Genetic parameters and selection gain in tropical wheat populations via Bayesian inference / Parâmetros genéticos e ganho de seleção em populações tropicais de trigo via inferência bayesiana

ABSTRACT: The development process of a new wheat cultivar requires time between obtaining the base population and selecting the most promising line. Estimating genetic parameters more accurately in early generations with a view to anticipating selection means important advances for wheat breeding programs. Thus, the present study estimated the genetic parameters of F2 populations of tropical wheat and the genetic gain from selection via the Bayesian approach. To this end, the authors assessed the grain yield per plot of 34 F2 populations of tropical wheat. The Bayesian approach provided an adequate fit to the model, estimating genetic parameters within the parametric space. Heritability (h2) was 0.51. Among those selected, 11 F2 populations performed better than the control cultivars, with genetic gain of 7.80%. The following populations were the most promising: TbioSossego/CD 1303, CD 1303/TbioPonteiro, BRS 254/CD 1303, Tbio Duque/Tbio Aton, and Tbio Aton/CD 1303. Bayesian inference can be used to significantly improve tropical wheat breeding programs.

RESUMO: O processo de desenvolvimento de uma nova cultivar de trigo requer tempo entre a obtenção da população base e a seleção da linhagem mais promissora. Estimar parâmetros genéticos com mais precisão nas primeiras gerações com vistas a antecipar a seleção significa avanços importantes para os programas de melhoramento de trigo. Assim, o presente estudo estima os parâmetros genéticos de populações F2 de trigo tropical e o ganho genético da seleção via abordagem Bayesiana. Para tanto, os autores avaliaram a produtividade de grãos por parcela de 34 populações F2 de trigo tropical. A abordagem Bayesiana proporcionou um ajuste adequado ao modelo, estimando parâmetros genéticos dentro do espaço paramétrico. A herdabilidade (h2) foi de 0,51. Dentre as selecionadas, 11 populações F2 obtiveram desempenho superior às cultivares controle, com ganho genético de seleção de 7,80%. As seguintes populações foram as mais promissoras: Tbio Sossego/CD 1303, CD 1303/Tbio Ponteiro, BRS 254/CD 1303, Tbio Duque/Tbio Aton e Tbio Aton/CD 1303. A inferência Bayesiana pode ser usada para melhorar significativamente programas de melhoramento de trigo tropical.

AgroReg: main regression models in agricultural sciences implemented as an R Package

Regression analysis is highly relevant to agricultural sciences since many of the factors studied are quantitative. Researchers have generally used polynomial models to explain their experimental results, mainly because much of the existing software perform this analysis and a lack of knowledge of other models. On the other hand, many of the natural phenomena do not present such behavior; nevertheless, the use of non-linear models is costly and requires advanced knowledge of language programming such as R. Thus, this work presents several regression models found in scientific studies, implementing them in the form of an R package called AgroReg. The package comprises 44 analysis functions with 66 regression models such as polynomial, non-parametric (loess), segmented, logistic, exponential, and logarithmic, among others. The functions provide the coefficient of determination (R2), model coefficients and the respective p-values from the t-test, root mean square error (RMSE), Akaike's information criterion (AIC), Bayesian information criterion (BIC), maximum and minimum predicted values, and the regression plot. Furthermore, other measures of model quality and graphical analysis of residuals are also included. The package can be downloaded from the CRAN repository using the command: install.packages("AgroReg"). AgroReg is a promising analysis tool in agricultural research on account of its user-friendly and straightforward functions that allow for fast and efficient data processing with greater reliability and relevant information.

Production costs and land appraisal: A case study of Polatlı, Turkey / Custos de produção e avaliação de terras: Um estudo de caso de Polatlı, Turquia

ABSTRACT: In this study, the share of land rent in the fixed costs of wheat production was examined, and the aim of the study was to find land values using cost tables. To this purpose, we showed the effect of these on land values from the difference between field rents and net income. The study covered the district of Polatlı in Ankara province. Data on wheat production in Polatlı in 2017 was collected from six villages and 37 farms by means of a questionnaire. In selecting the farms, the ability to determine the land rent was taken into account as a selection criterion. The farms examined used on average per hectare, 11.9 hours of labor, 7.7 hours of draft power, 354.3 kg of fertilizer, 205.5 kg of seed, and 1.5 liters of agricultural chemicals. The average wheat production cost per hectare was $865.42; the average unit production cost was $0.23, and the production value was reported to be $1012.40/da. In this study, the land rent was of $225.40, and the net income from the land was reported to be $372.42. It was reported an evaluation performed using the taxation tables that land values according to rental incomes were $4508.80/ha, and $7448.40 when the land was worked by the landowner. Land rent constituted 26.05% of total production costs, and were equivalent to 22.26% of production value. When crop prices increased by 1%, income from the land increased by 4.49%.

RESUMO: Neste estudo, a participação do arrendamento da terra nos custos fixos da produção de trigo foi examinada, e o objetivo do estudo foi encontrar os valores da terra usando tabelas de custos. Para tanto, buscou-se mostrar o efeito destes nos valores dos terrenos a partir da diferença entre os aluguéis dos campos e a receita líquida. O estudo cobriu o distrito de Polatlı na província de Ancara. Os dados sobre a produção de trigo em Polatlı, em 2017, foram coletados em seis aldeias e 37 fazendas por meio de um questionário. Na seleção das fazendas, a capacidade de determinar o aluguel da terra foi levada em consideração como um critério de seleção. As fazendas examinadas consumiam em média por hectare 11,9 horas de mão de obra, 7,7 horas de força de tracção, 354,3 kg de fertilizante, 205,5 kg de semente e 1,5 litro de agroquímicos. O custo médio de produção de trigo por hectare foi de $ 865,42; o custo de produção unitário médio foi de $ 0,23, e o valor de produção foi de $ 1.012,40 / da. Neste estudo, o arrendamento da terra foi determinado em $ 225,40 e a renda líquida da terra em $ 372,42. A partir de uma avaliação realizada com base nas tabelas de tributação, verificou-se que os valores dos terrenos de acordo com a renda do arrendamento eram de $ 4508,80 / ha e $ 7.448,40 quando a terra era trabalhada pelo proprietário. A renda da terra constituiu 26,05% dos custos totais de produção e foi equivalente a 22,26% do valor da produção. Quando os preços das safras aumentaram 1%, a renda da terra aumentou 4,49%.

Meta-analysis of the experimental coefficient of variation in wheat using the Bayesian and Frequentist approaches

A large set of variables is assessed for progeny selection in a plant-breeding program and other agronomic fields. The meta-analysis of the coefficient of variation (CVe) produces information for researchers and breeders on the experimental quality of trials. This analysis can also be applied in the decision-making process of the experimental plan regarding the experimental design, the number of repetitions, and the treatments and plants/progenies to be measured. In this study, we evaluated the dataset distribution and the descriptive statistics of CVe through the Frequentist and Bayesian approaches, aiming to establish the credibility and confidence intervals. We submitted CVe data of ten wheat (Triticum aestivum L.) traits reported in 1,068 articles published to the Bayesian and Frequentist analyses. Sample data were analyzed via Gamma and normal models. We selected the model with the lowest Akaike Information Criterion (AIC) value, and then we tested three link functions. In the Bayesian analysis, uniform distributions were used as non-informative priors for the Gamma distribution parameters with three ranges of q~U (a,b,). Thus, the prior probability density function was given by: [formula] The Bayesian and Frequentist approaches with the Gamma model presented similar results for CVe; however, the range Bayesian credible intervals was narrower than the Frequentist confidence intervals. Gamma distribution fitted the CVe data better than the normal distribution. The credible and confidence intervals of CVe were successfully applied to wheat traits and could be used as experimental accuracy measurements in other experiments.(AU)

Evaluating tree survival and modeling initial growth for Atlantic Forest restoration / Avaliação da sobrevivência e modelagem do desenvolvimento inicial de árvores para restauração da Mata Atlântica

ABSTRACT: Ecological restoration has become an important complementary practice to protect natural resources and preserve biodiversity. However, native species may be used in restoration programs in ways that do not optimize their performance. This research evaluated the survival and to model the initial growth of 15 native tree species planted in "filling" and "diversity" lines in the post-planting phase of a restoration experiment in the subtropics of the Brazilian Atlantic Forest. We measured survival rate (%) one year after planting and collar diameter (mm), total height (m), crown projection area (m²) and crown volume (m³) in the first 48 months after planting. Growth modeling for each variable and species was based on the non-linear mathematical Logistic, Gompertz, and Chapman-Richards models. Model selection for each variable/species was supported by the Akaike Information Criterion, standard error of the estimate, and coefficient of determination. The highest survival rates were reported for Cordia americana, Gochnatia polymorpha, Inga uruguensis, Peltophorum dubium, Prunus sellowii e Zanthoxylum rhoifolium (91.7%) and for Solanum mauritianum (90.3%). The species with faster growth were, by increasing order, Mimosa scabrella, Trema micrantha, Solanum mauritianum and Croton urucurana. With a better understanding of the initial developmental potential of tree species, it is possible to increase the species and functional diversity of the filling group. There was no single model capable of describing the variables analyzed and different models were needed to describe different characteristics and species.

RESUMO: A restauração ecológica tornou-se uma importante atividade complementar para proteger os recursos naturais e conservar a biodiversidade. No entanto, as espécies nativas podem estar a ser utilizadas em programas de restauração de formas que não otimizam as suas características. O objetivo deste trabalho foi avaliar a sobrevivência e modelar o desenvolvimento inicial de 15 espécies arbóreas nativas plantadas em linhas de "preenchimento" e "diversidade" na fase de pós-plantio numa experiência de restauração nos subtrópicos da Mata Atlântica Brasileira. Avaliou-se a taxa de sobrevivência (%) um ano após o plantio e o diâmetro do colo (mm), a altura total (m), a área de projeção de copa (m²) e o volume de copa (m³) nos primeiros 48 meses após o plantio. A modelagem de crescimento para cada variável e espécie foi baseada nos modelos matemáticos não lineares: Logístico, Gompertz e Chapman-Richards. A seleção do modelo para cada variável/espécie teve como base o Critério de Informação de Akaike, erro padrão da estimativa e coeficiente de determinação. Os percentuais de sobrevivência mais altos foram para Cordia americana, Gochnatia polymorpha, Inga uruguensis, Peltophorum dubium, Prunus sellowii e Zanthoxylum rhoifolium (91,7%) e para Solanum mauritianum (90,3%). As espécies de crescimento mais rápido, por ordem crescente, foram: Mimosa scabrella, Trema micrantha, Solanum mauritianum e Croton urucurana. Com o conhecimento do potencial de desenvolvimento inicial das espécies, é possível aumentar a diversidade de espécies e funcional do grupo de preenchimento. Não houve um modelo único capaz de descrever todas as variáveis de desenvolvimento analisadas. Foram necessários diferentes modelos para descrever as diferentes características e as diferentes espécies.

Repeatability estimates in longitudinal data on guava trees

The use of longitudinal measurements is an essential practice both in Psidium guajava L. breeding and in other perennial crops in which covariance structures can be introduced to explain the form of dependence between measurements. Hence, this study aimed to analyze six covariance structures to identify one that best described the correlation between the repeated measurements in time in traits of guava full-sib families. The repeatability coefficient for each trait was estimated and the minimum number of evaluations required for estimates representing the population was determined. The work was performed based on average data of three yield-related variables from nine harvests of a guava tree population evaluated from 2011 to 2018. The best model was chosen based on the Akaike and Schwarz Bayesian information criterion. The autoregressive covariance structure best represented the dependencies among families between crops for all traits. The number of variables of fruits and total yield per plant presented repeatability estimates higher than 0.5 and may be essential traits for indirect selection of others, such as fruit mass, which had an estimated repeatability of 0.24, proving low regularity in the repetition of the character from one cycle to another. It was also possible to define four harvests as the minimum acceptable number of observations necessary on the same individual for these traits; therefore, the repetitions represented the individuals.(AU)

Mathematical model for estimating the leaf area of cured dry tobacco using linear measurements / Modelo matemático para estimar a área foliar do tabaco seco curado por meio de medidas lineares

Leaf area of dried Flue-cured tobacco is a reflection of climate and stage of growth of fresh tobacco in field; it also serves as the foundation for calculating a number of significant physical properties of tobacco. So the purpose of this paper was to establish a model to estimate the leaf area of dried Flue-cured tobacco in China from linear dimensions. Three Hundred eight tobacco leaves from different growing area and stalk position were sampled randomly and separated for model selection among linear, proportional and power model type and external evaluation individually. Results showed that there was a significant and strong correlation between leaf area and length×width , The equation LA = 0.495(L×W), where LA is the leaf area and L×W is the product of leaf length and width, was optimum and adequate for the estimation of leaf area of dried tobacco in China examined by Fisher's test, Akaike delta information criterion (AIC) and Bayesian information criterion (BIC). Growing area and stalk position had minor effect on the parameter before (L×W). The equation can sufficiently predict the area of leaf for external evaluation.

A área foliar do tabaco curado pelo Flue seco é um reflexo do clima e do estágio de crescimento do tabaco fresco no campo; também serve como base para o cálculo de várias propriedades físicas significativas do tabaco. Portanto, o objetivo deste artigo foi estabelecer um modelo para estimar a área foliar do tabaco curado por Flue seco na China a partir de dimensões lineares. Foram amostradas aleatoriamente 308 folhas de tabaco de diferentes áreas de cultivo e posição do colmo e separadas para seleção de modelos entre tipo linear, proporcional e de potência e avaliação externa individualmente. Os resultados mostraram que houve uma correlação significativa e forte entre área foliar e comprimento×largura. A equação LA = 0,495 (L×W), em que LA é a área foliar e L×W é o produto do comprimento e largura da folha, ótima e adequada para a estimativa da área foliar de tabaco seco na China examinada pelo teste de Fisher, critério de informação delta de Akaike (AIC) e critério de informação bayesiana (BIC). A área de cultivo e a posição do caule tiveram efeito menor no parâmetro antes (C×L). A equação pode prever suficientemente a área da folha para avaliação externa.

Production costs and land appraisal: A case study of Polatli, Turkey / Custos de produção e avaliação de terras: Um estudo de caso de Polatli, Turquia

In this study, the share of land rent in the fixed costs of wheat production was examined, and the aim of the study was to find land values using cost tables. To this purpose, we showed the effect of these on land values from the difference between field rents and net income. The study covered the district of Polatli in Ankara province. Data on wheat production in Polatli in 2017 was collected from six villages and 37 farms by means of a questionnaire. In selecting the farms, the ability to determine the land rent was taken into account as a selection criterion. The farms examined used on average per hectare, 11.9 hours of labor, 7.7 hours of draft power, 354.3 kg of fertilizer, 205.5 kg of seed, and 1.5 liters of agricultural chemicals. The average wheat production cost per hectare was $865.42; the average unit production cost was $0.23, and the production value was reported to be $1012.40/da. In this study, the land rent was of $225.40, and the net income from the land was reported to be $372.42. It was reported an evaluation performed using the taxation tables that land values according to rental incomes were $4508.80/ha, and $7448.40 when the land was worked by the landowner. Land rent constituted 26.05% of total production costs, and were equivalent to 22.26% of production value. When crop prices increased by 1%, income from the land increased by 4.49%.

Neste estudo, a participação do arrendamento da terra nos custos fixos da produção de trigo foi examinada, e o objetivo do estudo foi encontrar os valores da terra usando tabelas de custos. Para tanto, buscou-se mostrar o efeito destes nos valores dos terrenos a partir da diferença entre os aluguéis dos campos e a receita líquida. O estudo cobriu o distrito de Polatli na província de Ancara. Os dados sobre a produção de trigo em Polatli, em 2017, foram coletados em seis aldeias e 37 fazendas por meio de um questionário. Na seleção das fazendas, a capacidade de determinar o aluguel da terra foi levada em consideração como um critério de seleção. As fazendas examinadas consumiam em média por hectare 11,9 horas de mão de obra, 7,7 horas de força de tracção, 354,3 kg de fertilizante, 205,5 kg de semente e 1,5 litro de agroquímicos. O custo médio de produção de trigo por hectare foi de $ 865,42; o custo de produção unitário médio foi de $ 0,23, e o valor de produção foi de $ 1.012,40 / da. Neste estudo, o arrendamento da terra foi determinado em $ 225,40 e a renda líquida da terra em $ 372,42. A partir de uma avaliação realizada com base nas tabelas de tributação, verificou-se que os valores dos terrenos de acordo com a renda do arrendamento eram de $ 4508,80 / ha e $ 7.448,40 quando a terra era trabalhada pelo proprietário. A renda da terra constituiu 26,05% dos custos totais de produção e foi equivalente a 22,26% do valor da produção. Quando os preços das safras aumentaram 1%, a renda da terra aumentou 4,49%.

Determination of optimal number of independent components in yield traits in rice

The principal component regression (PCR) and the independent component regression (ICR) are dimensionality reduction methods and extremely important in genomic prediction. These methods require the choice of the number of components to be inserted into the model. For PCR, there are formal criteria; however, for ICR, the adopted criterion chooses the number of independent components (ICs) associated to greater accuracy and requires high computational time. In this study, seven criteria based on the number of principal components (PCs) and methods of variable selection to guide this choice in ICR are proposed and evaluated in simulated and real data. For both datasets, the most efficient criterion and that drastically reduced computational time determined that the number of ICs should be equal to the number of PCs to reach a higher accuracy value. In addition, the criteria did not recover the simulated heritability and generated biased genomic values.

Evaluation of Bayesian methods of genomic association via chromosomic regions using simulated data

The development of efficient methods for genome-wide association studies (GWAS) between quantitative trait loci (QTL) and genetic values is extremely important to animal and plant breeding programs. Bayesian approaches that aim to select regions of single nucleotide polymorphisms (SNPs) proved to be efficient, indicating genes with important effects. Among the selection criteria for SNPs or regions, selection criterion by percentage of variance can be explained by genomic regions (%var), selection of tag SNPs, and selection based on the window posterior probability of association (WPPA). To also detect potentially associated regions, we proposed measuring posterior probability of the interval PPint), which aims to select regions based on the markers of greatest effects. Therefore, the objective of this work was to evaluate these approaches, in terms of efficiency in selecting and identifying markers or regions located within or close to genes associated with traits. This study also aimed to compare these methodologies with single-marker analyses. To accomplish this, simulated data were used in six scenarios, with SNPs allocated in non-overlapping genomic regions. Considering traits with oligogenic inheritance, WPPA criterion followed by %var and PPint criteria were shown to be superior, presenting higher values of detection power, capturing higher percentages of genetic variance and larger areas. For traits with polygenic inheritance, PPint and WPPA criteria were considered superior. Single-marker analyses identified SNPs associated only in oligogenic inheritance scenarios and was lower than the other criteria.(AU)

The impact of heterogeneity of variances on the genetic evaluation of performance traits in Nellore cattle

The objective was to evaluate the existence of heterogeneity of variances and its impact on the genetic evaluation of ponderal performance in sires of the Nellore breed. We used records of adjusted body weights at 210 (W210), 365 (W365), and 450 (W450) days of age. Both W365 and W450 were combined by principal component analyses using the first component (PC). Average daily gain (ADG) was obtained by difference between W450 and W210. The classes of standard deviations (SD) for W210, PC, and ADG were obtained by the standardization of means of herd-year means subclasses, with positive values composing the high SD and values equal and less than zero composing the SD. The model included the fixed effects of contemporary group and age at calving as a covariate, random genetic additive, and maternal genetic (except for PC) effects, and the permanent maternal environment. Variance components were obtained by Gibbs sampling. Posterior means of heritability in analyses without considering heterogeneity of variances ranged from 0.15±0.01 to 0.31±0.01. Posterior means of genetic correlations between the two classes of SD for W210, PC, and ADG were equal to 0.85±0.04, 0.83±0.03, and 0.71±0.08, respectively. Spearman correlation to breeding values of sires for ADG as the selection intensity increased in them, and the correlations between breeding values in general analyses were more correlated with those predicted in the high DP. Therefore, when there is a higher selection intensity on the sires only for the ADG criterion, there is a significant presence of the heterogeneity of variances and impact on the genetic evaluation of the sires. Thus, for ADG, the predictions of breeding values obtained by the genetic evaluation model in which the heterogeneity of variances are not considered are more weighted by the class of greater heterogeneity.(AU)

Genetic parameters and trends of growth traits in Nelore cattle raised in the Northern region of Brazil / Parâmetros genéticos e tendências de características de crescimento em gado Nelore criado na região norte do Brasil

The objective of this study was to estimate (co)variances and genetic parameters and to predict genetic trends for weight at 120 (W120), 210 (W210), 365 (W365), and 450 (W450) days of age in Nelore cattle raised in the northern region of Brazil. The database comprised records of 30,387 animals born between 2000 and 2013 in the Brazilian North. Estimates were calculated by the Restricted Maximum Likelihood (REML) method, in single- and multi-trait analyses in an animal model. Heritability as obtained using single- and multi-trait models for W120 (0.22 and 0.31), W210 (0.20 and 0.34), W365 (0.51 and 0.51), and W450 (0.49 and 0.51) indicated moderate to high magnitudes, with the possibility of genetic selection and incorporation into the herd. Genetic correlations between growth traits were favorable, ranging from 0.78 to 0.96. Genetic trends for W120 and W210 varied largely, from -0.31 to 4.68 and -0.53 to 7.62 kg/year, respectively. Smaller fluctuations were observed in genetic trends for W365 and W450, which ranged from -1.08 to 10.90 and -1.29 to 12.51 kg/year, respectively. Selection for W365 and W450 proved to be the criterion of choice for Nelore herds raised in the region; however, it may compromise adult performance because of higher costs and time for production. A thorough analysis of mattings is recommended to allow the selection of earlier-developing animals.(AU)

O presente trabalho foi delineado para estimar as (co) variâncias, parâmetros genéticos e de predizer as tendências genéticas para o peso aos 120 (W120), 210 (W210), 365 (W365) e 450 (W450) dias de idade de gado Nelore criado na região norte do Brasil. A base de dados foi constituituída por registro de 30387 animais, nascidos entre 2000 e 2013 no norte do Brasil. As estimativas foram calculadas pelo método de máxima restrição de probabilidade (REML) em um modelo animal com análises isoladas e multi variadas. A herdabilidade obtida para os modelos utilizados foi: W120 (0,22 e 0,31); W210 (0,20 e 0,34); W365 (0,51 e 0,51) e W450 (0,49 e 0,51), indicando moderada e alta magnitude com a possibilidade de seleção genética e incorporação no rebanho. As correlações genéticas entre grupos de tendências foram favoráveis variando de 0,78 a 0,96. As tendências genéticas para W120 e W210 apresentaram ampla variação de -0,31 a 4,68 e -0,53 a 7,62 kg/ano, respectivamente. Menores flutuações foram observadas nas tendências genéticas para W365 e W450, as quais variaram de -1,08 a 10,90 e -1,29 a12,51 kg/ano, respectivamente. Foi constatado que a seleção para W365 e W450 deve ser um critério de escolha para os rebanhos Nelore criados na região; contudo ela pode comprometer a performance dos adultos devido aos elevados custos e da duração da produção. Uma completa análise de cruzamentos é recomendada para possibilitar a seleção de animais jovens em desenvolvimento.(AU)

Genetic evaluation of oocyte and embryo production in dairy Gir cattle using repeatability and random regression models

The objective of this work is to estimate genetic parameters and breeding values to improve embryo and oocyte production, using repeatability and random regression models (RRM) for Gir dairy cattle. We used 11,398 records of ovum pick-up from 1,747 dairy Gir donors and evaluated sixteen different models: the traditional repeatability model and fifteen RRM, each of which considered a different combination of Legendre polynomial regressors to describe the additive genetic and permanent environment effects. The 4G1P model (four regressors for the genetic effect and one regressor for the permanent environment effect) is the most suitable model to analyze the number of viable and total oocytes, while the 3G1P is the best model to analyze the number of cleaved and viable embryos, according to the values of the Akaike information criterion (AIC) and the Bayesian information criterion (BIC). The heritability estimated with the RRM was higher than that estimated with the repeatability model. The high repeatability reported for oocyte and embryo count traits indicates that donors, which had high oocyte and embryo counts in the first ovum pick-up, should maintain this result in the next ovum pick-up. Genetic correlations between adjacent ages were high and positive, while genetic correlations between extreme ages were weak. We observed a reranking of the top sires and females (heifers and cows) over the period evaluated. The reliability of the estimated breeding values by RRM showed changes across age, and the expected genetic gains by RRM are larger. This shows that RRM is most suitable alternative for the evaluation and selection of oocyte and embryo count traits.(AU)

Fit and genetic parameters of the growth curve of Polled Nellore cattle / Ajuste e parâmetros genéticos da curva de crescimento em bovinos da raça Nelore Mocho

This study was undertaken to compare different non-linear models for fitting growth curves of Polled Nellore animals as well as to estimate genetic parameters for the components of the growth curve. The study involved body weight-age data of 6,717 Polled Nellore cattle from birth to 650 days of age, which belonged to the Brazilian Association of Zebu Breeders (ABCZ), corresponding to the period from 1980 to 2011. Four non-linear models (Brody, Bertalanffy, Logistic, and Gompertz) were fitted and compared by the adjusted coefficient of determination (R2adj), mean absolute deviation of residuals (MAD), root mean square error (RMSE), Akaike information criterion (AIC), and Bayesian information criterion (BIC). To estimate the genetic parameters and genetic values of asymptotic weight (A), integration constant (B), and maturation rate (K), the Bayesian inference method was adopted. The Brody model showed the lowest values of MAD, RMSE, AIC, and BIC and the highest R2adj. Heritability estimates for parameters A, B, and K were 0.11, 0.16, and 0.30, respectively, whereas genetic correlations were 0.01 (A-B), -0.91 (A-K), and 0.24 (B-K). The Brody model provided the best fit. The K parameter shows enough genetic variability for selection in the herd. Heavier animals in adulthood tend to exhibit lower growth rates. Despite the low heritability estimate of parameter A, there were genetic gains, indicating that selection is being efficient on asymptotic weight.(AU)

O objetivo deste estudo foi comparar diferentes modelos não lineares para o ajuste das curvas de crescimento de animais da raça Nelore Mocho e estimar os parâmetros genéticos para os componentes da curva de crescimento. Foram utilizados dados de peso corporal-idade do nascimento aos 650 dias de idades de 6.717 bovinos da raça Nelore Mocho, pertencentes à Associação Brasileira de Criadores de Zebu (ABCZ), referentes ao período de 1980 e 2011. Quatro modelos não lineares (Brody, Bertalanffy, Logístico e Gompertz) foram ajustados e comparados pelo coeficiente de determinação ajustado (R2adj), desvio médio absoluto dos resíduos (DMA), raiz quadrada do quadrado médio do resíduo (RMSE), critério de informação de Akaike (AIC) e o critério de informação bayesiano (BIC). Para estimativas dos parâmetros genéticos e valores genéticos do peso assintótico (A), constante de integração (B) e taxa de maturação (K), utilizou-se o método de inferência Bayesiana. O modelo Brody apresentou os menores valores de DMA, RMSE, AIC e BIC e o maior R2adj. As estimativas de herdabilidade foram 0,11; 0,16 e 0,30 para os parâmetros A, B e K, respectivamente, enquanto as correlações genéticas foram de 0,01 (A-B), -0,91 (A-K) e 0,24 (B-K). Constatou-se que o modelo Brody forneceu o melhor ajuste. O parâmetro K apresenta variabilidade genética suficiente para seleção no rebanho. Animais com maior peso na idade adulta tendem a apresentar menores taxas de crescimento. Apesar da baixa estimativa de herdabilidade do parâmetro A, observou-se ganhos genéticos, indicando que a seleção está sendo eficiente sobre o peso assintótico.(AU)

Interrelations between productive, vegetative, and fruit quality traits in Tahiti acid lime through Bayesian inference / Inter-relações entre características produtivas, vegetativas e de qualidade de fruto em lima ácida Tahiti através de inferência Bayesiana

Although the fruit yield has a core importance in Tahiti acid lime breeding programs, other traits stand out among the quality fruit and vegetative traits as ones that still need to be improved in selection of superior genotypes. Appling efficient tools aiming selection, such as the Bayesian inference, becomes an alternative in perennial crops. This study applied Bayesian inference in the genetic evaluation of Tahiti acid lime genotypes and estimated the interrelation between vegetative, productive and fruit quality traits. Twenty-four acid lime genotypes were evaluated for number of fruits, fruit yield, canopy volume, stem diameter, soluble solids content, shell thickness, and juice yield traits. The genotypic values were estimated through Bayesian inference and models with different residual structure were tested via deviance information criterion. Pearson's correlation and the path analysis were estimated, removing the multicollinearity effect. The Bayesian inference estimates genotypic values with high selective accuracy. The correlations obtained between traits from different groups can be useful in selection strategies for improvement of Tahiti acid lime. The Bayesian inference demonstrated to be an important tool and should be considered in perennial breeding programs.

Embora a produtividade seja uma característica fundamental em programas de melhoramento da lima ácida Tahiti, outras características se destacam por proporcionar uma seleção mais eficiente ou mesmo influenciar na expressão de atributos produtivos. A aplicação de inferência Bayesiana, pode tornar o processo de identificação de indivíduos superiores e o estudo das correlações entre as características ainda mais acurado. Objetivou-se, por meio deste estudo, estimar valores genéticos em genótipos de lima ácida Tahiti através de inferência Bayesiana e estimar coeficientes de correlação e de trilha entre características vegetativas, produtivas e de qualidade de frutos. Vinte e quatro genótipos de lima ácida foram avaliados durante dois anos para peso e número de frutos, volume de copa, diâmetro de caule, teor de sólidos solúveis dos frutos, espessura de casca e rendimento de suco. Os valores genéticos foram estimados por meio de inferência Bayesiana e modelos com diferentes estruturas residuais foram testados via critério de informação de deviance. Coeficiente de correlação de Pearson e de análise de trilha foram determinados, removendo o efeito de multicolinearidade. A estimação de valores genéticos via inferência Bayesiana apresentou alta acurácia seletiva. As correlações obtidas entre caracteres de diferentes grupos podem ser úteis em estratégias de seleção para melhoramento da lima ácida Tahiti. A inferência Bayesiana demonstrou ser uma ferramenta importante e deve ser considerada em programas de melhoramento de culturas perenes.

Models for optimizing selection based on adaptability and stability of cotton genotypes / Modelos para otimizar a seleção baseada em adaptabilidade e estabilidade de genótipos de algodão

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.(AU)

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.(AU)

Estimation of genetic parameters for weaning and yearling weights in a composite population used to form the Purunã breed

We aimed to evaluate the effects of sex and the linear and quadratic components of age of dam at calving, as well as apply a mixed model including maternal effect for the genetic evaluation of weaning (WW) and yearling (YW) weights. The phenotypic database was composed by Charolais, Caracu, Aberdeen Angus, and Canchim purebred and crossbred animals. Single-trait analyses were performed using models that included the maternal effect for WW and YW traits, and a model ignoring this effect on YW (YWNM). The Deviance Information Criterion (DIC), model posterior probabilities (MPP), accuracy of breeding values (ACC), and Spearman's rank correlation were applied to compare the models including and ignoring the maternal effect on YW. Sex and age of dam at calving had significant effects on WW and YW. The direct heritability estimates were 0.21±0.03 and 0.05±0.02, and the maternal heritabilities were 0.11±0.02 and 0.02±0.01 for WW and YW, respectively. The heritabilities estimated for YW may have been influenced by the several genetic groups in the population and by used conventional animal model, which may not have been the better fit model to evaluate YW in this population. The DIC, MPP, and ACC values indicated that YW outperformed the YWNM model, but the rank correlation and percentages of individuals selected in common suggested that the best animals would be selected independently of the model chosen.

Coffea canephora breeding: estimated and achieved gains from selection in the Western Amazon, Brazil / Melhoramento do Coffea canephora: ganhos de seleção estimados e realizados na Amazônia Ocidental

Gain from selection is an important criterion in quantifying the efficiency of breeding programs. This study quantified the selection gain estimated under experimental conditions and realized gain achieved in the field, seeking to interpret the efficiency of the Coffea canephora selection. For that purpose, we considered experiments that began in 2004 with directed hybridizations to obtain new hybrid progenies. From a breeding population composed of 288 hybrid individuals, 12 genotypes were selected in experimental conditions from 2005 to 2012, with amplitude in the estimated gains from 127.70 to19.19%. Those genotypes were evaluated from 2012 to 2018 in clonal tests in four environments of the Western Amazon. The environment that exhibited the greatest correlation between the predicted genetic values and the realized genetic gain observed in the field was the environment of Ouro Preto do Oeste, RO (0.67), the location in which the plants were selected, followed by the environments of Alta FlorestaD´Oeste, RO (0.44), Rio Branco, AC (0.43), and Porto Velho, RO (0.37).Experimental conditions showed that the effect due to dominance deviations was approximately three times greater than the additive effect. Nine clones exhibited higher genetic gains in the experimental conditions and at field, and two clones exhibited lower estimated gains and lower field performance.The clone G17-P7 exhibited high genetic gain under experimental conditions and low field performance. The selection in experimental conditions was positively correlated with plant performance in the field (r=0.55), which allows reduction of the original breeding population to a set of more promising clones to be grown in multiple environments, optimizing time and resources.(AU)

O ganho com a seleção é um dos critérios mais importantes para avaliar a eficiência de programas de melhoramento de plantas. O objetivo desse trabalho é quantificar a associação entre o ganho de seleção estimado em condições experimentais e o ganho de seleção realizado em campo, buscando quantificar a eficiência do melhoramento do Coffea canephora. Para isso, foram considerados experimentos iniciados com a hibridação direcionada para obtenção de progênies no ano de 2004, a avaliação de testes de progênies em condições experimentais no período de 2005 a 2012, e avaliações em diferentes ambientes da Amazônia Ocidental no período de 2012 a 2018. De uma população composta por 288 indivíduos estruturados em nove progênies de irmãos completos foram selecionados 12 genótipos com amplitude de 127,70 a -19,19% em suas estimativas de ganho com a seleção, para serem avaliados em quatro ambientes da Amazônia Ocidental. O ambiente que apresentou maior correlação entre os valores genéticos preditos e o ganho realizado foi Ouro Preto do Oeste - RO (0,67), local em que as plantas foram selecionadas, seguido pelos ambientes de Alta Floresta D´Oeste - RO (0,44), Rio Branco - AC (0,43) e Porto Velho - RO (0,37). Avaliações em condições experimentais mostraram que os efeitos devido aos desvios de dominância foram aproximadamente três vezes maiores do que os efeitos aditivos. Nove clones apresentaram maiores estimativas de ganho em condições experimentais e nos ensaios de campo, e dois clones apresentaram menores estimativas em ambas condições. O clone G17-P7 apresentou altas estimativas de ganho em condições experimentais e baixo desempenho em campo. A seleção em único ambiente esteve positivamente correlacionada com o desempenho dos cafeeiros em campo (r=0,55), permitindo reduzir a população de melhoramento original em um conjunto de clones de maior potencial agronômico.(AU)

Quantification of biogenic amines in fabrication steps of Gorgonzola-type cheese / Quantificação de aminas biogênicas nas etapas de fabricação do queijo tipo Gorgonzola

During the Gorgonzola-type cheese preparation there are proteolysis and lipolysis which may be influenced by the type of starter culture chosen. Six manufacturing steps were selected to identify which of them is most suitable for biogenic amines (BA) formation (1- milk, 2- lactic acid bacterial culture and fungus addition, 3- curd, 4- dry salting, 5- maturation at 30 days and maturation at 60 days); perform research on enterobacteria; accomplish the research of BA-producing bacteria (BAPB); detect and quantify the most abundant BA (putrescine, cadaverine, tyramine, histamine, spermidine and spermine) in the six steps of Gorgonzola cheese production and in bacterial isolates using high performance liquid chromatography and UV-Vis SPD/10AV detector and define if the presence of enterobacteria and BAPB would be correlated with BA production in this cheese. The bacterial culture used increased its log population by 7 log cycles and reached its highest level in batch 2 during cheese maturation. There was a decrease in the enterobacterial population in 2 log cycles after 60 days of maturation in batch 1. Tyramine was the BA with the highest concentration 306.32 mg.Kg-1 quantified in step 6 (60 days maturation) in batch 1. Criterion is requiered in bacterial starter culture selection because it is a quality determinant factor in relation to BA production and more rigor in raw material selection.

Durante a elaboração do queijo tipo Gorgonzola ocorre proteólise a partir das bactérias e dos fungos adicionados ao leite que podem levar a formação de aminas biogênicas (AB) neste tipo de queijo. Portanto, no presente estudo foi feito o acompanhamento com coleta de amostras em seis etapas na fabricação deste queijo paraidentificar em qual delas haveria maior formação de aminas biogênicas (AB). As amostras coletadas em três diferentes lotes foram o leite cru (1), leite pasteurizado adicionado de cultura de bactérias ácido-láticas (2), massa coalhada (3), queijo após a etapa de salga seca (4), queijo após 30 dias de maturação (5) e queijo após 60 dias de maturação (6). Também foram realizadas a pesquisa de enterobactérias e bactérias ácido-láticas com característica capacidade de descarboxilação de aminoácidos e produção de aminas biogênicas (BPAB); detecção e quantificação da AB mais abundante (putrescina, cadaverina, tiramina, histamina, espermidina e espermina) nas seis etapas de fabricação do queijo tipo Gorgonzola e nos isolados bacterianos utilizando cromatografia líquida de alta eficiência e detector UV-Vis SPD/10AV e a verificação se a presença de enterobactérias e BPAB estariam correlacionadas com a produção de AB nesse queijo. A cultura bacteriana utilizada cresceu aumentando em sete ciclos logarítmicos sua população e alcançou seu maior nível no lote 2 na etapa de maturação do queijo. Houve diminuição da população enterobactérias em 2 ciclos logarítmicos após 60 dias de maturação no lote 1. A tiramina foi a AB com concentração mais elevada 306,32 mg.Kg-1 quantificada na etapa 6 (60 dias de maturação) no lote 1. É necessário dar mais atenção em duas etapas na elaboração dos queijos: mais critério na seleção da cultura bacteriana iniciadora por ser um fator determinante na qualidade em relação à produção de AB e mais rigor na seleção da matéria-prima.Palavras chaves: cromatografia, cultura iniciadora, detector SPD/10AV UV­Vis, maturação, tiramina.

Best linear model to explain variability in the growth in Blanco Orejinegro cattle and effect of the serological status for bovine viral diarrhea and bovine leukosis / Melhor modelo linear para explicar a variabilidade no crescimento de bovinos Blanco Orejinegro e efeito do status sorológico para diarreia viral bovina e leucose bovina

The cattle breed Blanco Orejinegro (BON) is an important animal genetic resource in Colombia that needs to be studied to identify its productive benefits for Colombian livestock. The aim of this work was to establish the best linear model that explains the variability for birth weight, weaning weight and yearling weight, and estimate the effect of the serological status for Bovine Viral Diarrhea (BVD) and Bovine Leukosis (BL) in BON cattle in Colombia. The information on animal weighings belonging to 14 BON cattle herds, was collected and cleansed. Using the least squares method, 12 linear models were evaluated including as fixed effects, factors such as herd, sex, weighing month, birth order, season (rainy or dry), birth year, and contemporary group (formed by the concatenation of the factors herd, sex, and birth year). The weighing age was included as a covariate for weaning and yearling weights. For the selection of a model that best describes each parameter, the criteria for choosing models, such as Akaike information criterion (AIC), Bayesian Information criterion (BIC), coefficient of determination (R2 ), and the sum of squares of the error (SSE), were considered. The model that included the contemporary group showed the best fit, being also the best to describe the three parameters evaluated, since, of the four criteria considered for its evaluation, AIC and SSE showed the lowest values and the highest R2 . With this model, weight predictions with higher precision were able to be performed. Employing indirect ELISA screening tests of blood plasma, the serological status of each animal was estimated for BVD and BL viral infections. The serological status of these two viral infections was included in the best-fit model. There was no significant effect of the serological status on the parameters evaluated, so there are indications that animals that came in contact with the virus were not affected during growth.(AU)

A raça bovina Blanco Orejinegro (BON) é um importante recurso genético animal da Colômbia que requer estudos que identifiquem seus benefícios produtivos para a bovinocultura colombiana. O objetivo deste trabalho foi identificar o melhor modelo linear que explique a variabilidade do peso ao nascimento, ao desmame e ao ano e estimar o efeito do status sorológico para diarréia viral (BVD) e leucose bovina (BL) em gado BON da Colômbia. As informações sobre a pesagem de animais pertencentes a 14 fazendas dedicadas à criação de BON foram coletadas e depuradas. Utilizando o método dos mínimos quadrados, foram avaliados 12 modelos lineares nos quais foram incluídos como efeitos fixos fatores de rebanho, sexo, mês de pesagem, ordem de parição, época de nascimento (chuvosa ou seca), ano de nascimento e grupo de contemporâneos; a idade no momento da pesagem foi incluída como covariável para as características peso ao desmame e peso ao ano. Para a escolha do modelo que melhor descreve cada característica, foram considerados os critérios para escolha dos modelos AIC, BIC, coeficiente de determinação (R2 ) e soma dos quadrados dos erros (SCE). Verificou-se que o modelo que incluía o grupo de contemporâneos apresentou o melhor ajuste, sendo o melhor para descrever as três características avaliadas, uma vez que, dentre os quatro critérios levados em consideração para a sua avaliação, o AIC e a SCE apresentaram os menores valores e os R2 mais altos. Com este modelo, foi possível fazer predições de peso com maior acurácia. Os testes ELISA de rastreamento indireto estimaram o status sorológico de cada animal para infecções virais por BVD e BL. O efeito do status sorológico nessas duas infecções virais foi incluído no modelo que apresentou melhor ajuste. Não houve efeito do status sorológico sobre as características avaliadas, portanto há indicações de que os animais que tiveram contato com o vírus não foram afetados durante o crescimento.(AU)