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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., Competing Interests: The authors have declared that no competing interests exist.

The performance of inbred lines in advanced endogamous generation is commonly evaluated in successive generations of testing and selection, which we defined as "multistage field trials" (MSFT). MSFT data routinely exhibit heterogeneity of (co)variances at several levels due to genetic and/or statistical imbalance. Nowadays, mixed models have been widely used to deal with unbalanced data. However, few studies on common bean have addressed the use of a mixed model approach with modeling of (co)variance structures for random effects in MSFT. Furthermore, factor analysis and genotype‐ideotype distance (FAI‐BLUP) selection index was originally proposed using best linear unbiased predictions from individual analysis. In this regard, we aimed to study the implications of modeling (co)variance structures for random effects in the estimation of genetic parameters and evaluate the accuracy and efficiency of inbred line selection by the modeled FAI‐BLUP approach. A total of five trials were evaluated from 2018 to 2020. The results revealed that the unstructured covariance matrix fitted better for grain yield, whereas the matrix with uniform correlation and heterogeneity of variances fitted better for grain aspect and plant architecture. The modeled FAI‐BLUP approach increased the values of selection accuracy and selection efficiency. Our results suggest that modeling the different structures of (co)variances and selecting the best‐performing genotypes by modeled FAI‐BLUP approach should be used in common bean assays involving unbalanced data. Core Ideas: Genetic and/or statistical imbalance is a reality of plant breeding programs.Selecting the best fitted (co)variance structure for unbalanced data increased the selection accuracy.Low magnitude estimates of genetic correlation indicated the predominance of the complex part of the G × E interaction.The modeled FAI‐BLUP approach increased the selection efficiency by an average of 13.95%. [ABSTRACT FROM AUTHOR]

In breeding of autogamous plants, breeders often deal with the evaluation of progenies derived from multiple populations. We hypothesize that selection strategies that account for the heterogeneous genotypic variability of progenies within these populations associated with the population means may improve progeny selection. Thus, the objective of this work was to use two mixed models with progenies nested to population effects to obtain and evaluate indexes for the genotypic values of progenies. We used simulations and a real dataset from a multipopulation recurrent selection program of common bean (Phaseolus vulgaris L.). Progenies from 20 populations were evaluated for grain yield in two different generations. The three studied indexes consider the merit of populations, but differently account for the genotypic variability of progenies within populations: index gM uses a mean estimate, index gH is based on heterogeneous estimates, and the index gW also uses a mean estimate but is weighted by the selection accuracy within populations. The studied populations were highly diverse in both generations, justifying the implementation of the two models to obtain the population means and specific estimates of genotypic variability of progenies for each population. The comparison among indexes suggested that index gW more appropriately explored the information from the genotypic profiles of the common bean studied populations in the genotypic values of progenies. Thus, the index gW has the potential to help breeders of self-pollinated plant species to improve progeny selection from multiple populations. [ABSTRACT FROM AUTHOR]

In diallel analysis, using mixed models, it is possible to estimate the variance components of general combining ability (GCA), specific combining ability (SCA), reciprocal GCA (RGCA), reciprocal SCA (RSCA), and parents, even in unbalanced datasets. These variances can be estimated by likelihood maximization via numerical algorithms (e.g., expectation maximization [EM] and average information [AI]), which have different advantages. Thus, the objective of this study was to describe and implement the EM‐AI algorithm (combination of EM and AI) in R software to estimate the variance components of RGCA, RSCA, and parents effects in diallel analysis. Two real datasets and three diallel models (Griffing's Model 1, Griffing's Model 1 + RGCA, and Model 3, a general diallel model with the effects of GCA, SCA, RGCA, RSCA, and parents) were used to evaluate the efficiency of the algorithms AI, EM, and EM‐AI. The AI algorithm failed to converge for the three diallel models in both datasets. The other algorithms (EM and EM‐AI) converged normally, and the estimated variance components with these algorithms were similar for the three diallel models in both datasets. However, the EM‐AI algorithm was more efficient than the EM algorithm, and the general diallel model (Model 3) provided more accurate estimates of variance parameters. Thus, the EM‐AI algorithm with routine implemented in R has potential for use in diallel analyses in plant breeding. [ABSTRACT FROM AUTHOR]

The goal of breeding programs is selection toward the ideal plant type. In this study, field experiments were performed to select common bean inbred progenies that maximize the probability of extracting superior lines. A total of 124 inbred progenies of three consecutive generations (F2:3, F2:4, and F2:5) were conducted in field experiments over three different environments (one generation in each environment). Seven different traits, related to disease severity, commercial acceptance grain, and yield, were evaluated by best linear unbiased prediction. This work underscored the importance of incorporating population information into the statistical model as a means of comparing progenies from different populations with higher efficacy, even when kinship information between populations is not available. Toward the common bean ideotype, 20 inbred progenies of greater potential were selected using the factor analysis and genotype-ideotype distance (FAI-BLUP) index. This index is based on the structural equation models by joining the factor analysis technique (exploratory factor analysis) with the ideotype design (confirmatory factor analysis). The predicted genetic gain was increased for all the traits in all generations. Selection strategies that capture the multitrait information capitalize the progenies × growth season interactions and are based on the ideotype, such as as the FAI-BLUP index, have the potential for use in genetic breeding toward the common bean ideotype and can accelerate the release of more adapted cultivars. [ABSTRACT FROM AUTHOR]