Schedule

Note: The schedule is subject to changes!

Date	Day	Time	Topic	Room	Lecturer
09-04-2026	Thu	08-10	Introduction	S09	N.N.
13-04-2026	Mon	08-10	Genetic diversity	S09	N.N.
16-04-2026	Thu	08-10	Genomic variation: Genotyping and sequencing	S09	N.N.
20-04-2026	Mon	08-10	Phylogenetic analysis	S09	N.N.
20-04-2026	Mon	12-14	Computer lab: Genetic diversity & Genomic variation	PC6	N.N.
20-04-2026	Mon	16-18	Computer lab: Phylogenetic analysis	PC6	N.N.
23-04-2026	Thu	08-10	Population structure	S09	N.N.
27-04-2026	Mon	08-10	Gene flow	S09	N.N.
27-04-2026	Mon	14-16	Computer lab: Population structure	PC6	N.N.
27-04-2026	Mon	16-18	Computer lab: Gene flow	PC6	N.N.
30-04-2026	Thu	08-10	Biodiversity	S09	N.N.
04-05-2026	Mon	08-10	Crop diversity and systematics	S09	N.N.
04-05-2026	Mon	14-16	Coalescent theory	PC6	N.N.
04-05-2026	Mon	16-18	Computer lab: Coalescent theory	PC6	N.N.
07-05-2026	Thu	08-10	Crop domestication	S09	N.N.
11-05-2026	Mon	08-10	Genetics of crop evolution	S09	N.N.
11-05-2026	Mon	14-16	Tests of selection	PC6	N.N.
11-05-2026	Mon	16-18	Computer lab: Tests of selection	PC6	N.N.
14-05-2026	Thu		Ascension day - No class
18-05-2026	Mon	08-10	History of PGR & Legislation for PGR	S09	N.N.
18-05-2026	Mon	14-16	Demographic analysis	PC6	N.N.
18-05-2026	Mon	16-18	Computer lab: Demographic analysis	S09	N.N.
21-05-2026	Thu	08-10	Conservation of plant genetic resources	S09	N.N.
			Pentecost break (Excursion planned)
01-06-2026	Mon	08-10	Core collections	S09	N.N.
01-06-2026	Mon	14-16	Allele mining in PGR	PC6	N.N.
01-06-2026	Mon	16-18	Computer lab: Core collections & Allele mining	PC6	N.N.
04-06-2026	Thu		Corpus Christi day - No class
08-06-2026	Mon	08-10	Analysis of phenotypic diversity	S09	N.N.
08-06-2026	Mon	14-16	Genetic mapping of useful alleles	PC6	N.N.
08-06-2026	Mon	16-18	Computer lab: Analysis of phenotypic diversity & Genetic mapping	PC6	N.N.
11-06-2026	Thu	08-10	Genetic resources in plant breeding	S09	N.N.
17-07-2026	Fri	23:55	Deadline submission of data analysis report
XX-07-2026			Written exam (Exam period 1)
XX-09-2026			Written exam (Exam period 2)

Course organisation

• Syllabus: HTML
• Computer labs:
  • The computer labs will take place in PC Room 3 where we have access to windows PCs. You can either work with them or bring your own laptop.
  • We will use R and Rstudio for the computer exercises. If you want to install R and Rstudio on your own computer: R download and R studio
  • We will work with the same data set for many of the computer exercises. To avoid having to prepare the data each time, we will do it only once using these instructions and save the prepared data. You will need the following data files: genetic data, list with teosinte samples, list with landraces, and list with improved varieties. If you encounter any problems you can also download the prepared data here.
• Data analysis project: Download the datasets and the assignment of each student to the data here.

Topics

Introduction and motivation

• Slides | Lecture notes
• Video: Introduction (30 min)

Genetic diversity

• Slides | Lecture notes
• Videos: 1-Types of genetic diversity (22 min) 2-Diversity in PGR (14 min) 3-Measuring diversity (18 min) 4-DNA sequence diversity (18 min) 5-Complex diversity (10 min)
• In class exercise
• Computer lab:
  • Data preparation: HTML | Markdown
  • Analysis of genetic diversity: HTML | Markdown

Genomic variation: Genotyping and sequencing

• Slides | Lecture notes
• Videos: 1-Genetic variation and genotyping (21 min) 2-Sequencing (19 min) 3-Bioinformatics (15 min)
• In class exercise
• Computer lab: No computerlab for this topic

Additional reading materials:

• A field guide to whole-genome sequencing, assembly and annotation by R Eckblom and JBW Wolf (2014)

Phylogenetic analysis

• Slides | Lecture notes
• Video: 1-Key concepts (14 min) 2-Phylogenetic trees (14 min) 3-Methods tree construction (8 min) 4-UPGMA clustering (10 min) 5-Further methods and PGR examples (20 min)
• In class exercise
• Computer lab: HTML | Markdown

Biodiversity

• Slides | Lecture notes
• Video: 1-Introduction (19 min) 2-Economic value (5 min) 3-Agrobiodiversity (13 min) 4-Changes in biodiversity (10 min)
• In class exercises

Crop diversity and systematics

• Slides | Lecture notes
• Video: 1-Plant phylogeny (15 min) 2-Plant architecture (20 min) 3-Crop phylogeny (17 min)
• In class exercise

Crop domestication

• Slides | Lecture notes
• Videos: 1-History (21 min) 2-Centres (23 min) 3-Old-World (17 min)
• In class discussion

Population structure

• Slides | Lecture notes | 3-D PCA of Amaranth domestication: HTML (loading may take a while)
• Videos: 1-Introduction and phylogeny (10 min) 2-PCA (14 min) 3-Modelbased inference (20 min)
• In class exercise:
• Computer lab: HTML | Markdown

Gene flow and reticulate evolution

• Slides | Lecture notes
• Videos: 1-Introduction (19 min) 2-Reticulate evolution (9 min) 3-Examples (28 min)
• In class discussion

Coalescent theory

• Slides | Lecture notes
• Videos: 1-Theory and genealogies (24 min) 2-Mutations (22 min) 3-Demography and applications (26 min)
• Computer lab: HTML | Markdown

Tests of selection

• Slides | Lecture notes
• Videos: 1-Introduction (20 min) 2-Concepts (13 min) 3-Selection tests (25 min)
• Computer lab: HTML | Markdown

Genetics of crop evolution

• Slides | Lecture notes
• Videos: 1-Domestication syndrome (15 min) 2-Genetics of maize domestication (15 min) 3-Molecular genetics of teosinte branched 1 (24 min)
• In class discussion (only questions 1 to 4).

Demographic analysis of crop evolution

• Slides | Lecture notes
• Videos: 1-Introduction (19 min) 2-Selection at tb1 (20 min) 3-Genome-wide selection detection (11 min)
• In class discussion (only questions 5 to 8).

History of plant genetic resources

• Slides | Lecture notes
• Videos: 1-Introduction (10 min) 2-World-changing plants (14 min) 3-Collection expeditions (29 min) 4-German genebank history (5 min) 5-International developments (20 min)

International legislation for plant genetic resources

• Slides | Lecture notes
• Videos: 1-Introduction (20 min) 2-International Treaty (9 min) 3-SMTA (14 min) 4-Nagoya-Protocol (13 min)
• Additional videos: ABS - Simply explained (5 min) What is ABS? (2.5 min) ABS monitoring (6 min)
• In class exercise: PDF

Conservation of plant genetic resources

• Slides | Lecture notes
• Videos: 1-Introduction (26 min) 2-Ex situ conservation (17 min) 3-In situ conservation (31 min)
• In class discussion

Core collections

• Slides | Lecture notes
• Videos: 1-Background (7 min) 2-Construction of core collections (24 min) 3-Examples (5 min)
• Computer lab: PDF, data

Allele mining in PGR

• Slides | Lecture notes
• Videos: 1-Introduction (19 min) 2-FIGS (16 min) 3-Popgen-based allele mining (6 min)
• In class discussion (part 1)

Genetic mapping of useful alleles

• Slides | Lecture notes
• Videos: 1-Introduction (16 min) 2-Basic principles (16 min) 3-Methods and caveats (18 min) 4-Genetic mapping in PGR (9 min)
• In class discussion (part 2)

Analysis of phenotypic diversity

• Lecture notes
• Videos: 1-Background (11 min) 2-Mapping populations (22 min) 3-Phenotyping technologies (24 min)
• Computer lab: Rmd, dataset

Genetic resources in plant breeding

• Slides | Lecture notes
• Video: 1-Introduction (12 min) 2-Prebreeding (25 min) 3-Breeding methods (17 min) 4-Genomic selection (45 min) 5-Introgression libraries (9 min) 6-Genetic engineering (8 min) Note: No video on genome editing, check out the lecture notes
• In class discussion

Course literature

• Jack Harlan: Crops and Man (1992) PDF