PBR-36804 Markers in Quantitative Genetics and Plant Breeding (online)


Credits 4.00

Teaching methodContact hours
Knowledge clip0
Distance group work0
E-learning material0
Course coordinator(s)dr. ir. CA Maliepaard
Lecturer(s)dr. ir. JC Goud
dr. ir. CA Maliepaard
dr. ir. RE Niks
Examiner(s)dr. ir. JC Goud
dr. ir. RE Niks
dr. ir. CA Maliepaard

Language of instruction:


Assumed knowledge on:

PBR-31803 Genetics (DL); PBR-22803 Principles of Plant Breeding (DL); MAT-25303 Advanced Statistics (DL)
-Note: It is necessary to have followed an online course at Wageningen University before, or the special Onboarding course for distance learning. To get access to the Onboarding course, send an email to: onboarding.wur@wur.nl.

Continuation courses:

PBR-32302; PBR-32802; PBR-31802; PBR-35803


Note 1: This course can not be combined in an individual programme with ABG-30806 Modern Statistics for the Life Sciences (MSLS) and/or PBR-21803 Pre-breeding

Note 2: This course has a maximum number of participants. The deadline for registration is one week earlier than usual. See Academic Year.(http://www.wageningenur.nl/en/Education-Programmes/Current-Students/Agenda-Calendar-Academic-Year.htm) -> Registration for Courses.
Note 3: The period mentioned below is the period in which this course starts. For the exact academic weeks see the courseplanning on www.wur.eu/schedule.

Note 4: This course is offered online and it takes about 20 hours to complete the weekly task. There are assignments with deadlines and non-synchronous interaction with teachers and fellow students. An online exam is offered in the last week of the course (usually at the last Friday of the course)

Note 5: This is an online course, but it can also be followed by on-campus students after consultation of the course coordinator.

Note 6: Because of overlap between this online course and on-campus courses, it is not possible to combine this course with PBR-21803 Pre-breeding in your study program to obtain a minimum amount of credits.

In this course, the students will be made familiar with the use of molecular markers in genetic research and plant breeding, the estimation of genetic distance based on marker genotype frequencies in different types of segregating populations, the construction of linkage maps, concepts and applications of quantitative genetics, the analysis of quantitative trait loci (QTLs) and the discovery and application of markers in research and for selection in breeding programs, both for qualitative and quantitative traits.

Learning outcomes:

After successful completion of this course students are expected to be able to:
- understand the concept of genetic markers in genetic research and breeding;
- understand the use of polymorphic markers in segregating populations;
- use sequence information for discovery of single-nucleotide polymorphisms (SNPs) and understand how these can be used as molecular markers for genetic mapping, QTL analysis and marker-aided selection;
- analyse genetic segregations, including cases where genetic linkage occurs;
- infer linkage/non-linkage and to calculate genetic distance from genotype frequencies in a segregating population;
- use software to construct a genetic map from marker genotyping data in a segregating population and interpret the result;
- distinguish and contrast genetic and physical maps;
- comprehend and contrast the inheritance of qualitative vs. quantitative traits and the consequences for plant breeding. The inheritance of monogenic vs. polygenic traits and the relationship to qualitative and quantitative traits.;
- comprehend the importance of quantitative traits in breeding and possibilities and consequences for selection over shorter and longer periods;
- comprehend the concepts of additivity, dominance, incomplete (partial) dominance and overdominance in single-locus and multi-locus genetic models. Comprehend the concept of epistasis and recognize different forms of two-locus epistasis;
- comprehend how dominance and overdominance can be involved in the explanation of heterosis and consequences for breeding (choice pure line or hybrid cultivars, maintaining heterozygosity in OPV, inbreeding depression after sib mating or selfing);
- calculate midparent value, (net) additive effect, (net) dominance effect and (means based) dominance ratio from the means of a trait in basic generations such as BC1, F2, RILs, including parental generations P1 and P2 and F1. Interpret results in terms of consequences for breeding;
- comprehend the concepts of additive genetic variance, dominance genetic variance, dominance ratio and their expectations in different breeding generations /research populations;
- use quantitative genetics models and statistical methods to quantify additive genetic variance, dominance genetic variance, (variance based) dominance ratio in basic breeding and research populations;
- comprehend the concepts of genetic and environmental variance, narrow-sense and wide-sense heritability;
- understand that heritability estimates are specific for certain traits in certain populations tested in certain environments with a certain experimental design but also have a wider interpretation outside those specific contexts;
- use quantitative genetics models and statistical methods to estimate variance components (genetic variance, environmental variance, variance associated with G*E interaction) and to estimate wide-sense and narrow-sense heritability;
- comprehend the concepts of Selection Differential, selection intensity, Response to selection, genetic correlation, indirect selection and Correlated Response to Selection, and the so-called breeders' equation. Understand how the response to selection may vary according to the heritability, the selection intensity, the type of material, the stage at which the trait can be evaluated (before/after flowering!). Understand indirect selection in terms of these concepts.
- understand the relevance of response to selection in terms of progress per time unit for selectable traits in a breeding program. Understand the relationship between quantitative genetic theory of indirect selection and applications in indirect selection, notably in marker-assisted selection of quantitative traits and/or genomic selection on breeding values of quantitative traits;
- calculate response to selection and correlated response to selection, given a heritability estimate, intensity of selection, selection differential;
- apply quantitative genetics theory and methodology to compare expected effectiveness of different possible breeding strategies (e.g. breeding hybrid vs. pure line cultivar) under given assumptions and limitations;
- map a gene involved in a qualitative trait in a mapping population;
- understand the concept of QTL analysis using a genotyped mapping population, a linkage map for that population and a quantitative phenotypic trait scored in the population;
- distinguish and contrast QTL mapping procedures based on single marker analyses, interval mapping, composite interval mapping;
- perform QTL analyses using QTL mapping software and interpret the results;
- understand the principles of bulked-segregant analysis and selective genotyping;
- understand the application of molecular markers in indirect selection for phenotypic traits in breeding programs.


Study knowledge clips, E-learning modules, individual and group exercises, online discussions, application of software.


Examination will be an online written examination with open questions and/or multiple choice questions. An online exam is offered in the last week of the course (usually at the last Friday of the course).


E-learning modules, scientific papers, texts of Piet Stam on mapping and QTL analysis, Kearsey and Pooni The Genetical analysis of quantitative traits, Chapters 1 - 4.3, 15.5 to 15.8.

Compulsory for: MPSPlant SciencesMScF: Plant Breeding6DL