• Spring 2022
  • Location: Plant Sciences Hall (room 272)
  • Time: Tuesday and Thursday 11:00-12:15 am
  • Office Hour: Thursday 12:15-1:00 pm (except for 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

  • 01-18 (Tue): [Lecture] Introduction about crop improvement
    • [Canvas materials]
  • 01-20 (Thu): [Lab] Research Project Management using RStudio, HCC, and GitHub

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

Week 2: Experimental design for selection scan

  • 01-25 (Tue): [Lecture] Experimental design and basic population genetics terminology
    • [Canvas materials]
    • Reading: Hahn 2019. Chapter 1 and 2
  • 01-27 (Thu): [Lab] Slurm job and Wright-Fisher simulation

Week 3: Next-generation sequencing and diversity measurement

  • 02-01 (Tue): [Lecture] Next-generation sequencing and diversity measurement
    • [Canvas materials] and [HTML]
      • Reading: Hahn 2019. Chapter 3
  • 02-03 (Thu): [Lab] Theta calculation

Week 4: Population differentiation

Week 5: Scan for direct selection

  • 02-15 (Tue): [Lecture] Direct selection
    • [Hahn 2019, Chapter 7]
    • [Canvas materials] and [HTML]
  • 02-17 (Thu): [Lab] Submitting slurm jobs

Week 6: Linked selection

  • 02-22 (Tue): [Lecture] Linked selection
    • [Hahn 2019, Chapter 8]
    • [HTML]
  • 02-24 (Thu): [Lab] Breaking down statistics into genomic features

Week 7: Wrap up the population genomics session

  • 03-01 (Tue): [Lecture] Population genomics summary
    • [Hahn 2019, Chapter 10] and [Canvas materials]
  • 03-03 (Thu): [Lab] Popular popgen software

Part II. Conventional Breeding: Mating Design and Heritability Estimation

Week 8: Transition from Pop Gen to Quant Gen

  • 03-08 (Tue): [Lecture] Definition of breeding populations
    • [Bernardo, Chapter 2]
    • [HTML]
  • 03-10 (Thu): [Lecture] Phenotypic and genotypic values
    • [Bernardo, Chapter 3]
    • [HTML]

Week 9:

  • 3-13 to 3-20: Spring Break

Week 10: Breeding population means and variances

  • 03-22 (Thu): [Lecture] Phenotypic and genetic variances
    • [Bernardo, Chapter 6]
    • [HTML]
    • [Due date for Mid-term paper: March 25th]
  • 03-24 (Thu): [Lab] Compute phenotypic values and variances

Week 11: Mating designs and Estimating Genetic Variances

  • 03-29 (Tue): [Lecture] Mating design
    • [Bernardo, Chapter 7] or [Lynch and Walsh, Chapter 18]
    • [HTML]
  • 03-31 (Thu): [Lab] Genetics variances calculation

Part III. Genome-enabled Breeding and GWAS

Week 12: Best linear unbiased prediction

  • 04-05 (Tue): [Lecture] BLUP introduction and Matrix operations
    • [Bernardo, Chapter 10] or [Lynch and Walsh, Chapter 8]
    • [HTML]
  • 04-07 (Thu): [Lecture] BLUP calculation for breeding populations

Week 13: Genome-enabled selection

  • 04-12 (Tue): [Lecture] Genomic selection
    • [Bernardo, Chapter 11]
    • [HTML]
  • 04-14 (Thu): [Lab] Genomic selection in practice (1)

Week 14: GS and GWAS via mixed models

  • 04-19 (Tue): [Lab] Genomic selection in practice (2)
    • [Canvas materials] and [HTML]
  • 04-21 (Thu): [Lecture] Genome-wide association study
    • [Bernardo, Chapter 11]
    • [HTML]

Week 15: Association mapping via mixed models

Part IV. Emerging Technologies in Plant Breeding

Week16: