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Open Access Research article

The importance of phenotypic data analysis for genomic prediction - a case study comparing different spatial models in rye

Angela-Maria Bernal-Vasquez1, Jens Möhring1, Malthe Schmidt2, Manfred Schönleben3, Chris-Carolin Schön3 and Hans-Peter Piepho1*

Author Affiliations

1 Bioinformatics Unit, Institute of Crop Science, University of Hohenheim, Fruwirthstrasse 23, 70599 Stuttgart, Germany

2 KWS LOCHOW GMBH, Ferdinand-von-Lochow-Strasse 5, 29303 Bergen, Germany

3 Plant Breeding, Technische Universität München, Liesel-Beckmann-Strasse 2, 85354 Freising, Germany

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BMC Genomics 2014, 15:646  doi:10.1186/1471-2164-15-646

Published: 4 August 2014

Abstract

Background

Genomic prediction is becoming a daily tool for plant breeders. It makes use of genotypic information to make predictions used for selection decisions. The accuracy of the predictions depends on the number of genotypes used in the calibration; hence, there is a need of combining data across years. A proper phenotypic analysis is a crucial prerequisite for accurate calibration of genomic prediction procedures. We compared stage-wise approaches to analyse a real dataset of a multi-environment trial (MET) in rye, which was connected between years only through one check, and used different spatial models to obtain better estimates, and thus, improved predictive abilities for genomic prediction. The aims of this study were to assess the advantage of using spatial models for the predictive abilities of genomic prediction, to identify suitable procedures to analyse a MET weakly connected across years using different stage-wise approaches, and to explore genomic prediction as a tool for selection of models for phenotypic data analysis.

Results

Using complex spatial models did not significantly improve the predictive ability of genomic prediction, but using row and column effects yielded the highest predictive abilities of all models. In the case of MET poorly connected between years, analysing each year separately and fitting year as a fixed effect in the genomic prediction stage yielded the most realistic predictive abilities. Predictive abilities can also be used to select models for phenotypic data analysis. The trend of the predictive abilities was not the same as the traditionally used Akaike information criterion, but favoured in the end the same models.

Conclusions

Making predictions using weakly linked datasets is of utmost interest for plant breeders. We provide an example with suggestions on how to handle such cases. Rather than relying on checks we show how to use year means across all entries for integrating data across years. It is further shown that fitting of row and column effects captures most of the heterogeneity in the field trials analysed.

Keywords:
Stage-wise analysis; Genomic prediction; Cross validation; Spatial models; Multi-environment trials (MET); Restricted maximum likelihood (REML)