Abstract
Formalized breeding schemes are a key component of breeding program design and a gateway to conducting plant breeding as a quantitative process. Unfortunately, breeding schemes are rarely defined, expressed in a quantifiable format, or stored in a database. Furthermore, the continuous review and improvement of breeding schemes is not routinely conducted in many breeding programs. Given the rapid development of novel breeding methodologies, it is important to adopt a philosophy of continuous improvement regarding breeding scheme design. Here, we discuss terms and definitions that are relevant to formalizing breeding pipelines, market segments and breeding schemes, and we present a software tool, Breeding Pipeline Manager, that can be used to formalize and continuously improve breeding schemes. In addition, we detail the use of continuous improvement methods and tools such as genetic simulation through a case study in the International Institute of Tropical Agriculture (IITA) Cassava east-Africa pipeline. We successfully deploy these tools and methods to optimize the program size as well as allocation of resources to the number of parents used, number of crosses made, and number of progeny produced. We propose a structured approach to improve breeding schemes which will help to sustain the rates of response to selection and help to deliver better products to farmers and consumers.
Highlights
A breeding program is the sum of breeding pipelines to achieve breeding targets for a set of market/target segments1 Only after rigorous market and social studies have been carried out and an impactful pipeline investment case is presented to the leadership of an organization/institution, a breeding pipeline is created to carry out trait discovery, population improvement, product development, introgression efforts, seed dissemination/commercialization or a combination of one or several of these
To demonstrate the use of the continuous improvement methodologies to optimize breeding processes leveraging from measuring tools like the breeding pipeline manager (BPM) and stochastic simulation, we engaged in discussions with the Institute of Tropical Agriculture (IITA) Cassava program
We found the IITA-cassava program to be composed of five breeding pipelines and on average tackling six market segments
Summary
A breeding program is the sum of breeding pipelines to achieve breeding targets for a set of market/target segments Only after rigorous market and social studies have been carried out and an impactful pipeline investment case is presented to the leadership of an organization/institution, a breeding pipeline is created to carry out trait discovery, population improvement, product development, introgression efforts, seed dissemination/commercialization or a combination of one or several of these (tiers). A market segment is defined by the target population of environments in which the final. Improving Breeding Schemes product is grown, as well as descriptions of the target clients and product traits that are valued for production and consumption by farmers and end-users. Products to be placed in a market segment are described through product profiles/concepts; detailed descriptions of the traits and their thresholds (or range of values) to be found in the desired product or variety (sometimes based on current variety in the market) that aims to increase the likelihood of acceptance in the market. A breeding pipeline within a program may target one or more market segments and the associated product profiles using one or more breeding schemes. Breeding schemes are a collection of crossing, evaluation, and selection (CES) tasks and decisions which vary across breeding stages (e.g., in the crossing block vs. advanced yield testing in plants) and define a breeding strategy (Henryon et al, 2014; Yabe et al, 2017; Cobb et al, 2019; Pook et al, 2020; Gaynor et al, 2021; Figure 1)
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