Dataset Information

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

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.

SUBMITTER: Bernal-Vasquez AM

PROVIDER: S-EPMC4133075 | biostudies-literature | 2014 Aug

REPOSITORIES: biostudies-literature

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Publications

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

Bernal-Vasquez Angela-Maria AM Möhring Jens J Schmidt Malthe M Schönleben Manfred M Schön Chris-Carolin CC Piepho Hans-Peter HP

BMC genomics 20140804

<h4>Background</h4>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 mul ...[more]

PMID: 25087599

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Project description:BackgroundMultilevel and spatial models are being increasingly used to obtain substantive information on area-level inequalities in cancer survival. Multilevel models assume independent geographical areas, whereas spatial models explicitly incorporate geographical correlation, often via a conditional autoregressive prior. However the relative merits of these methods for large population-based studies have not been explored. Using a case-study approach, we report on the implications of using multilevel and spatial survival models to study geographical inequalities in all-cause survival.MethodsMultilevel discrete-time and Bayesian spatial survival models were used to study geographical inequalities in all-cause survival for a population-based colorectal cancer cohort of 22,727 cases aged 20-84 years diagnosed during 1997-2007 from Queensland, Australia.ResultsBoth approaches were viable on this large dataset, and produced similar estimates of the fixed effects. After adding area-level covariates, the between-area variability in survival using multilevel discrete-time models was no longer significant. Spatial inequalities in survival were also markedly reduced after adjusting for aggregated area-level covariates. Only the multilevel approach however, provided an estimation of the contribution of geographical variation to the total variation in survival between individual patients.ConclusionsWith little difference observed between the two approaches in the estimation of fixed effects, multilevel models should be favored if there is a clear hierarchical data structure and measuring the independent impact of individual- and area-level effects on survival differences is of primary interest. Bayesian spatial analyses may be preferred if spatial correlation between areas is important and if the priority is to assess small-area variations in survival and map spatial patterns. Both approaches can be readily fitted to geographically enabled survival data from international settings.

Dataset Information

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

Background

Results

Conclusions

Publications

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

Similar Datasets

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