• Spring 2025
• 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.

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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

• Basic R: Quick online reference for data input, basic statistics, and plots.
• Advanced R by Hadley Wickham.
• R Markdown: The definitive Guide by Yihui Xie et al.,
• STHDA: Statistical tools for high-throughput data analysis.

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Schedule 2025

Week 1: Introduction and Overview

• 01-21 (Tue): [Lecture] Introduction about crop improvement
  • [Canvas materials]
• 01-23 (Thu): [Lab] Research Project Management using RStudio, HCC, and GitHub
  • Reading: [hcc doc] and [hcc-usage in the J. Yang lab]
  • [HTML]

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

Week 2: Experimental design for selection scan

• 01-28 (Tue): [Lecture] Experimental design and basic population genetics terminology
  • [Canvas materials]
  • Reading: Hahn 2019. Chapter 1 and 2
• 01-30 (Thu): [Lab]Wright-Fisher simulation
  • [HTML]

Week 3: Next-generation sequencing and diversity measurement

• 02-04 (Tue): [Lecture] Next-generation sequencing and diversity measurement
  • [Canvas materials] and [HTML]
  • Reading: Hahn 2019. Chapter 3
• 02-06 (Thu): [Lab] Guest lecture by HCC

Week 4: Population differentiation

• 02-11 (Tue): [Lecture] Measuring population differentiation
  • [Canvas materials] and [HTML]
  • Reading: Hahn 2019. Chapter 5
• 02-13 (Thu): [Lab] Calculate Fst and XP-CLR using NGS data
  • [HTML]
  • Computational resources:
    • [ANGSD website]

Week 5: Population genomics in a case study

• 02-18 (Tue): [Lab] Calculate Fst and XP-CLR using NGS data
  • [HTML]
  • Computational resources:
    • [Basic Linux/Unix Commands with Examples]
    • [A Beginner’s Guide to Vim]
• 02-20 (Thu): [Seminar] Designing NUE maize using a PopGen approach
  • Change to room Keim 150 for a Departmental seminar

Week 6: Scan for direct selection

• 02-25 (Tue): [Lecture] Direct selection
  • [Hahn 2019, Chapter 7]
  • [HTML]
• 02-27 (Thu): [Lab] Fst and genomic features
  • [HTML]