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Application of mixed model and spatial analysis methods in multi-environmental and agricultural field trials.

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Agricultural experimentation involves selection of experimental materials, selection of experimental units, planning of experiments, and collection of relevant information, analysis and interpretation of the results. An overall work of this thesis is on the importance, improvement and efficiency of variety contrast by using linear mixed mode with spatial-variance covariance compare to the usual ANOVA methods of analysis. A need of some considerations on the recently widely usage of a bi-plot analysis of genotype plus genotype by environment interaction (GEE) on the analysis of multi-environmental crop trials. An application of some parametric bootstrap method for testing and selecting multiplicative terms in GGE and AMMI models and to show some statistical methods for handling missing data using multiple imputations principal component and other deterministic approaches. Multi-environment agricultural experiments are unbalanced because several genotypes are not tested in some environments or missing of a measurement from some plot during the experimental stage. A need for imputation of the missing values sometimes is necessary. Multiple imputation of missing data using the cross-validation by eigenvector method and PCA methods are applied. We can see the advantage of these methods having easy computational implementation, no need of any distributional or structural assumptions and do not have any restrictions regarding the pattern or mechanism of missing data in experiments. Genotype by environment (G×E) interaction is associated with the differential performance of genotypes tested at different locations and in different years, and influences selection and recommendation of cultivars. Wheat genotypes were evaluated in six environments to determine the G×E interactions and stability of the genotypes. Additive main effects and multiplicative interactions (AMMI) was conducted for grain yield of both year and it showed that grain yield variation due to environments, genotypes and (G×E) were highly significant. Stability for grain yield was determined using genotype plus genotype by environment interaction (GGE) biplot analysis. The first two principal components (PC1 and PC2) were used to create a 2-dimensional GGE biplot. Which-won where pattern was based on six locations in the first and five locations in the second year for all the twenty genotypes? The resulting pattern is one realization among many possible outcomes, and its repeatability in the second was different and a future year is quite unknown. A repeatability of which won-where pattern over years is the necessary and sufficient condition for mega-environment delineations and genotype recommendation. The advantages of mixed models with spatial variance-covariance structures, and direct implications of model choice on the inference of varietal performance, ranking and testing based on two multi-environmental data sets from realistic national trials. A model comparison with a ᵪ2-test for the trials in the two data sets (wheat and barley data) suggested that selected spatial variance-covariance structures fitted the data significantly better than the ANOVA model. The forms of optimally-fitted spatial variance-covariance, ranking and consistency ratio test were not the same from one trial (location) to the other. Linear mixed models with single stage analysis including spatial variance-covariance structure with a group factor of location on the random model also improved the real genotype effect estimation and their ranking. The model also improved varietal performance estimation because of its capacity to handle additional sources of variation, location and genotype by location (environment) interaction variation and accommodating of local stationary trend. The knowledge and understanding of statistical methods for analysis of multi-environmental data analysis is particularly important for plant breeders and those who are working on the improvement of plant variety for proper selection and decision making of the next level of improvement for country agricultural development.


Doctor of Philosophy in Statistics. University of KwaZulu-Natal, Pietermaritzburg 2015.


Environmental impact analysis--Statistical methods., Plant breeding--Statistical methods., Agriculture--Experimentation--Statistical methods., Crop yields., Multi-environmental field trials., Agricultural field trials., Theses--Statistics.