SimpleMating: R‐package for prediction and optimization of breeding crosses using genomic selection
Abstract Selecting parents and crosses is a critical step for a successful breeding program. The ability to design crosses with high means that will maintain genetic variation in the population is the goal for long‐term applications. Herein, we describe a new computational package for mate allocatio...
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| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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Wiley
2025-03-01
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| Series: | The Plant Genome |
| Online Access: | https://doi.org/10.1002/tpg2.20533 |
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| _version_ | 1850048116542144512 |
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| author | Marco Antônio Peixoto Rodrigo Rampazo Amadeu Leonardo Lopes Bhering Luís Felipe V. Ferrão Patrício R. Munoz Márcio F. R. Resende Jr. |
| author_facet | Marco Antônio Peixoto Rodrigo Rampazo Amadeu Leonardo Lopes Bhering Luís Felipe V. Ferrão Patrício R. Munoz Márcio F. R. Resende Jr. |
| author_sort | Marco Antônio Peixoto |
| collection | DOAJ |
| description | Abstract Selecting parents and crosses is a critical step for a successful breeding program. The ability to design crosses with high means that will maintain genetic variation in the population is the goal for long‐term applications. Herein, we describe a new computational package for mate allocation in a breeding program. SimpleMating is a flexible and open‐source R package originally designed to predict and optimize breeding crosses in crops with different reproductive systems and breeding designs. Divided into modules, SimpleMating first estimates the cross performance (criterion), such as mid‐parental value, cross total genetic value, and/or usefulness of a set of crosses. The second module implements an optimization algorithm to maximize a target criterion while minimizing next‐generation inbreeding. The software is flexible, enabling users to specify the desired number of crosses, set maximum and minimum crosses per parent, and define the maximum allowable parent relationship for creating crosses. As an outcome, SimpleMating generates a mating plan from the target parental population using single or multi‐trait criteria. For example, we implemented and tested SimpleMating in a simulated maize breeding program obtained through stochastic simulations. The crosses designed via SimpleMating showed a large genetic mean over time (up to 22% more genetic gain than conventional genomic selection programs, with lesser loss of genetic diversity over time), supporting the use of this tool, as well as the use of data‐driven decisions in breeding programs. |
| format | Article |
| id | doaj-art-e5b98c1ba59847c390d37f95ab469a13 |
| institution | DOAJ |
| issn | 1940-3372 |
| language | English |
| publishDate | 2025-03-01 |
| publisher | Wiley |
| record_format | Article |
| series | The Plant Genome |
| spelling | doaj-art-e5b98c1ba59847c390d37f95ab469a132025-08-20T02:54:03ZengWileyThe Plant Genome1940-33722025-03-01181n/an/a10.1002/tpg2.20533SimpleMating: R‐package for prediction and optimization of breeding crosses using genomic selectionMarco Antônio Peixoto0Rodrigo Rampazo Amadeu1Leonardo Lopes Bhering2Luís Felipe V. Ferrão3Patrício R. Munoz4Márcio F. R. Resende Jr.5Laboratório de Biometria Universidade Federal de Viçosa Viçosa Minas Gerais BrazilBlueberry Breeding and Genomics Lab University of Florida Gainesville Florida USALaboratório de Biometria Universidade Federal de Viçosa Viçosa Minas Gerais BrazilBlueberry Breeding and Genomics Lab University of Florida Gainesville Florida USABlueberry Breeding and Genomics Lab University of Florida Gainesville Florida USASweet Corn Breeding and Genomics Lab University of Florida Gainesville Florida USAAbstract Selecting parents and crosses is a critical step for a successful breeding program. The ability to design crosses with high means that will maintain genetic variation in the population is the goal for long‐term applications. Herein, we describe a new computational package for mate allocation in a breeding program. SimpleMating is a flexible and open‐source R package originally designed to predict and optimize breeding crosses in crops with different reproductive systems and breeding designs. Divided into modules, SimpleMating first estimates the cross performance (criterion), such as mid‐parental value, cross total genetic value, and/or usefulness of a set of crosses. The second module implements an optimization algorithm to maximize a target criterion while minimizing next‐generation inbreeding. The software is flexible, enabling users to specify the desired number of crosses, set maximum and minimum crosses per parent, and define the maximum allowable parent relationship for creating crosses. As an outcome, SimpleMating generates a mating plan from the target parental population using single or multi‐trait criteria. For example, we implemented and tested SimpleMating in a simulated maize breeding program obtained through stochastic simulations. The crosses designed via SimpleMating showed a large genetic mean over time (up to 22% more genetic gain than conventional genomic selection programs, with lesser loss of genetic diversity over time), supporting the use of this tool, as well as the use of data‐driven decisions in breeding programs.https://doi.org/10.1002/tpg2.20533 |
| spellingShingle | Marco Antônio Peixoto Rodrigo Rampazo Amadeu Leonardo Lopes Bhering Luís Felipe V. Ferrão Patrício R. Munoz Márcio F. R. Resende Jr. SimpleMating: R‐package for prediction and optimization of breeding crosses using genomic selection The Plant Genome |
| title | SimpleMating: R‐package for prediction and optimization of breeding crosses using genomic selection |
| title_full | SimpleMating: R‐package for prediction and optimization of breeding crosses using genomic selection |
| title_fullStr | SimpleMating: R‐package for prediction and optimization of breeding crosses using genomic selection |
| title_full_unstemmed | SimpleMating: R‐package for prediction and optimization of breeding crosses using genomic selection |
| title_short | SimpleMating: R‐package for prediction and optimization of breeding crosses using genomic selection |
| title_sort | simplemating r package for prediction and optimization of breeding crosses using genomic selection |
| url | https://doi.org/10.1002/tpg2.20533 |
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