Master's course Plant Breeding - Markers in Quantitative Genetics and Plant Breeding

Join this academic-level online course that is designed for working professionals in the plant breeding sector who want to enhance their knowledge of molecular markers and their application in genetic research and plant breeding. Participants will learn about the use of molecular markers for genetic mapping, QTL analysis, and marker-aided selection for both qualitative and quantitative traits. The course covers the estimation of genetic distance, the construction of linkage maps, the analysis of quantitative trait loci (QTLs), and the inheritance of qualitative and quantitative traits. Upon completion of this course, participants will have a comprehensive understanding of molecular markers and their application in genetic research and breeding, including how to estimate heritability, perform QTL analysis, and understand the concepts of indirect selection and genomic selection.

Organised by Wageningen Academy

Mon 27 May 2024 until Fri 5 July 2024

Duration 6 weeks, 20 hours per week (4 ECTS)
Price EUR 1,640.00

Registration deadline: 7 April 2024

Exam date: 4 July 2024

Why follow this online course?

In this course, participants 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. 

Is this online course for you?

If you are a working professional in the plant breeding sector, this course is the perfect opportunity for you to expand your knowledge and sharpen your skills. This comprehensive course will provide you with the tools you need to succeed and advance in your career, especially in combination with other advanced Online Master's Courses Plant Breeding

This course is also part of the Online Master's course series - Plant Breeding: Markers in Quantitative Genetics & Quality

What you'll learn

After successful completion of this online course, you will 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 recognise 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; distinguish QTL analysis from genome-wide association studies (GWAS);
  • understand the concept of GWAS and LD and LD decay, the issue of population structure and kinship correction in GWAS, the use of Manhattan plots and QQ-plots of p-values in the context of GWAS studies;
  • understand the concept of genomic selection in breeding and statistical procedures used for genomic selection;
  • 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.

Learning methods

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

Practical information

STAP budget

When enrolling in this course, you may apply for the use of the STAP budget. Check if you are eligible for the STAP-budget.


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 as course reference book and for more in-depth knowledge.

Software used in this course

R including R Studio.

Time investment

This course is quite time-intensive and requires approximately 20 hours per week for the average participant. There are assignments with deadlines. 

It's important to realise that, if you do not comply with these recommendations, you cannot claim extra support from the instructor and cannot claim a refund of the registration fee, if you decide to discontinue the course. 

Prerequisite knowledge

You should have sufficient knowledge on concepts and methodologies related to plant biology, such as genetics, plant breeding, plant physiology and molecular biology. If you are lacking certain knowledge or skills listed above, we strongly recommend you join the course “Principles of Plant Breeding” and/or "Advanced Statistics" first.

Self-Paced Online Course Getting Started with R
You need to have advanced knowledge of statistics and some experience with R and R Studio in order to perform statistical analyses. If the latter is not the case, you can follow the Self-Paced Online Course Getting Started with R. For more information and registration, please check this document.


Participation in the remotely proctored exam is optional. If you decide not to participate in the exam, you do not qualify for a certificate and/or Micro-credentials.

The date of examination is 04-07-2024 (4 July 2024) from 08:30 - 22:00 (Amsterdam Time Zone). The duration of an exam is 3 hours. The resit will be scheduled in the week of 15 July 2024.


Upon successful completion - passing the exam and making assignments - , a digital certificate with 4 study credits (ECTS) is issued. This certificate offers no immediate rights to apply for a formal degree programme at a university, but might support your request for admission. In case you've also completed the Master's Course Germplasm and Seed Technology successfully, you can obtain a Micro-credentials certificate. 

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More information & Registration

You can register for this course. Have any questions? Contact Wageningen Academy.