Key messageA flexible and user-friendly spatial method called SpATS performed comparably to more elaborate and trial-specific spatial models in a series of sorghum breeding trials.AbstractAdjustment for spatial trends in plant breeding field trials is essential for efficient evaluation and selection of genotypes. Current mixed model methods of spatial analysis are based on a multi-step modelling process where global and local trends are fitted after trying several candidate spatial models. This paper reports the application of a novel spatial method that accounts for all types of continuous field variation in a single modelling step by fitting a smooth surface. The method uses two-dimensional P-splines with anisotropic smoothing formulated in the mixed model framework, referred to as SpATS model. We applied this methodology to a series of large and partially replicated sorghum breeding trials. The new model was assessed in comparison with the more elaborate standard spatial models that use autoregressive correlation of residuals. The improvements in precision and the predictions of genotypic values produced by the SpATS model were equivalent to those obtained using the best fitting standard spatial models for each trial. One advantage of the approach with SpATS is that all patterns of spatial trend and genetic effects were modelled simultaneously by fitting a single model. Furthermore, we used a flexible model to adequately adjust for field trends. This strategy reduces potential parameter identification problems and simplifies the model selection process. Therefore, the new method should be considered as an efficient and easy-to-use alternative for routine analyses of plant breeding trials.
Modelling spatial trends in sorghum breeding field trials using a two-dimensional P-spline mixed model
J. G. Velazco,M. Rodríguez-Álvarez,M. Boer,D. Jordan,P. Eilers,M. Malosetti,F. V. van Eeuwijk
Published 2017 in Theoretical and Applied Genetics
ABSTRACT
PUBLICATION RECORD
- Publication year
2017
- Venue
Theoretical and Applied Genetics
- Publication date
2017-04-03
- Fields of study
Agricultural and Food Sciences, Medicine, Biology
- Identifiers
- External record
- Source metadata
Semantic Scholar, PubMed
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EXTRACTION MAP
CLAIMS
CONCEPTS
- anisotropic smoothing
A smoothing scheme that allows different degrees of smoothness in the two field directions.
- genetic effects
Genotype-related effects estimated in the mixed model alongside the spatial terms.
- genotypic values
Genotype-specific values predicted from the field-trial data.
Aliases: predictions of genotypic values
- sorghum breeding field trials
A series of large, partially replicated sorghum experiments used to evaluate genotypes.
Aliases: sorghum breeding trials
- spatial trends
Continuous variation across the field layout that can affect observed trial values.
Aliases: field trends, continuous field variation
- spats model
A mixed-model spatial analysis approach built around two-dimensional P-splines and anisotropic smoothing.
Aliases: SpATS
- standard spatial models
Conventional spatial-analysis models used as comparators in each trial, typically with autoregressive residual correlation.
Aliases: more elaborate standard spatial models, trial-specific spatial models, best fitting standard spatial models
- two-dimensional p-splines
A bivariate spline basis used to represent smooth variation across field rows and columns.
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