Evaluating the impact of modeling the family effect for clonal selection in potato-breeding programs.

Because of its wide distribution, high yield potential, and short cycle, the potato has become essential for global food security. However, the complexity of tetrasomic inheritance, the high level of heterozygosity of the parents, the low multiplication rate of tubers, and the genotype-by-environment interactions impose severe challenges on tetraploid potato-breeding programs. The initial stages of selection take place in experiments with low selection accuracy for many of the quantitative traits of interest, for example, tuber yield. The goal of this study was to investigate the contribution of incorporating a family effect in the estimation of the total genotypic effect and selection of clones in the initial stage of a potato-breeding program. The evaluation included single trials (STs) and multi-environment trials (METs). A total of 1,280 clones from 67 full-sib families from the potato-breeding program at Universidade Federal de Lavras were evaluated for the traits total tuber yield and specific gravity. These clones were distributed in six evaluated trials that varied according to the heat stress level: without heat stress, moderate heat stress, and high heat stress. To verify the importance of the family effect, models with and without the family effect were compared for the analysis of ST and MET data for both traits. The models that included the family effect were better adjusted in the ST and MET data analyses for both traits, except when the family effect was not significant. Furthermore, the inclusion of the family effect increased the selective efficiency of clones in both ST and MET analyses via an increase in the accuracy of the total genotypic value. These same models also allowed the prediction of clone effects more realistically, as the variance components associated with family and clone effects within a family were not confounded. Thus, clonal selection based on the total genotypic value, combining the effects of family and clones within a family, proved to be a good alternative for potato-breeding programs that can accommodate the logistic and data tracking required in the breeding program.

Accounting for spatial trends in multi-environment diallel analysis in maize breeding.

Spatial trends represent an obstacle to genetic evaluation in maize breeding. Spatial analyses can correct spatial trends, which allow for an increase in selective accuracy. The objective of this study was to compare the spatial (SPA) and non-spatial (NSPA) models in diallel multi-environment trial analyses in maize breeding. The trials consisted of 78 inter-populational maize hybrids, tested in four environments (E1, E2, E3, and E4), with three replications, under a randomized complete block design. The SPA models accounted for autocorrelation among rows and columns by the inclusion of first-order autoregressive matrices (AR1 ⊗ AR1). Then, the rows and columns factors were included in the fixed and random parts of the model. Based on the Bayesian information criteria, the SPA models were used to analyze trials E3 and E4, while the NSPA model was used for analyzing trials E1 and E2. In the joint analysis, the compound symmetry structure for the genotypic effects presented the best fit. The likelihood ratio test showed that some effects changed regarding significance when the SPA and NSPA models were used. In addition, the heritability, selective accuracy, and selection gain were higher when the SPA models were used. This indicates the power of the SPA model in dealing with spatial trends. The SPA model exhibits higher reliability values and is recommended to be incorporated in the standard procedure of genetic evaluation in maize breeding. The analyses bring the parents 2, 10 and 12, as potential parents in this microregion.

Genetic diversity of Euterpe edulis martius based on fruit traits / Diversidade genética de Euterpe edulis martius com base em características de frutos

Juçara (Euterpe edulis Martius) is a palm species from the Atlantic Forest whose fruits are important as a source of food to several individuals from the fauna of the region. Despite its ecological importance, juçara is found in the list of endangered species, due to the fragmentation of the forests and the illegal extraction of the heart of palm. We aimed to evaluate the inter- and intra-populational genetic diversity of E. edulis based on fruit and seed traits in forest fragments of the Espírito Santo State in Brazil. The aim was to generate information to be used in E. edulis breeding programs, or in the delineation of more efficient management and reforestation strategies. The study was carried out in 20 forest fragments and 198 fruit plants were sampled. Positive genetic association was observed between the evaluated traits, with the longitudinal diameter of the fruit (LDF) and the seed mass (SM) greatly affecting fruit mass (FM). The existence of inter- and intra-populational genetic divergence was proved. The genetic divergence found in E. edulis suggests that there is genetic material that can be explored in breeding programs and this information may also contribute to management strategies that can increase the species genetic diversity

Juçara (Euterpe edulis Martius) é uma espécie de palmeira da Mata Atlântica, que é importante como fonte de alimento para vários indivíduos da fauna. Apesar de sua importância ecológica, juçara é encontrada na lista de espécies ameaçadas à extinção, devido à fragmentação florestal e à extração ilegal do palmito. Nós tivemos como objetivo avaliar a diversidade genética inter e intra populacional de E. edulis com base em caracteres de frutos e sementes, em fragmentos florestais do Estado do Espírito Santo no Brasil, com o objetivo de gerar informações a serem utilizadas nos programas de melhoramento de E. edulis ou na delimitação de estratégias de manejo e reflorestamento mais eficientes. O estudo foi realizado em 20 fragmentos florestais e 198 plantas frutíferas foram amostradas. Foi observada uma grande associação genética positiva entre os caracteres avaliados, com as características diâmetro longitudinal dos frutos (LDF) e massa de sementes (SM) apresentando efeitos maiores do que a massa característica da fruta (FM). A existência de divergência genética inter e intrapopulacional foi comprovada. A divergência genética encontrada neste trabalho para E. edulis sugere a presença de material genético que vale a pena ser explorado em programas de melhoramento e essa informação também pode contribuir com estratégias de manejo para aumentar a diversidade genética das espécies.

Unraveling candidate genes underlying biomass digestibility in elephant grass (Cenchrus purpureus).

BACKGROUND: Elephant grass [Cenchrus purpureus (Schumach.) Morrone] is used for bioenergy and animal feed. In order to identify candidate genes that could be exploited for marker-assisted selection in elephant grass, this study aimed to investigate changes in predictive accuracy using genomic relationship information and simple sequence repeats for eight traits (height, green biomass, dry biomass, acid and neutral detergent fiber, lignin content, biomass digestibility, and dry matter concentration) linked to bioenergetics and animal feeding. RESULTS: We used single-step, genome-based best linear unbiased prediction and genome association methods to investigate changes in predictive accuracy and find candidate genes using genomic relationship information. Genetic variability (p < 0.05) was detected for most of the traits evaluated. In general, the overall means for the traits varied widely over the cuttings, which was corroborated by a significant genotype by cutting interaction. Knowing the genomic relationships increased the predictive accuracy of the biomass quality traits. We found that one marker (M28_161) was significantly associated with high values of biomass digestibility. The marker had moderate linkage disequilibrium with another marker (M35_202) that, in general, was detected in genotypes with low values of biomass digestibility. In silico analysis revealed that both markers have orthologous regions in other C4 grasses such as Setaria viridis, Panicum hallii, and Panicum virgatum, and these regions are located close to candidate genes involved in the biosynthesis of cell wall molecules (xyloglucan and lignin), which support their association with biomass digestibility. CONCLUSIONS: The markers and candidate genes identified here are useful for breeding programs aimed at changing biomass digestibility in elephant grass. These markers can be used in marker-assisted selection to grow elephant grass cultivars for different uses, e.g., bioenergy production, bio-based products, co-products, bioactive compounds, and animal feed.

Repeatability analysis of guava fruit and leaf characteristics / Análise de repetibilidade de características de frutos e folhas de goiaba

Psidium guajava L. (guava) is an important species that presents high genetic variability due to its mixed reproductive system, which is desired in breeding programs. Repeatability is an important tool for the selection of genotypes in pre-breeding studies. When genetic variability is present, the knowledge regarding the number of samples to be used in repeatability studies is indispensable. This study aims to determine the number of necessary measures while optimizing resources and maintaining the reliability of the results for the variables evaluated in P. guajava. The experiment was carried out with genotypes from three Brazilian States: Espírito Santo, São Paulo, and Minas Gerais, and a total of 79 P. guajava genotypes were collected. The following characteristics were evaluated: young leaf length and width; developed leaf length and width; fruit length; fruit diameter and fruit cavity diameter; and fruit weight and pulp weight. For the evaluated characteristics, deviance, permanent phenotypic and temporary environment variance, coefficients of repeatability and determination, accuracy and the number of estimated measurements required were determined. We established that the number of measurements required in repeatability analysis for a coefficient of repeatability with a reliability of 80% is four, for the measurements of developed leaf width, pulp weight, fruit diameter, and fruit cavity diameter

Psidium guajava L. (goiaba) é uma espécie importante que apresenta alta variabilidade genética devido ao seu sistema reprodutivo misto, o que é desejado em programas de melhoramento. A repetibilidade é uma ferramenta importante para a seleção de genótipos em estudos de pré-melhoramento.Quando a variabilidade genética está presente, o conhecimento sobre o número de amostras a serem usadas em estudos de repetibilidade é indispensável. Este estudo tem como objetivo determinar o número de medidas necessárias, otimizando recursos e mantendo a confiabilidade dos resultados para as variáveis avaliadas em P. guajava. O experimento foi conduzido com genótipos de três estados brasileiros: Espírito Santo, São Paulo e Minas Gerais, e um total de 79 genótipos de P. guajava foram coletados. As seguintes características foram avaliadas: comprimento e largura das folhas jovens; comprimento e largura das folhas desenvolvidas; comprimento do fruto; diâmetro do fruto e diâmetro da cavidade do fruto; e peso do fruto e peso da polpa. Para as características avaliadas, foram determinados os desvios, a variância fenotípica permanente e temporária do ambiente, os coeficientes de repetibilidade e determinação, a precisão e o número estimado de medidas necessárias. Foi estabelecido que o número de medições necessárias na análise de repetibilidade para um coeficiente de repetibilidade com uma confiabilidade de 80% é igual a quatro, para as medidas de largura de folha desenvolvida, peso da polpa, diâmetro do fruto e diâmetro da cavidade do fruto.

Genetic insights into elephantgrass persistence for bioenergy purpose.

Persistence may be defined as high sustained yield over multi-harvest. Genetic insights about persistence are essential to ensure the success of breeding programs and any biomass-based project. This paper focuses on assessing the biomass yield persistence for bioenergy purpose of 100 elephantgrass clones measured in six growth seasons in Brazil. To assess the clones' persistence, an index based on random regression models and genotype-ideotype distance was proposed. Results suggested the existence of wide genetic variability between elephantgrass clones, and that the yield trajectories along the harvests generate genetic insights into elephantgrass clones' persistence and G x E interaction. A gene pool that acts over the biomass yield (regardless of the harvest) was detected, as well as other gene pools, which show differences on genes expression (these genes are the major responsible for clones' persistence). The lower and higher clones' persistence was discussed based on genome dosage effect and natural biological nitrogen fixation ability applied to bioenergy industry. The huge potential of energy crops necessarily is associated with genetic insights into persistence, so just this way, breeding programs could breed a new cultivar that fulfills the bioenergy industries.

Repeatability of biometric characteristics of Juçara palm fruit / Repetibilidade de características biométricas de frutos de palmito Juçara

Juçara is a plant that occurs in the Brazilian Atlantic Forest which presents high ecological importance to the biodiversity and is present on the list of endangered species. The fruits are known as super fruits because they present chemical characteristics of great importance. Due to its elevated economic importance and for the low number of researches with this species, the first step is to make the pre-breeding of the species. This consists in morphological characterization, which is very dependent on time and labour. Thus, the decrease of the number of evaluated measurements by individual is of great importance to the phases of pre-breeding and breeding. The objective of this work was to obtain estimates of the coefficients of repeatability and determination of six Euterpe edulis fruit characteristics to enable the prediction of the necessary number of measurements required to achieve given levels of certainty for the real values for each of the six fruit characteristics. The performances of various methods for repeatability estimation were compared. The characteristics longitudinal diameters of the fruits, longitudinal diameters of the seeds, equatorial diameters of the fruits, equatorial diameters of the seeds, fruit weights and seed weights of juçara palm fruits were measured, and the deviances, the coefficients of repeatability, the coefficients of determination, and the necessary numbers measurements for an accurate prediction of the real value of the population were estimated. The methods used do not differ as to estimate the repeatability coefficient to the longitudinal diameter characteristics of the fruit, seed equatorial diameter, fruit mass and seed mass. With 95% reliability is possible to use four (4) for mass measurements of fruit and five (5) measurements for longitudinal diameter of fruit, seed equatorial diameter, fruit mass and seed mass.

A juçara é uma planta de ocorrência da Mata Atlântica brasileira e apresenta grande importância ecologia para a biodiversidade e se encontra na lista de espécies ameaçadas de extinção. Os frutos são conhecidos como super frutos por apresentarem características químicas de grande importância. Devido a sua grande importância econômica e pelo baixo número de pesquisas com esta espécie, o primeiro passo é fazer o pré-melhoramento. Este consiste em caracterização morfológica, a qual é muito dispendiosa de tempo e mão de obra. Sendo assim, a diminuição do número de medições avaliadas por indivíduo é de suma importância durante as fases de pré-melhoramento e melhoramento. O objetivo deste trabalho foi obter estimativas dos coeficientes de repetibilidade e de determinação, predizer o número adequado de medições capaz de proporcionar níveis de certeza da predição do valor real dos indivíduos para cada uma das seis características analisadas de Euterpe edulis, e comparar diferentes métodos de estimação da repetibilidade. Foram mensuradas seis características nos frutos de juçara e posteriormente estimou-se a deviance, o coeficiente de repetibilidade, o coeficiente de determinação e o número de medições necessárias para uma predição adequada do valor real dos indivíduos. As metodologias utilizadas não diferem quanto à estimativa do coeficiente de repetibilidade para as características diâmetro longitudinal do fruto, diâmetro equatorial da semente, massa do fruto e massa da semente. Com 95% de confiabilidade é possível utilizar quatro (4) medições para massa do fruto e cinco (5) medições para diâmetro longitudinal do fruto, diâmetro equatorial do fruto, diâmetro longitudinal da semente, diâmetro equatorial da semente e massa da semente.