EiB breeding scheme optimization manuals

In order to deliver higher rates of genetic gain and variety turnover, breeding programs targeting low- to middle-income countries must adopt standard best practices in breeding scheme design in order to enable a continuous process of optimization to deliver on breeding targets (product profiles).

The CGIAR Excellence in Breeding Platform has developed this series of practical and conceptual manuals to set a common terminology and conceptual framework to visualize the main steps in a breeding process. 


Breeding as a process




Trait and diversity pipelines

A. Managing diversity

1. Germplasm and trait introgression


Breeding pipelines

A. Evaluation decisions

1. Heritability: Meaning and computation

B. Selection decisions

1. Estimating surrogates of genetic value

2. Selection intensity

3. Selection indices (practical guidelines)


Field trials

A. Design and analysis

1. Practical guidelines

2. Theoretical background


Program performance indicators

A. Genetic gain

1. Genetic gain as a high-level key performance indicator

See also: Webinar on Rate of response to selection (genetic gain)

See also: Cheatsheet on realized genetic gain

See also: Cheatsheet on predicted genetic gain


Scripts and datasets 

The simulated data sets and R scripts to recreate the analysis mentioned in any of the “how to” manuals can be found in the Excellence in Breeding (EiB) GitLab page:



Germplasm and trait introgression
This manual provides guidelines for the introgression of traits and germplasm while maintaining closed recurrent selection programs.
Giovanny E. Covarrubias-Pazaran
Heritability: Meaning and computation
This manual explains the concept of heritability and shows how to compute it by different methods along with recommendations.
Giovanny E. Covarrubias-Pazaran
Estimating surrogates of genetic value
This manual describes and compares different methods of estimating genetic value.
Ian Mackay, Giovanny E. Covarrubias-Pazaran
Genetic gain as a high-level key performance indicator
This manual describes how to use genetic gain as a key performance indicator of breeding processes
Giovanny E. Covarrubias-Pazaran
Selection intensity
This manual describes selection intensity, how to calculate it, and its importance in determining response to selection.
Ian Mackay, Giovanny E. Covarrubias-Pazaran
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Video URL
[Webinar] Rate of response to selection (genetic gain): Concept, methods and recommendations
Presentation delivered during the webinar "Enhancing and measuring Genetic Gain in crop breeding", 19 Nov 2020.
Giovanny E. Covarrubias-Pazaran
Cheatsheat on how to calculate realized genetic gain
Recommendations on how to set experiments, organize the data and analyze it to provide accurate estimates of realized genetic gain
Giovanny E. Covarrubias-Pazaran
Cheatsheet on how to calculate predicted genetic gain
Provides a template and guidelines to calculate predicted genetic gain for continuous assessment and reporting.
Giovanny E. Covarrubias-Pazaran
Guideline for the practical implementation of selection indices
A step-by-step approach to implement selection indices.
Giovanny E. Covarrubias-Pazaran
Design and analysis of field trials - 2. Theoretical background
A brief introduction to the theoretical background of field experimentation, multi-environmental trials and GxE interaction.
Christian R. Werner
Design and analysis of field trials - 1. Practical guidelines
Guidelines on the design and statistical analysis of plant breeding field trails with a focus on breeders who do not have access to permanent biometric support
Christian R. Werner