Modelling spatial trends in sorghum breeding field trials using a two-dimensional P-spline mixed model

Julio G. Velazco, María Xosé Rodríguez-Álvarez, Martin P. Boer, David R. Jordan, Paul H.C. Eilers, Marcos Malosetti, Fred A. van Eeuwijk*

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

14 Citations (Scopus)

Abstract

Key message: A 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. Abstract: Adjustment 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.
Original languageEnglish
Pages (from-to)1375-1392
JournalTheoretical and Applied Genetics
Volume130
Issue number7
DOIs
Publication statusPublished - 2017

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Sorghum
Breeding
field experimentation
breeding
Spatial Analysis
Genotype
plant breeding
methodology

Cite this

Velazco, Julio G. ; Rodríguez-Álvarez, María Xosé ; Boer, Martin P. ; Jordan, David R. ; Eilers, Paul H.C. ; Malosetti, Marcos ; van Eeuwijk, Fred A. / Modelling spatial trends in sorghum breeding field trials using a two-dimensional P-spline mixed model. In: Theoretical and Applied Genetics. 2017 ; Vol. 130, No. 7. pp. 1375-1392.
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Modelling spatial trends in sorghum breeding field trials using a two-dimensional P-spline mixed model. / Velazco, Julio G.; Rodríguez-Álvarez, María Xosé; Boer, Martin P.; Jordan, David R.; Eilers, Paul H.C.; Malosetti, Marcos; van Eeuwijk, Fred A.

In: Theoretical and Applied Genetics, Vol. 130, No. 7, 2017, p. 1375-1392.

Research output: Contribution to journalArticleAcademicpeer-review

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