EiB breeding scheme optimization manuals

A series of manuals outlining best practices in breeding scheme design and optimization.

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


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: Document on Cheatsheet realized genetic gain.pdf


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