Breeding scheme optimization

Breeding definitions for non-experts

(Note that these definitions are to help increase understanding for those not familiar with plant breeding science. They may lack nuance or precision for technical documents or audiences)


Biofortification: This involves breeding crops to increase their nutritional value, such as developing rice varieties with higher vitamin A content to combat malnutrition.

Archetype for implementing Rapid Cycle Genomic Selection (RCGS) in CGIAR-NARES-SME breeding network pipelines

The rapid cycle genomic selection (RCGS) archetype, developed by Accelerated Breeding Initiative’s ACCELERATE Work Package, seeks to enable selection and recycling of new parents as fast as possible – preferably two-to-three-year cycles, using data that is accurately representing the target population of environments (TPE) in which the future potential varieties will grow.

Breeding scheme design using quantitative genetics: 10 session course

This training is a professional development course designed by the Excellence in Breeding (EiB) Platform to increase the skillset of plant breeders to design breeding schemes. Across the public and private sector there is a gap on how to design breeding schemes and instead breeding schemes are normally inherited from one breeder to the other. EiB’s Module 2 and collaborators from seed industry have addressed this issue by developing and making this training available. 

Breeding pipeline manager

This tool aims to help breeding professionals to formalize the market segments, product profiles and breeding schemes associated to their breeding program(s). It serves as repository of valuable information that can be used for different purposes, e.g. discussions with leadership on proper targets, level of investment in different markets, breeding scheme optimization discussions to allocate resources more efficiently, share information with partners remotely, among others. The resulting documents can be considered the “blueprints” of the design step in the breeding process.

Characterization of rice quality traits to improve breeding for Latin America and the Caribbean

In this Story of Excellence, Juan Arbelaez (the University of Illinois at Urbana-Champaign) and Maribel Cruz (Latin American Fund for Irrigated Rice) present their work on genetic and phenotypic characterization of rice grain quality traits to define breeding strategies for improving rice milling, appearance, and cooking qualities in Latin America and the Caribbean.

National breeding institutes deliver initial program costing at in-person training course

A new costing tool is helping national breeding programs get the financial data needed to improve their efficiency, effectiveness and transparency. And now, in its first in-person event since the beginning of the pandemic, CGIAR Excellence in Breeding (EiB) has prepped six African National Agricultural Research and Extension Systems (NARES) to fully cost their programs.  

Basics of Genomic Selection 5. Mid-density Genotyping

Eng Hwa Ng and Rajaguru Bohar present the current genotyping shared services available from EiB to enable low, mid and high-density genotyping for the application in genomic selection. The link to trait augmentation is presented and the logistical challenges involved in starting to genotype the early-stage materials from programs is discussed. A network strategy for genotyping is presented to breeders. Costs, workflows, panels available and crop status are discussed by Rajaguru.

Basics of Genomic Selection 4. Selection Intensity and Cycle Time

Giovanny Covarrubias-Pazaran presents how to implement genomic prediction to change selection intensity. It is possible to increase selection intensity at an additional cost (although lower than the cost of phenotyping) or maintain the same intensity and accuracy with reduced costs.

Additionally, Covarrubias-Pazaran presents how to implement genomic prediction to reduce cycle time. This implies predicting individuals that have not been observed before while also predicting haplotypes that have not been observed before.

Webinar: Costing for breeding programs

The “Breeding Costing Tool” is a powerful solution for allowing users to estimate the cost of crop breeding and its associated research activities and to help breeders make decisions about resource allocation. The costing tool is designed to calculate the cost of running a crop breeding activity, or an entire breeding pipeline, using the prices, costs and salaries from a single year. The software is freely available from the Queensland Alliance for Agriculture and Food Innovation and the University of Queensland in Australia.

Optimal program sizes

What is an optimal program size?

The size of the breeding program is something that can increase the genetic gain by taking advantage of factors such as selection intensity or the among- and within-family variance.

These simulation reports demonstrate the trade-offs between of number of parents, crosses and progeny per cross, and provide practical advice on how to set the level of each.