Plant Breeding: Markers in Quantitative Genetics and 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: 6 April 2025

Please note that the dates for the academic year of 2024-2025 are yet to be confirmed, so they might still change.

Target audience

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.

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 (can be found under Related courses in the right-hand column). 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.

Learning outcomes

After successful completion of this programme, you will be able to:

  • Understand the use of polymorphic markers in segregating populations.
  • 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.
  • 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.
  • Comprehend the concepts of additivity, dominance, incomplete (partial) dominance and overdominance in single-locus and multi-locus genetic models, and recognise different forms of two-locus epistasis.
  • 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.
  • Map a gene involved in a qualitative trait in a mapping population.
  • 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.
  • 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.
  • Distinguish and contrast genetic and physical maps.
  • 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 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 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.
  • Understand the concept of genetic markers in genetic research and breeding.
  • Use software to construct a genetic map from marker genotyping data in a segregating population and interpret the result.
  • 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).
  • 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.
  • 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.
  • Understand the relevance of response to selection in terms of progress per time unit for selectable traits in a breeding program.


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.

This course is an online course at master level that you follow in a cohort. Learners participate at different time points and from different time zones, as most learners also have a job. The programme therefor offers learning activities that allow you to supervised self-study at your own pace, with deadlines for assignments, and includes knowledge clips, e-learning modules, read literature, online individual and group exercises and assignments, online discussions, and in some courses occasionally live question hours through MS Teams at specific dates and times. There are no online live classes. The exam has a fixed date.

Scientific papers, texts of Piet Stam on mapping and QTL analysis and 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. Links to relevant papers and articles will be provided through the online learning environment.

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

Software used in this course: R, including R studio.

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 first. For more information and registration, please check the document linked in the right-hand column.

This course is also part of the Online Master's course series Plant Breeding: Markers in Quantitative Genetics & Quality and the Online Master's course series Plant Breeding: Markers in Quantitative Genetics, Germplasm & Seed Technology.


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-credential.

The date of examination is 3 July 2025 from 08:30 - 22:00 (Amsterdam Time Zone). The duration of an exam is 3 hours. The resit is scheduled on 17 July 2025.


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 or the Master's Course Breeding for Quality successfully, you can obtain a Micro-credentials certificate.

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