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Gregor Gorjanc, Ivan Pocrnic, Steph Smith, Laura Strachan, and Gabriela M. Fortuna

This online course will equip participants with an understanding of computer modelling of breeding programmes to enhance genetic improvements in agriculture. The modelling is done through the AlphaSimR package.

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This online course will equip participants with an understanding of computer modelling of breeding programmes to enhance genetic improvements in agriculture. The modelling is done through the AlphaSimR package.

The package provides a set of functions that represent breeding activities. The combination of these functions in an R script allows the modelling of simple and arbitrarily complex breeding programmes. It also allows evaluation of the effects of alternative breeding scenarios on the rate of genetic improvement and other key performance indicators.

The course is taught by experts in the field and is applicable to a range of breeding programmes as demonstrated through local and global case studies.

Wheat field image by Alf Ceplitis.

What you'll learn

1) Recall the key steps in setting up and designing a computer (in-silico) breeding programme to simulate and study a chosen population and understand the objectives that the in-silico breeding programme is being tailored to address.

2) Apply and build a breeding programme with AlphaSimR and use it to simulate and analyse a range of scenarios for a chosen population using an online R platform, which allows participants to access, manipulate, and run code.

3) Evaluate different breeding scenarios best suited to different species, populations, and available resources. Use information from the course to create a breeding programme which meets these objectives and derive tangible interpretations based on the simulation results.

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What's inside

Syllabus

Week 1: Introduction to breeding programme modelling
Week 2: Relationship between DNA & traits
Week 3: DNA Lottery
Week 4: Response to selection
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Week 5: Modelling complex breeding programmes

Good to know

Know what's good
, what to watch for
, and possible dealbreakers
In-silico breeding programme simulations, like the ones taught here, offer an environment that is both dynamic and responsive. This is highly valuable for learners who want to create in-silico experiments that are iterative in nature
This course provides learners with an opportunity to learn by doing thanks to the simulations. These simulations help students learn by engaging in trial and error
AlphaSimR, the software which will be the focus of this course, is open-source and boasts an active community of users. This community is useful for students who want supplemental support as they work through the course materials
Using in-silico computer models to study plant breeding is a forward-thinking approach in which more and more experts are securing funding. Familiarity with these models is a competitive edge
The case studies in this course are international in scope. This broadens the range of issues and topics covered. In turn, more learners will be able to relate to the material
This is a foundational course for students who are new to computer simulation modeling

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Activities

Be better prepared before your course. Deepen your understanding during and after it. Supplement your coursework and achieve mastery of the topics covered in Breeding Programme Modelling with AlphaSimR with these activities:
Review 'Genetics for Plant Breeders' By Allard
The text 'Genetics for Plant Breeders' is an introductory text on the principles of genetics and how it relates to plant breeding. It will provide a helpful background on the key principles of genetics that are applied throughout the course.
Show steps
  • Carefully read each chapter and take notes
  • Complete the exercises at the end of each chapter
  • Consider creating a summary of the key ideas and concepts
Review Genetics and Statistics
Strengthen foundational knowledge in genetics and statistics, which are essential for understanding the concepts covered in the course.
Browse courses on Genetics
Show steps
  • Review basic genetic principles: Mendelian inheritance, gene expression, DNA structure, and mutations
  • Review statistical concepts: probability distributions, hypothesis testing, and regression analysis
  • Apply genetics and statistics to solve problems related to breeding and genetic improvement
Read Quantitative Genetics in the Wild
Expand understanding of the genetic basis of quantitative traits and evolutionary processes by reading a foundational book in the field.
Show steps
  • Obtain a copy of the book
  • Read and understand the key concepts presented in the book
  • Apply the knowledge gained from the book to the breeding programme simulations in AlphaSimR
Seven other activities
Expand to see all activities and additional details
Show all ten activities
Attend a Workshop on AlphaSimR
Enhance understanding of AlphaSimR and its application in breeding programmes by attending a workshop led by experts in the field.
Show steps
  • Identify upcoming AlphaSimR workshops
  • Register for and attend the workshop
  • Participate actively in the workshop and ask questions
Complete the Chapter Quizzes
The chapter quizzes will help you to assess your understanding of the material covered in each chapter and to identify areas where you may need further study.
Browse courses on Response to Selection
Show steps
  • Go to the relevant chapter on edX
  • Click on the quiz link
  • Complete the quiz
  • Review your results and identify any areas where you need to improve
Practice Building AlphaSimR Scripts
Reinforce understanding of AlphaSimR and programming concepts by completing exercises that focus on building AlphaSimR scripts.
Show steps
  • Review AlphaSimR functions and syntax
  • Complete coding exercises to build AlphaSimR scripts
  • Troubleshoot and debug scripts
Simulate a Wheat Breeding Programme in AlphaSimR
Practice modelling a breeding programme using AlphaSimR to solidify understanding of the concepts learned in the course.
Show steps
  • Install R and download AlphaSimR
  • Set up a simple breeding programme in AlphaSimR
  • Simulate the breeding programme and analyse the results
  • Experiment with different breeding scenarios
Mentor Junior Students in AlphaSimR
Reinforce knowledge and understanding of AlphaSimR by mentoring junior students on the basics of the software and its applications in breeding programmes.
Show steps
  • Identify opportunities to mentor junior students
  • Provide guidance and support to students on using AlphaSimR
  • Answer questions and troubleshoot issues
Design and Present a Breeding Programme
Demonstrate mastery of breeding programme design by creating and presenting a plan that addresses specific objectives and incorporates the principles learned in the course.
Show steps
  • Identify the breeding objectives
  • Design the breeding programme
  • Simulate the breeding programme and evaluate the results
  • Prepare a presentation to showcase the breeding programme
Assist in a Breeding Programme
Gain practical experience and contribute to real-world breeding efforts by volunteering at a research institution or agricultural organization.
Show steps
  • Identify opportunities to volunteer at breeding programmes
  • Contact the organization and express interest in volunteering
  • Assist with tasks related to breeding, such as data collection, record keeping, or lab work

Career center

Learners who complete Breeding Programme Modelling with AlphaSimR will develop knowledge and skills that may be useful to these careers:
Crop and Soil Scientist
Crop and Soil Scientists play a vital role in the agricultural industry by applying their knowledge of plant and soil science to improve crop production and soil management. This course would be particularly useful for Crop and Soil Scientists who want to gain a deeper understanding of computer modelling of breeding programmes to enhance genetic improvements in agriculture.
Quantitative Geneticist
Quantitative Geneticists use mathematical and statistical methods to study the inheritance of traits in plants and animals. This course would be helpful for Quantitative Geneticists who want to learn how to use computer modelling to simulate and study breeding programmes.
Plant Geneticist
Plant Geneticists use their knowledge of genetics and plant breeding to improve the quality and yield of crops. This course would be helpful for Plant Geneticists who want to learn how to use computer modelling to simulate and study breeding programmes.
Animal Geneticist
Animal Geneticists use their knowledge of genetics and animal breeding to improve the quality and yield of livestock. This course would be helpful for Animal Geneticists who want to learn how to use computer modelling to simulate and study breeding programmes.
Data Scientist
Data Scientists use their knowledge of data analysis and machine learning to solve problems in a variety of industries. This course would be helpful for Data Scientists who want to learn how to use computer modelling to simulate and study breeding programmes.
Software Engineer
Software Engineers design, develop, and maintain software systems. This course may be helpful for Software Engineers who want to learn how to develop software for computer modelling of breeding programmes.
Biostatistician
Biostatisticians use their knowledge of statistics to design and analyse experiments in the life sciences. This course would be helpful for Biostatisticians who want to learn how to use computer modelling to simulate and study breeding programmes.
Agricultural Economist
Agricultural Economists use their knowledge of economics to analyse the agricultural industry. This course would be helpful for Agricultural Economists who want to learn how to use computer modelling to simulate and study breeding programmes.
Science Writer
Science Writers write about scientific topics for a variety of audiences. This course may be helpful for Science Writers who want to learn about computer modelling of breeding programmes.
Science Teacher
Science Teachers teach science at the secondary school level. This course may be helpful for Science Teachers who want to learn about computer modelling of breeding programmes.
Rancher
Ranchers raise livestock. This course may be helpful for Ranchers who want to learn about computer modelling of breeding programmes.
Farmer
Farmers grow crops and raise livestock. This course may be helpful for Farmers who want to learn about computer modelling of breeding programmes.
Ecologist
Ecologists study the interactions between organisms and their environment. This course may be helpful for Ecologists who want to learn about computer modelling of breeding programmes.
Wildlife Biologist
Wildlife Biologists study the behaviour and ecology of wildlife. This course may be helpful for Wildlife Biologists who want to learn about computer modelling of breeding programmes.
Environmental Scientist
Environmental Scientists study the environment and the impact of human activities on the environment. This course may be helpful for Environmental Scientists who want to learn about computer modelling of breeding programmes.

Reading list

We've selected ten books that we think will supplement your learning. Use these to develop background knowledge, enrich your coursework, and gain a deeper understanding of the topics covered in Breeding Programme Modelling with AlphaSimR.
Provides a comprehensive overview of the principles and methods used in field crop breeding, including the genetic basis of traits and the different breeding methods.
This classic textbook provides a comprehensive overview of experimental design and analysis techniques, including practical examples and exercises.
Provides a comprehensive overview of the statistical methods used in the analysis of biological data, including methods for sequence analysis, gene expression analysis, and protein-protein interaction networks.
Examines the application of molecular genetic techniques to plant breeding, including the use of molecular markers, genetic transformation, and gene editing.
Provides a comprehensive overview of the genetic and genomic approaches used in crop breeding, including the use of molecular markers and genomic selection.
Provides a comprehensive overview of the principles and methods used in plant breeding and biotechnology, including the use of molecular markers, genetic transformation, and gene editing.
Provides a comprehensive overview of the statistical methods used in the analysis of human genetic data, including methods for linkage analysis and association studies.
Provides a foundational overview of statistical methods used in agricultural research, including experimental design, analysis of variance, and regression analysis.
Provides a solid foundation in statistical theory and methods that are essential for designing and analyzing agricultural experiments.
Provides a concise introduction to plant breeding principles and methods, suitable for undergraduate students and non-specialists.

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