materials] and [HTML]
  • 02-20 (Thu): [Lab] Breaking down theta statistics into genomic features

Part II. Conventional Breeding: Mating Design and Heritability Estimation

Week 7: Transition from PopGen to QuantGen

Week 8: Breeding population means and variances

  • 03-03 (Tue): [Lecture] Phenotypic and genotypic values
  • 03-05 (Thu): [Lecture] Phenotypic and genetic variances

Week 9: Mating designs and Estimating Genetic Variances

  • 03-10 (Tue): [Lecture] Mating design
    • [Bernardo, Chapter 7] or [Lynch and Walsh, Chapter 18]
    • [HTML]
  • 03-12 (Thu): [Lab] Genetics variances calculation

Week 10: Genotype x environment interaction Class cancelled due to the Coronavirus

  • 03-17 (Tue): [Guest Lecture]
  • 03-19 (Thu): [Guest Lab]
    • [Due date for Mid-term paper review]

Week11:

  • 3-22 to 3-29: Spring Break

Part III. Genome-enabled Breeding and GWAS

  • Note: our course switch to Zoom online course because of the Covid-19 pandemic

Week 12: Best linear unbiased prediction

  • 03-31 (Tue): [Lecture] BLUP introduction and Matrix operations
    • [Bernardo, Chapter 10] or [Lynch and Walsh, Chapter 8]
    • [HTML]
  • 04-02 (Thu): [Lecture] BLUP calculation for breeding populations

Week 13: Genome-enabled selection

  • 04-07 (Tue): [Lecture] Genomic selection
    • [Bernardo, Chapter 11]
    • [Canvas materials] and [HTML]
  • 04-09 (Thu): [Lab] Genomic selection in practice
    • [Canvas materials] and [HTML]

Week 14: Association mapping via mixed models

  • 04-14 (Tue): [Lecture] Genome-wide association study
    • [Bernardo, Chapter 11]
    • [Canvas materials] and [HTML]
  • 04-16 (Thu): [Lab1] GWAS in practice (1)
  • 04-21 (Tue): [Lab2] GWAS in practice (2)

Part IV. Emerging Technologies in Plant Breeding

Week15:

  • 4-23 (Thu): Summary and emerging technologies
    • [Due date for final paper and final code]
    • [Slides in Canvas]
    • HW Keys: [HTML]

Week16:

  • 4-28 (Tue): [Final project presentation]
  • 4-30 (Thu): [Final project presentation] [Due date for final code review]