Breeding Programme Modelling with AlphaSimR from edX

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.

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

Traffic lights

Read about what's good

what should give you pause

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

Reviews summary

Alphasimr for genetic breeding programs

According to learners, this course provides an invaluable foundation for computer modelling of breeding programmes using the powerful AlphaSimR package. Students frequently highlight the clarity of complex concepts presented by expert instructors and the strong emphasis on practical application to real breeding scenarios. While the course content is considered cutting-edge and highly beneficial for research, some learners note it is very demanding and requires a strong grasp of R and genetic principles as prerequisites. There are occasional mentions of the online R platform having minor glitches and the forum support not always being quick, suggesting areas for potential improvement. Overall, it is highly recommended for advanced learners in the field.

Taught by knowledgeable experts who clarify complex topics effectively.

"The instructors explain complex concepts clearly."

"The experts teaching it clearly know their stuff and made the theory very accessible through examples."

"The hands-on labs were crucial for understanding."

Offers critical skills for designing and simulating breeding programs.

"Absolutely invaluable for my research. The ability to simulate complex scenarios and evaluate different strategies using AlphaSimR is a game changer."

"This course filled a critical gap in my understanding of breeding program design. The step-by-step approach to building models was excellent."

"I especially valued the practical application to real breeding scenarios."

Occasional issues with the online R platform and forum support.

"I appreciated the online R platform, though sometimes it had minor glitches."

"The support on the forums wasn't always quick."

Requires strong prior knowledge of R and genetic principles.

"A very informative course, but be warned: you need a strong grasp of R and genetic principles coming in."

"Content is great, but it's very demanding. I struggled without an extensive background in R, and the course felt like it sometimes assumed more familiarity than I had."

"Definitely for advanced learners."

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

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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.

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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

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Strengthen foundational knowledge in genetics and statistics, which are essential for understanding the concepts covered in the course.

Browse courses on Genetics

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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

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Expand understanding of the genetic basis of quantitative traits and evolutionary processes by reading a foundational book in the field.

View Evolution and Selection of Quantitative Traits on Amazon

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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

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Attend a Workshop on AlphaSimR

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Enhance understanding of AlphaSimR and its application in breeding programmes by attending a workshop led by experts in the field.

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Identify upcoming AlphaSimR workshops
Register for and attend the workshop
Participate actively in the workshop and ask questions

Complete the Chapter Quizzes

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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

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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

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Reinforce understanding of AlphaSimR and programming concepts by completing exercises that focus on building AlphaSimR scripts.

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Review AlphaSimR functions and syntax
Complete coding exercises to build AlphaSimR scripts
Troubleshoot and debug scripts

Simulate a Wheat Breeding Programme in AlphaSimR

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Practice modelling a breeding programme using AlphaSimR to solidify understanding of the concepts learned in the course.

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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

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Reinforce knowledge and understanding of AlphaSimR by mentoring junior students on the basics of the software and its applications in breeding programmes.

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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

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Demonstrate mastery of breeding programme design by creating and presenting a plan that addresses specific objectives and incorporates the principles learned in the course.

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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

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Gain practical experience and contribute to real-world breeding efforts by volunteering at a research institution or agricultural organization.

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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.

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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.

See salaries and explore the career path for Plant Geneticist

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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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Farmer

Farmers grow crops and raise livestock. This course may be helpful for Farmers who want to learn about computer modelling of breeding programmes.

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Rancher

Ranchers raise livestock. This course may be helpful for Ranchers who want to learn about computer modelling of breeding programmes.

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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.

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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.

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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.

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