Multi-trait Genomic Selection Methods for Crop Improvement

Abstract Plant breeders make selection decisions based on multiple traits, such as yield, plant height, flowering time, and disease resistance. A commonly used approach in multi-trait genomic selection is index selection, which assigns weights to different traits relative to their economic importanc...

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Bibliographic Details
Published in:Genetics (Austin) 2020-08, Vol.215 (4), p.931-945
Main Authors: Moeinizade, Saba, Kusmec, Aaron, Hu, Guiping, Wang, Lizhi, Schnable, Patrick S
Format: Article
Language:English
Subjects:
Agricultural production
Algorithms
Corn
Crop improvement
Datasets
Decisions
Disease resistance
Economic importance
Experimentation
Flowering
Genetics
Investigations
Methods
Multiple objective analysis
Objectives
Optimization
Pareto optimization
Plant breeding
Population
Simulation
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Summary:Abstract Plant breeders make selection decisions based on multiple traits, such as yield, plant height, flowering time, and disease resistance. A commonly used approach in multi-trait genomic selection is index selection, which assigns weights to different traits relative to their economic importance. However, classical index selection only optimizes genetic gain in the next generation, requires some experimentation to find weights that lead to desired outcomes, and has difficulty optimizing nonlinear breeding objectives. Multi-objective optimization has also been used to identify the Pareto frontier of selection decisions, which represents different trade-offs across multiple traits. We propose a new approach, which maximizes certain traits while keeping others within desirable ranges. Optimal selection decisions are made using a new version of the look-ahead selection (LAS) algorithm, which was recently proposed for single-trait genomic selection, and achieved superior performance with respect to other state-of-the-art selection methods. To demonstrate the effectiveness of the new method, a case study is developed using a realistic data set where our method is compared with conventional index selection. Results suggest that the multi-trait LAS is more effective at balancing multiple traits compared with index selection.
ISSN:1943-2631
0016-6731
1943-2631
DOI:10.1534/genetics.120.303305