Abstract The objective of this work was to compare the use of noninformative and informative priors in Bayesian models, as well as to evaluate the viability of including informative priors in the estimation of variance components and genetic values in soybean breeding programs. The used phenotypic data refer to the evaluation of 80 soybean genotypes in ten environments over three years. For each evaluated crop year, informative and noninformative priors were used, and the parameters were estimated using the Gibbs sampler algorithm. Parameter estimates from the previous crop year were used as prior information for the next evaluated crop year. The goodness-of-fit was calculated using the deviance information criterion (DIC). Selective accuracy showed the highest values for the models chosen through DIC for both crop years. However, the intervals of the highest posterior density are narrower for all models that adopted informative priors. Adding information into Bayesian inference does not always result in a better model fitting. programs 8 years algorithm goodnessoffit goodness fit DIC. . (DIC) However fitting (DIC

Resumo O objetivo deste trabalho foi comparar o uso de a priori não informativas e informativas em modelos bayesianos, bem como avaliar a viabilidade da inclusão de a priori informativas na estimativa dos componentes de variância e dos valores genotípicos em programas de melhoramento de soja. Os dados fenotípicos utilizados referem-se à avaliação de 80 genótipos de soja, em dez ambientes, ao longo de três anos. Para cada safra avaliada, foram utilizadas a priori informativas e não informativas, e os parâmetros foram estimados com uso do algoritmo de amostragem de Gibbs. As estimativas dos parâmetros da safra anterior foram utilizadas como informação prévia para a próxima safra avaliada. A qualidade do ajuste foi calculada com uso do critério de informação de desvio (DIC). A acurácia seletiva apresentou maiores valores nos modelos escolhidos por meio do DIC, para ambas as safras. No entanto, os intervalos de maior densidade a posteriori são menores para todos os modelos que adotaram a priori informativas. Adicionar informações à inferência bayesiana nem sempre resulta em melhor ajuste ao modelo. bayesianos soja referemse referem se 8 ambientes anos avaliada Gibbs DIC. DIC . (DIC) safras entanto modelo (DIC

Resumo O objetivo deste trabalho foi estimar os parâmetros genéticos e avaliar a diversidade genética de 12 genótipos de lima ácida 'Tahiti' (Citrus latifolia) enxertados em dois porta-enxertos. O experimento foi conduzido de julho de 2017 a janeiro de 2019, no município de São Mateus, no estado de Espírito Santo, Brasil. Foram mensuradas características vegetativas (diâmetro de caule, diâmetro de projeção de copa e altura de planta), produtivas (rendimento e número de frutos) e de qualidade de frutos (diâmetros de fruto, teor de sólidos solúveis e rendimento de suco). Utilizou-se modelo misto para estimar os coeficientes de herdabilidade e repetibilidade, bem como predizer os valores genéticos. A diversidade entre os enxertos foi obtida por meio da diferença da distância euclidiana média padronizada, e os genótipos foram agrupados pelo método de Tocher modificado. A qualidade do agrupamento e a importância dos caracteres foi avaliada pela análise de componentes principais (ACP). Observou-se variabilidade genética, o que indica a possibilidade de seleção de genótipos superiores. O método de Tocher mostrou a presença de três grupos de genótipos, o que foi congruente com os resultados da ACP. O uso de técnicas multivariadas permite a seleção e a recomendação de genótipos superiores de lima ácida 'Tahiti'. 1 Tahiti 'Tahiti Citrus latifolia portaenxertos. portaenxertos porta enxertos. porta-enxertos 201 2019 Mateus Santo Brasil caule planta, planta , planta) diâmetros fruto suco. suco . suco) Utilizouse Utilizou se repetibilidade padronizada modificado ACP (ACP) Observouse Observou Tahiti. 20 (ACP 2

Abstract The objective of this work was to estimate the genetic parameters and to evaluate the genotypic diversity of 12 'Tahiti' acid lime (Citrus latifolia) genotypes grafted onto two rootstocks. The experiment was carried out from July 2017 to January 2019, in the municipality of São Mateus, in the state of Espírito Santo, Brazil. Vegetative (stem diameter, canopy projection diameter, and plant height), productive (yield and fruit number), and fruit quality (fruit diameter, soluble solids content, and juice yield) traits were determined. A mixed model was used to estimate heritability and repeatability coefficients, as well as to predict clonal values. Scion diversity was determined through the standardized mean difference of Euclidean distances, and genotypes were clustered by modified Tocher. Clustering quality and trait importance were evaluated using the principal component analysis (PCA). Genotypic variance was observed, which is indicative of the possibility of selection of superior genotypes. The Tocher method showed the presence of three clusters, which is in alignment with the PCA results. The multivariate analyses allows of the selection and the recommendation of superior 'Tahiti' acid lime genotypes. 1 Tahiti 'Tahiti Citrus latifolia rootstocks 201 2019 Mateus Santo Brazil stem diameter height, height , height) yield number, number number) content coefficients values distances PCA. . (PCA) observed clusters results 20 (PCA 2

ABSTRACT. Multi-trait multi-environment (MTME) models were fitted to eucalyptus breeding trials data to assess residual variance structure, genetic stability and adaptability. To do so, 215 eucalyptus clones were evaluated in a randomized complete block design with 30 replicates and one plant per plot in four environments. At 36 months of age, tree diameter at breast height (DBH) and pilodyn penetration (PP) were measured. Two MTME models were fitted, for which residuals were considered homoscedastic and heteroscedastic, with the best MTME model selected using Bayesian information criterion. The harmonic mean of the relative performance of the genotypic values (HMRPGV) was used to determine stability and adaptability. Of the two models, the heteroscedastic MTME model had better fit and provided greater accuracy. In addition, genotype-by-environment interaction was complex, and there was low genetic correlation between DBH and PP. Rank correlation between the clones selected by the MTME models was high for DBH but low for PP. The HMRPGV facilitated clone selection through simultaneous evaluation of stability, adaptability, and productivity. Thus, our results suggest that heteroscedastic MTME model / HMRPGV can be efficiently applied in the genetic evaluation and selection of eucalyptus clones. ABSTRACT Multitrait Multi trait multienvironment multi environment (MTME structure adaptability so 21 3 environments age (DBH PP (PP measured criterion (HMRPGV accuracy addition genotypebyenvironment genotype complex productivity Thus 2

Abstract Genetic selection efficiency is measured by accuracy. Model selection relies on hypothesis testing with effectiveness given by statistical significance (p-value). Estimates of selection accuracy are based on variance parameters and precision. Model selection considers the amount of genetic variability and significance of effects. Questions arise as to which one to use: accuracy or p-value? We show there is a link between the two and both may be used. We derive equations for accuracy in multi-environment trials and determine numbers of repetitions and environments to reach accuracy. We propose a new methodology for accuracy classification based on p-values. This enables a better understanding of the level of accuracy being accepted when certain p-value is used. Accuracy of 90% is associated with p-value of 2%. Use of p-values up to 20% (accuracies above 50%) are acceptable to verify significance of genetic effects. Sample sizes for desired p-values are found via accuracy values.

ABSTRACT: The Fisher’s infinitesimal model is traditionally used in quantitative genetics and genomic selection, and it attributes most genetic variance to additive variance. Recently, the dominance maximization model was proposed and it prioritizes the dominance variance based on alternative parameterizations. In this model, the additive effects at the locus level are introduced into the model after the dominance variance is maximized. In this study, the new parameterizations of additive and dominance effects on quantitative genetics and genomic selection were evaluated and compared with the parameterizations traditionally applied using the genomic best linear unbiased prediction method. As the parametric relative magnitude of the additive and dominance effects vary with allelic frequencies of populations, we considered different minor allele frequencies to compare the relative magnitudes. We also proposed and evaluated two indices that combine the additive and dominance variances estimated by both models. The dominance maximization model, along with the two indices, offers alternatives to improve the estimates of additive and dominance variances and their respective proportions and can be successfully used in genetic evaluation.

ABSTRACT Forest plantations are strong allies in preserving natural resources, providing social and economic benefits. The plantations carried out in the coming years will be vital to meet the growing demand for forest products. To ensure the continuity of genetic progress and the good results achieved with the improvement of forest species, statistical methods that accurately selects superior genotypes are desirable. Multi-trait multi-environment trials are preferred over single-trait single-environment trials, since they can exploit the covariance between traits and environments, increasing the analysis’s prediction power. The Bayesian multi-trait multi-environments approach (BMTME) combines the cited advantages with the parsimony of Bayesian statistics promoting a more informative data analysis. Thus, the aims of this study were to estimate genetic parameters, evaluate genetic variability, and select eucalyptus clones through BMTME models. To this end, a data set with 215 eucalyptus clones evaluated in four environments for diameter at breast height and Pilodyn penetration was used. The Markov Chain Monte Carlo algorithm was applied to estimate the variance components and genetic parameters and to predict the genotypic values. The Smith-Hazel index was used to simultaneously achieve gains with selection for both traits. The BMTME approach provided high accuracies, being a good strategy to the evaluation of multiple environmental trials of Eucalyptus for breeding purposes.

RESUMO: A interação genótipo × ambiente (G × E) desempenha um papel essencial na expressão fenotípica e pode provocar dificuldades na seleção genética. Assim, o presente estudo teve como objetivo estimar parâmetros genéticos e comparar diferentes estratégias de seleção no contexto de modelos mistos para melhoramento da soja. Para isso, foram utilizados dados referentes à avaliação de 30 genótipos em dez ambientes, referentes à característica produtividade de grãos. Os componentes de variância foram estimados pela máxima verossimilhança restrita (REML) e os valores genotípicos foram preditos pela melhor previsão imparcial linear (BLUP). Efeitos significativos dos genótipos e interação G × E foram detectados pelo teste da razão de verossimilhança (LRT). Correlação genotípica baixa foi obtida entre os ambientes indicando interação G × E do tipo complexa. A acurácia seletiva foi muito alta, indicando alta confiabilidade. Os resultados mostraram que os genótipos de soja mais produtivos apresentam alta adaptabilidade e estabilidade.

ABSTRACT: The genotype × environment (G×E) interaction plays an essential role in phenotypic expression and can lead to difficulties in genetic selection. Thus, the present study aimed to estimate genetic parameters and to compare different selection strategies in the context of mixed models for soybean breeding. For this, data referring to the evaluation of 30 genotypes in 10 environments, regarding the grain yield trait, were used. The variance components were estimated through restricted maximum likelihood (REML) and genotypic values were predicted through best linear unbiased prediction (BLUP). Significant effects of genotypes and G×E interaction were detected by the likelihood ratio test (LRT). Low genotypic correlation was obtained across environments, indicating complex G×E interaction. The selective accuracy was very high, indicating high reliability. Our results showed that the most productive soybean genotypes have high adaptability and stability.

ABSTRACT. The selection of superior genotypes of soybean entails a simultaneous evaluation of a number of favorable traits that provide a comparatively superior yield. Disregarding the population effect in the statistical model may compromise the estimate of variance components and the prediction of genetic values. The present study was undertaken to investigate the importance of including population effect in the statistical model and to determine the effectiveness of the index based on factor analysis and ideotype design via best linear unbiased prediction (FAI-BLUP) in the selection of erect, early, and high-yielding soybean progenies. To attain these objectives, 204 soybean progenies originating from three populations were examined for various traits of agronomic interest. The inclusion of the population effect in the statistical model was relevant in the genetic evaluation of soybean progenies. To quantify the effectiveness of the FAI-BLUP index, genetic gains were predicted and compared with those obtained by the Smith-Hazel and Additive Genetic indices. The FAI-BLUP index was effective in the selection of progenies with balanced, desirable genetic gains for all traits simultaneously. Therefore, the FAI-BLUP index is an adequate tool for the simultaneous selection of important traits in soybean breeding.

Abstract The aims of this study were to estimate genetic parameters, predict genotypic values, and analyze the genotypic divergence in S0 and S1 peach trees evaluated in a subtropical environment by the mixed model methodology. For this, twenty-two clones were evaluated for plant and fruit traits. Genotypic variance among clones was significant. The individual broad-sense heritabilities ranged from 0.11 to 0.84, and the individual repeatability coefficients ranged from 0.15 to 0.89. The genotypic coefficients of variation were higher than 10% for most of the traits. Clustering based on plant and fruit traits led to the formation of two and five mutually exclusive groups, respectively. Multivariate analysis of principal components indicated that some traits could be excluded from genetic evaluation. Considering the yield trait and the selection of five clones, predicted gain from selection was 70%, which shows the possibility of considerable genetic progress from clonal selection in peach trees.

Abstract The genotype × environment (G×E) interaction plays an essential role in phenotypic expression and can lead to difficulties in genotypes recommendation. Thus, the objectives of this study were: i) propose the Multi-Environment Index Based on Factor Analysis and Ideotype-Design/Markov Chain Monte Carlo (FAI/MCMC index), and ii) apply it for soybean genotypes recommendation. To this end, a data set with 30 soybean genotypes evaluated in 10 environments for grain yield trait was used. Variance components, genetic parameters and genetic values were estimated through MCMC algorithm. Environmental stratification was conducted by factor analyses and the selection of soybean genotypes was performed using the FAI/MCMC index. The results indicated the existence of genotypic variability and G×E interaction. The environments were grouped into three factors. The predicted genetic gains from indirect selection was 4.81%. Thus, our results suggest that the FAI/MCMC index can be successfully used in soybean breeding.

RESUMO: Em ensaios multi-ambientes, grandes redes experimentais são utilizadas para a avaliação de genótipos, tentando contornar o efeito que a interação genótipo por ambiente desempenha na seleção genotípica. Neste estudo, objetivamos testar diferentes estruturas de variância residual e medir o ganho de seleção de genótipos de algodão, baseados em produtividade, adaptabilidade e estabilidade, simultaneamente. Doze genótipos de algodão foram plantados em 10 ambientes, sendo determinados o comprimento da fibra (CF), a resistência da fibra (RF), a micronaire (MIC) e produtividade de fibras (PF). A seleção do modelo para diferentes estruturas de variância residual (homogênea e heterogênea) foi testada usando o Critério de Informação de Akaike (AIC) e o Critério de Informação Bayesiano (BIC). Os componentes de variância foram estimados através de máxima verossimilhança restrita e os valores genotípicos foram preditos através da melhor predição linear não viesada. A média harmônica do desempenho relativo dos valores genéticos (HMRPGV) foram aplicadas para seleção simultânea para adaptabilidade, estabilidade e produtividade. De acordo com o BIC, a estrutura residual heterogênea apresentou o melhor ajuste para a característica PF, enquanto a estrutura residual homogênea apresentou o melhor ajuste para as características CF, RF e MIC. A acurácia seletiva foi alta, indicando confiabilidade da predição. O método HMRPGV foi capaz de selecionar para estabilidade, adaptabilidade e produtividade, simultaneamente, com notável ganho de seleção para cada característica.

ABSTRACT: In multi-environment trials (MET), large networks are assessed for results improvement. However, genotype by environment interaction plays an important role in the selection of the most adaptable and stable genotypes in MET framework. In this study, we tested different residual variances and measure the selection gain of cotton genotypes accounting for adaptability and stability, simultaneously. Twelve genotypes of cotton were bred in 10 environments, and fiber length (FL), fiber strength (FS), micronaire (MIC), and fiber yield (FY) were determined. Model selection for different residual variance structures (homogeneous and heterogeneous) was tested using the Akaike Information Criterion (AIC) and Bayesian Information Criterion (BIC). The variance components were estimated through restricted maximum likelihood and genotypic values were predicted through best linear unbiased prediction. The harmonic mean of relative performance of genetic values (HMRPGV) were applied for simultaneous selection for adaptability, stability, and yield. According to BIC heterogeneous residual variance was the best model fit for FY, whereas homogeneous residual variance was the best model fit for FL, FS, and MIC traits. The selective accuracy was high, indicating reliability of the prediction. The HMRPGV was capable to select for stability, adaptability and yield simultaneously, with remarkable selection gain for each trait.

Resumo: O objetivo deste trabalho foi selecionar progênies e indivíduos de cupuaçuzeiro (Theobroma grandiflorum) com base em características agronômicas e, indiretamente, identificar aqueles adaptados a um ambiente de sistema agroflorestal (SAF) na Amazônia brasileira. Para tanto, 25 progênies de irmãos completos foram plantadas e testadas em consórcio com pimenta-do-reino (Piper nigrum), banana (Musa spp.) e bacuri (Platonia insignis). O experimento foi realizado em delineamento de blocos ao acaso, com cinco repetições e três plantas por parcela, de 2005 a 2019. Para as análises estatísticas, foram utilizadas as médias fenotípicas de produção e incidência da vassoura de bruxa avaliadas durante 11 safras. Progênies e indivíduos superiores foram identificados pela metodologia de modelos mistos (REML/BLUP), o que resultou na seleção de dez plantas de cinco famílias com características agronômicas superiores. As progênies de cupuaçu 6, 36, 37, 49 e 52 são as que melhor se adaptam ao ambiente de um SAF multiespécies na região amazônica, em razão de suas características agronômicas em condições competitivas. Dez matrizes apresentam potencial agronômico e adaptação indireta ao SAF e podem ser utilizadas como cultivares clonais de cupuaçu nesse ambiente.

Abstract: The objective of this work was to select cupuaçu (Theobroma grandiflorum) tree progenies and individuals based on their agronomic traits, and, indirectly, to identify those adapted to an agroforestry system (AFS) environment in the Brazilian Amazon. For this purpose, 25 full-sib progenies were planted and tested in consortium with black pepper (Piper nigrum), banana (Musa spp.), and bacuri (Platonia insignis) trees. The experiment was carried out in a randomized complete block design, with five replicates and three plants per plot, from 2005 to 2019. For the statistical analyses, the phenotypic averages for production and incidence of witches’ broom disease, evaluated during 11 harvests, were used. Superior progenies and individuals were identified using the mixed model methodology (REML/BLUP), which led to the selection of ten plants from five families with superior agronomic traits. Cupuaçu tree progenies 6, 36, 37, 49, and 52 are the ones that best adapt to the environment of a multispecies AFS in the Amazon region because of their agronomic traits under competitive conditions. Ten matrices show agronomic potential and indirect adaptation to the AFS and can be used as clonal cupuaçu cultivars in this environment.

Abstract: The present study aimed to evaluate the applicability and efficiency of the FAI-BLUP index in the genetic selection of maize hybrids, using 84 maize hybrids that were evaluated for cycle, morphology, and yield traits in four environments. Models accounting for homogeneous and heterogeneous residual variances were tested, and variance components were estimated using the residual maximum likelihood. Genotypic values were predicted by best linear unbiased prediction, and factor analysis was applied to group the traits. The FAI-BLUP index was used for the selection of maize hybrids based on ideotype design. Three factors explained more than 70% of genotypic variability, with selective accuracies varying from low (0.46) to high (0.99). Predicted genetic gains were positive for traits related to yield and negative for traits related to cycle and morphology, as is desirable in maize crop.

ABSTRACT Tree breeders are prioritizing the increase of the interspecific diversity in the breeding programs due to the pronounced environmental changes, and expansion of the forest frontier to less productive areas. In this scenario, there is a growing interest for species of the genus Corymbia due to their good growth, resistance to biotic and abiotic factors, and industrial properties. Also, Corymbia spp. can cross with each other, generating interspecific hybrids. However, there are great difficulties on defining the best crosses. Thus, the objectives of this study were to evaluate the genetic variability of 64 progenies of Corymbia maculata and 64 progenies of Corymbia torelliana and to use the GGE biplot method to point the most appropriated crosses to broad and specific environments in order to generate stable and productive interspecific hybrids of C. maculata and C. torelliana. The GGE biplot was an efficient method for evaluating the genetic variability between progenies, for visualizing the genotype by environment interaction pattern and for identifying the best crosses in order to generate interspecific hybrids of the species. By adopting a selection intensity of 10%, the recommended progenies to generate interspecific hybrids for the Aracruz municipality (ARA) were 10, 40, 49, 64, 20, 9 and 47 of C. maculata and 24, 56, 41, 64, 43, 31 and 12 of C. torelliana. For Três Lagoas municipality (TLA), the recommended progenies were 11, 17, 1, 48, 7, 63 and 21 of C. maculata and 42, 46, 61, 44, 10, 63 and 28 of C. torelliana.

ABSTRACT An accurate, efficient and informative statistical method for analyses of genotype × environment (G × E) interactions is a key requirement for progress in any breeding program. Thus, the objective of this study was to quantify individual variation in reaction norms using random regression models fitted through Legendre polynomials in eucalyptus (Eucalyptus spp.) breeding. To this end, a data set with 215 eucalyptus clones of different species and hybrids evaluated in four environments for diameter at breast height (DBH) and Pilodyn penetration (PP) was used. Variance components were estimated by restricted maximum likelihood, and genetic values were predicted by best linear unbiased prediction. The best-fitted model for DBH and PP was indicated by the Akaike information criterion, and the significance of the genotype effects was tested using the likelihood ratio test. Genetic variability between eucalyptus clones and very high accuracies ( r g ^ g ≥ 0 . 90) were detected for both traits. Reaction norms and eigenfunctions generated genetic insights into G × E interactions. This is the first study that quantified individual variation in reaction norms using random regression models fitted through Legendre polynomials in eucalyptus breeding and demonstrated the great potential of this technique.