Abebe, Admas Alemu
- Department of Plant Breeding, Swedish University of Agricultural Sciences
Abstract
Genomic selection (GS) in plant breeding aims to identify individuals with superior genetic merit while maintaining genetic diversity within populations. In plant breeding, considering multiple traits simultaneously makes optimizing selection complex, especially under genetic relatedness constraints. In this study, we propose a binary quadratic programming framework for constructing a multi-trait selection index that maximizes genetic gain while minimizing average pairwise relatedness appropriate for identifying superior candidates for advancement in the breeding pipeline. The approach combines estimated breeding values (EBVs) across multiple traits by applying trait-specific economic weights, while simultaneously accounting for coancestry through the genomic relationship matrix. By formulating the selection problem as a constrained Quadratic Programing Multi-trait Selection Index (QPMSI), our method enables the identification of a fixed number of candidate individuals that jointly optimize selection index values and control genetic relatedness. We evaluated the performance of the proposed method using five real genomic datasets and demonstrated that it provides a more effective balance between selection response and control of genetic relatedness than the Linear Programming Multi-trait Selection Index (LPMSI). In particular, the QPMSI consistently outperformed the LPMSI in terms of the MV metric (gain-to-degree of relatedness ratio), achieving improvements of at least 53.8%. This framework offers a practical and computationally efficient tool for sustainable breeding strategies in multi-trait selection contexts.
Keywords
Plant breeding; Linear programming; Quadratic programing; Multi-trait index selection; Genetic diversity; Candidates individuals
Published in
Plant Methods
2026, volume: 22, number: 1, article number: 7
Publisher: BMC
SLU Authors
UKÄ Subject classification
Botany
Genetics and Genomics
Publication identifier
- DOI: https://doi.org/10.1186/s13007-025-01484-4
Permanent link to this page (URI)
https://res.slu.se/id/publ/146085