Revisiting superiority and stability metrics of cultivar performances using genomic data: derivations of new estimators.

The selection of highly productive genotypes with stable performance across environments is a major challenge of plant breeding programs due to genotype-by-environment (GE) interactions. Over the years, different metrics have been proposed that aim at characterizing the superiority and/or stability of genotype performance across environments. However, these metrics are traditionally estimated using phenotypic values only and are not well suited to an unbalanced design in which genotypes are not observed in all environments. The objective of this research was to propose and evaluate new estimators of the following GE metrics: Ecovalence, Environmental Variance, Finlay-Wilkinson regression coefficient, and Lin-Binns superiority measure. Drawing from a multi-environment genomic prediction model, we derived the best linear unbiased prediction for each GE metric. These derivations included both a squared expectation and a variance term. To assess the effectiveness of our new estimators, we conducted simulations that varied in traits and environment parameters. In our results, new estimators consistently outperformed traditional phenotype-based estimators in terms of accuracy. By incorporating a variance term into our new estimators, in addition to the squared expectation term, we were able to improve the precision of our estimates, particularly for Ecovalence in situations where heritability was low and/or sparseness was high. All methods are implemented in a new R-package: GEmetrics. These genomic-based estimators enable estimating GE metrics in unbalanced designs and predicting GE metrics for new genotypes, which should help improve the selection efficiency of high-performance and stable genotypes across environments.

Longitudinal Meta-Analysis of Peak Height Velocity in Young Female Athletes.

Growth patterns and biological milestones in youth sports are key to interpreting the development of young athletes. However, there is no analysis of longitudinal meta-analysis describing the growth of young female athletes. This longitudinal meta-analysis estimated growth curves and age at peak height velocity (PHV) in young female athletes based on anthropometric data from longitudinal studies found in the literature. Following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines, studies with repeated measurements in young female athletes were identified from searches of four databases (MEDLINE, Web of Science, SCOPUS, and SPORTDiscus) without date restrictions through August 2023. We adapted our bias assessment criteria using the Cochrane risk of bias tool for randomized controlled trials as a reference. Bayesian multilevel modeling was used to perform a longitudinal meta-analysis to extract stature growth curves and age at PHV. Fourteen studies met our eligibility criteria. Twenty-one independent samples could be included in the analysis. Conditional on the data and models, the predicted mean age at PHV for female athletes was 11.18 years (90% CI: 8.62; 12.94). When studies were aggregated by sport in the models, the models could not capture sport-specific growth curves for stature and estimate a corresponding age at PHV. We provide the first longitudinal meta-analytic summary of pubertal growth and derive age at PHV in young female athletes. The meta-analysis predicted that age at PHV occurs at similar ages to those in the general pediatric population. The data pool was limited in sports and geographic distribution, emphasizing the need to promote longitudinal research in females across different youth sports contexts.

Concurrent validity of the assessment tool for a health promotion program in Primary Health Care via telephone: a multilevel analysis / Validade concorrente do instrumento de avaliação de um programa de promoção de saúde na Atenção Primária à Saúde por telefone: uma análise multinível

This study aims to verify the concurrent validity of the paper, and the telephone versions of the instrument used to evaluate the effectiveness of the Vida Ativa Melhorando a Saúde (VAMOS) Pro-gram participants. The VAMOS Program is a community-based intervention aiming at motivating people to adopt an active and healthy lifestyle. The study population was adults registered at the Basic Health Units in the state of Santa Catarina, and the sample for the validity test was two groups that concluded the program. To compare each variable provided by paper and telephone format, multi-level generalized linear and logistic models were carried out, adjusted by age, sex, and educational level. As a result, it was possible to identify the validity of most of the questions, with variations in the frequency of cooked vegetable consumption, method of preparing animal meat, frequency of physical activity, and waist circumference. We concluded that the use of the telephone survey could be considered for VAMOS Program effectiveness evaluation

Este estudo teve como objetivo verificar a validade concorrente das versões papel e ligação telefônica do ins-trumento utilizado para avaliar a efetividade do Programa Vida Ativa Melhorando a Saúde ( VAMOS). O Programa VAMOS é uma intervenção de base comunitária, com o objetivo de motivar as pessoas a adotarem um estilo de vida ativo e saudável. A população do estudo foi de adultos registrados nas Unidades Básicas de Saúde do estado de Santa Catarina, e a amostra para o teste de validade considerou dois grupos que concluí-ram o programa. Para comparar cada variável fornecida pelo formato papel e telefone, foram realizados mo-delos lineares e logísticos generalizados multiníveis, ajustados por idade, sexo e nível de escolaridade. Como resultado, foi possível identificar a validade da maioria das questões, com variações na frequência de consumo de hortaliças cozidas, modo de preparo da carne animal, frequência de atividade física e circunferência da cintura. Concluímos que o uso da coleta por telefone pode ser considerado para a avaliação da efetividade do Programa VAMOS.

Dissecting the complex genetic basis of pre- and post-harvest traits in Vitis vinifera L. using genome-wide association studies.

Addressing the pressing challenges in agriculture necessitates swift advancements in breeding programs, particularly for perennial crops like grapevines. Moving beyond the traditional biparental quantitative trait loci (QTL) mapping, we conducted a genome-wide association study (GWAS) encompassing 588 Vitis vinifera L. cultivars from a Chilean breeding program, spanning three seasons and testing 13 key yield-related traits. A strong candidate gene, Vitvi11g000454, located on chromosome 11 and related to plant response to biotic and abiotic stresses through jasmonic acid signaling, was associated with berry width and holds potential for enhancing berry size in grape breeding. We also mapped novel QTL associated with post-harvest traits across chromosomes 2, 4, 9, 11, 15, 18, and 19, broadening our grasp on the genetic intricacies dictating fruit post-harvest behavior, including decay, shriveling, and weight loss. Leveraging gene ontology annotations, we drew parallels between traits and scrutinized candidate genes, laying a robust groundwork for future trait-feature identification endeavors in plant breeding. We also highlighted the importance of carefully considering the choice of the response variable in GWAS analyses, as the use of best linear unbiased estimators (BLUEs) corrections in our study may have led to the suppression of some common QTL in grapevine traits. Our results underscore the imperative of pioneering non-destructive evaluation techniques for long-term conservation traits, offering grape breeders and cultivators insights to improve post-harvest table grape quality and minimize waste.

Unveiling a differential metabolite modulation of sorghum varieties under increasing tunicamycin-induced endoplasmic reticulum stress.

Plants trigger endoplasmic reticulum (ER) pathways to survive stresses, but the assistance of ER in plant tolerance still needs to be explored. Thus, we selected sensitive and tolerant contrasting abiotic stress sorghum varieties to test if they present a degree of tolerance to ER stress. Accordingly, this work evaluated crescent concentrations of tunicamycin (TM µg mL-1): control (0), lower (0.5), mild (1.5), and higher (2.5) on the initial establishment of sorghum seedlings CSF18 and CSF20. ER stress promoted growth and metabolism reductions, mainly in CSF18, from mild to higher TM. The lowest TM increased SbBiP and SbPDI chaperones, as well as SbbZIP60, and SbbIRE1 gene expressions, but mild and higher TM decreased it. However, CSF20 exhibited higher levels of SbBiP and SbbIRE1 transcripts. It corroborated different metabolic profiles among all TM treatments in CSF18 shoots and similarities between profiles of mild and higher TM in CSF18 roots. Conversely, TM profiles of both shoots and roots of CSF20 overlapped, although it was not complete under low TM treatment. Furthermore, ER stress induced an increase of carbohydrates (dihydroxyacetone in shoots, and cellobiose, maltose, ribose, and sucrose in roots), and organic acids (pyruvic acid in shoots, and butyric and succinic acids in roots) in CSF20, which exhibited a higher degree of ER stress tolerance compared to CSF18 with the root being the most affected plant tissue. Thus, our study provides new insights that may help to understand sorghum tolerance and the ER disturbance as significant contributor for stress adaptation and tolerance engineering.

Peak height velocity in young athletes: A longitudinal meta-analysis.

The present longitudinal meta-analysis aimed to estimate the growth curves and age at peak height velocity (PHV) in young male athletes, considering anthropometric data from available longitudinal studies. Following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines, studies with repeated measurements in young male athletes were identified from searches across four databases (MEDLINE, SPORTDiscus, Web of Science, and SCOPUS). Estimations were based on multilevel polynomial models using a fully Bayesian framework. After a full-text screening of 317 studies meeting the eligibility criteria, 31 studies were considered. Studies were excluded mainly due to study design, repeated reporting, and incomplete reporting of the outcomes. Of the 31 studies analysed, 26 (84%) focused on young European athletes. The average age at PHV for the total sample of studies with young athletes was 13.1 years (90% credible interval: 12.9; 13.4). When considering data by sport, there was substantial variation in the age at PHV estimates (range: 12.4 to 13.5 years). As most studies in the meta-analysis focused on young European football players (52%), predictions for young athletes from other sports may be limited. The age at PHV in the available data occurred earlier than in general paediatric populations.

Metabolomic exhibits different profiles and potential biomarkers of Vitis spp. co-cultivated with Fusarium oxysporum for short, medium, and long times.

Differential rootstock tolerance to Fusarium spp. supports viticulture worldwide. However, how plants stand against the fungus still needs to be explored. We hypothesize it involves a differential metabolite modulation. Thus, we performed a gas chromatography coupled with mass spectrometry (GC-MS) analysis of Paulsen P1103 and BDMG573 rootstocks, co-cultured with Fusarium oxysporum (FUS) for short, medium, and long time (0, 4, and 8 days after treatment [DAT]). In shoots, principal component analysis (PCA) showed a complete overlap between BDMG573 non-co-cultivated and FUS at 0 DAT, and P1103 treatments showed a slight overlap at both 4 and 8 DAT. In roots, PCA exhibited overlapping between BDMG573 treatments at 0 DAT, while P1103 treatments showed overlapping at 0 and 4 DAT. Further, there is a complete overlapping between BDMG573 and P1103 FUS profiles at 8 DAT. In shoots, 1,3-dihydroxyacetone at 0 and 4 DAT and maltose at 4 and 8 DAT were biomarkers for BDMG573. For P1103, glyceric acid, proline, and sorbitol stood out at 0, 4, and 8 DAT, respectively. In BDMG573 roots, the biomarkers were ß-alanine at 0 DAT, cellobiose and sorbitol at both 4 and 8 DAT. While in P1103 roots, they were galactose at 0 and 4 DAT and 1,3-dihydroxyacetone at 8 DAT. Overall, there is an increase in amino acids, glycolysis, and tricarboxylic acid components in tolerant Paulsen P1103 shoots. Thus, it provides a new perspective on the primary metabolism of grapevine rootstocks to F. oxysporum that may contribute to strategies for genotype tolerance and early disease identification.

Food consumption scale validation in VAMOS Program: a proposal to assess eating behavior changes in Brazil / Validação da escala de consumo alimentar no Programa VAMOS: uma proposta para avaliar as mudanças no comportamento alimentar no Brasil

Abstract This study aimed to validate the frequency consumption scale (FCS) and establish cut-off points to assess changes in the eating behavior of participants in the VAMOS Program. The study was based on a community intervention conducted in 2019 in 70 Brazilian cities, with 458 adults from Primary Care. The questionnaire consisted of 12 questions about food frequency consumption. The questions were inserted into the analytical workflow, divided into the descriptive analysis, exploratory and confirmatory factor analysis (EFA), item response theory (IRT) modeling, and construction and validity of an applied questionnaire score. EFA indicated a two-factor structure, with three "healthy" (raw vegetables, fruits, and cooked vegetables) and three "unhealthy" (sugary drinks, sweets, and the replacement of meals with snacks) eating items. Items responses' probabilities indicate a daily consumption of two healthy and once or nonweekly consumption of unhealthy items. Finally, the four categories proposed for FCS can respond over time. Therefore, the FCS proposal can be used effectively for program nutrition evaluation. Furthermore, it is possible to attribute behavior change in Brazilian primary care users with six items.

Resumo Este estudo teve como objetivo validar a escala de consumo de frequência (ECF) e estabelecer pontos de corte para avaliar mudanças no comportamento alimentar dos participantes do Programa VAMOS. O estudo baseou-se em uma intervenção comunitária realizada em 2019 em 70 cidades brasileiras, com 458 adultos da Atenção Básica. O questionário era composto por 12 questões sobre o consumo de frequência alimentar. As questões foram inseridas no fluxo de trabalho analítico, divididas em análise descritiva, análise fatorial exploratória e confirmatória (EFA), modelagem da teoria de resposta ao item (TRI) e construção e validade de um escore de questionário aplicado. EFA indicou uma estrutura de dois fatores, com três itens alimentares "saudáveis" (vegetais crus, frutas e vegetais cozidos) e três "não saudáveis" (bebidas açucaradas, doces e a substituição de refeições por lanches). As probabilidades das respostas dos itens indicam um consumo diário de dois itens saudáveis e um consumo único ou não semanal de itens não saudáveis. Por fim, as quatro categorias propostas para o ECF podem fornecer respostas ao longo do tempo. A proposta do ECF pode ser usada efetivamente para avaliação nutricional do programa. Além disso, é possível atribuir a mudança de comportamento em usuários da atenção básica brasileira com seis itens.

Student-Athlete Identity Variation Across the Undergraduate Period: A Mixed-Methods Study.

We examined the influence of individual and contextual characteristics on student-athlete identities and then explored identity variations across the undergraduate college years. Our main analysis relied on a quantitative study of a large sample of cross-sectional data (n = 862: females = 490, males = 372) with follow-up data for 102 participants. We also used qualitative semi-structured interviews within a small sub-sample (n = 4) who participated in international competitions to provide deeper insight into their identities across time. We used the Portuguese version of the Baller Identity Measurement Scale (BIMS) to explore student-athlete identities, and we examined the influence of sex, student-athlete status (based on institution documents), the participant's competitive level in the sport, and the student athlete's university type. We modelled response probability on BIMS items with multilevel ordinal regression in a cumulative model based on the Bayesian framework. For the follow-up in-depth qualitative interviews of four participants competing at the international level, we used thematic analysis, with two independent researchers generating thematic codes. We found a non-significant trend toward a decreased student-athlete identity across the undergraduate years. Participants' statements reflected their difficulty combining both aspects of the student-athlete identity, such that they tried to shift their identities, depending on the circumstances, while their athletic identity seemed to be privileged. Hence, participants had difficulty combining a dual academic-sport career within a context oriented toward academic achievement and transition to professional life. The higher education context was unprepared to support student-athletes toward a dual academic-sport career.

Enviromic-based kernels may optimize resource allocation with multi-trait multi-environment genomic prediction for tropical Maize.

BACKGROUND: Success in any genomic prediction platform is directly dependent on establishing a representative training set. This is a complex task, even in single-trait single-environment conditions and tends to be even more intricated wherein additional information from envirotyping and correlated traits are considered. Here, we aimed to design optimized training sets focused on genomic prediction, considering multi-trait multi-environment trials, and how those methods may increase accuracy reducing phenotyping costs. For that, we considered single-trait multi-environment trials and multi-trait multi-environment trials for three traits: grain yield, plant height, and ear height, two datasets, and two cross-validation schemes. Next, two strategies for designing optimized training sets were conceived, first considering only the genomic by environment by trait interaction (GET), while a second including large-scale environmental data (W, enviromics) as genomic by enviromic by trait interaction (GWT). The effective number of individuals (genotypes × environments × traits) was assumed as those that represent at least 98% of each kernel (GET or GWT) variation, in which those individuals were then selected by a genetic algorithm based on prediction error variance criteria to compose an optimized training set for genomic prediction purposes. RESULTS: The combined use of genomic and enviromic data efficiently designs optimized training sets for genomic prediction, improving the response to selection per dollar invested by up to 145% when compared to the model without enviromic data, and even more when compared to cross validation scheme with 70% of training set or pure phenotypic selection. Prediction models that include G × E or enviromic data + G × E yielded better prediction ability. CONCLUSIONS: Our findings indicate that a genomic by enviromic by trait interaction kernel associated with genetic algorithms is efficient and can be proposed as a promising approach to designing optimized training sets for genomic prediction when the variance-covariance matrix of traits is available. Additionally, great improvements in the genetic gains per dollar invested were observed, suggesting that a good allocation of resources can be deployed by using the proposed approach.

Food consumption scale validation in VAMOS Program: a proposal to assess eating behavior changes in Brazil.

This study aimed to validate the frequency consumption scale (FCS) and establish cut-off points to assess changes in the eating behavior of participants in the VAMOS Program. The study was based on a community intervention conducted in 2019 in 70 Brazilian cities, with 458 adults from Primary Care. The questionnaire consisted of 12 questions about food frequency consumption. The questions were inserted into the analytical workflow, divided into the descriptive analysis, exploratory and confirmatory factor analysis (EFA), item response theory (IRT) modeling, and construction and validity of an applied questionnaire score. EFA indicated a two-factor structure, with three "healthy" (raw vegetables, fruits, and cooked vegetables) and three "unhealthy" (sugary drinks, sweets, and the replacement of meals with snacks) eating items. Items responses' probabilities indicate a daily consumption of two healthy and once or nonweekly consumption of unhealthy items. Finally, the four categories proposed for FCS can respond over time. Therefore, the FCS proposal can be used effectively for program nutrition evaluation. Furthermore, it is possible to attribute behavior change in Brazilian primary care users with six items.

Identidade do professor de educação física: uma revisão narrativa da literatura / Physical education teacher identity: a narrative literature review

RESUMO O estudo identitário por muito tempo vem ganhando novos paradigmas, gerando inclusive crises identitárias. O objetivo do estudo foi encontrar publicações desta temática em estudos brasileiros, com a pretensão de discutir o processo de (re)construção da identidade do Professor de Educação Física. Foi realizada uma revisão narrativa da literatura, para discutir junto as temáticas da Teoria conceituais da identidade, Contributos para a construção da identidade do professor, e a identidade do professor de Educação Física. Face aos achados, vale dizer que o cenário atual requer um debate mais reflexivo sobre o direcionamento e desenvolvimento da identidade profissional do professor de Educação Física. Em relação a literatura científica, ainda há muito a ser estudado, pois foi possível identificar algumas limitações nos estudos sobre identidade, como por exemplo, a falta de consenso sobre a definição e conceituação da identidade do professor de Educação Física, que podem dificultar a comparação e generalização de futuros resultados. Espera-se que pesquisadores e organizações públicas a privadas, se atentem aos cuidados necessários quanto à formação do docente, assim para qualquer desenvolvimento profissional, e que esses achados ganhem espaços nas discussões relacionadas a identidade profissional do professor de Educação Física.

ABSTRACT The identity study has long been gaining new paradigms, even generating identity crises. The aim of the study was to find publications on this theme in Brazilian studies, with the intention of discussing the process of (re)construction of the identity of the Physical Education Teacher. A narrative review of the literature was carried out, to discuss along with the themes of conceptual identity theory, contributions to the construction of teacher identity, and the identity of the physical education teacher. Given the findings, it is worth saying that the current scenario requires a more reflective debate on the direction and development of the professional identity of the physical education teacher. In relation to scientific literature, there is still much to be studied, as it was possible to identify some limitations in studies on identity, such as, for example, the lack of consensus on the definition and conceptualization of the identity of the physical education teacher, which may hinder comparison and generalization of future results. It is hoped that researchers and public and private organizations will pay attention to the necessary care regarding teacher training, as well as any professional development, and that these findings will gain space in discussions related to the professional identity of the physical education teacher.

Adaptation and Validation of the Constructivist Teaching Practices Inventory in Elementary Physical Education (CTPI-EPE) for Brazilian Physical Education Pre-Service Teachers.

Constructivism is used as a powerful theoretical outlook to support teaching, learning, and curriculum in physical education and sport. The Constructivist Teaching Practices Inventory in Elementary Physical Education (CTPI-EPE) is a valid instrument for assessing in-service teachers. However, there is a need to translate constructivist teaching practices for PE into other languages. This study examined the validity of the Portuguese version of the adapted CTPI-EPE for Brazilian physical education preservice teachers (PST). The sample comprised of 869 physical education PSTs from Brazil. Data were collected through an online form. Aiken's V was used to examine content validity, and Bayesian methods used for exploratory and confirmatory factor analysis. The results showed adequate content and internal structure of the translated and adapted questionnaire. This study highlighted the validity of the Portuguese version of the CTPI-EPE, which could be considered an important instrument for self-reflection by PSTs, and provide information for improved training in higher education toward constructivist teaching.

Genotyping marker density and prediction models effects in long-term breeding schemes of cross-pollinated crops.

KEY MESSAGE: In genomic recurrent selection, the more markers, the better because they buffer the linkage disequilibrium losses caused by recombination over cycles, and consequently, provide higher responses to selection. Reductions of genotyping marker density have been extensively evaluated as potential strategies to reduce the genotyping costs of genomic selection (GS). Low-density marker panels are appealing in GS because they entail lower multicollinearity and computing time and allow more individuals to be genotyped for the same cost. However, statistical models used in GS are usually evaluated with empirical data, using "static" training sets and populations. This may be adequate for making predictions during a breeding program's initial cycles but not for the long-term. Moreover, studies that focus on long selective breeding cycles generally do not consider GS models with the effect of dominance, which is particularly important for breeding outcomes in cross-pollinated crops. Hence, dominance effects are important and unexplored in GS for long-term programs involving allogamous species. To address it, we employed two approaches: analysis of empirical maize datasets and simulations of long-term breeding applying phenotypic and genomic recurrent selection (intrapopulation and reciprocal schemes). In both schemes, we simulated twenty breeding cycles and assessed the effect of marker density reduction on the population mean, the best crosses, additive variance, selective accuracy, and response to selection with models [additive, additive-dominant, general (GCA), and this plus specific combining ability (GCA + SCA)]. Our results indicate that marker reduction based on linkage disequilibrium levels provides useful predictions only within a cycle, as accuracy significantly decreases over cycles. In the long-term, without training set updating, high-marker density provides the best responses to selection. The model to be used depends on the breeding scheme: additive for intrapopulation and additive-dominant or GCA + SCA for reciprocal.

Age-, sex-, and maturity-associated variation in the phase angle after adjusting for size in adolescents.

Background: Applied research using the phase angle (PhA) in children and adolescents has increased notably. Using multilevel modeling in a fully Bayesian framework, we examined the relationships between PhA, age, sex, biological maturity status, and body size in 10-16-year-old adolescents. Methods: The sample comprised 519 adolescents (women, n = 241; men, n = 278) from Campinas, São Paulo, Brazil. Biological maturity status was assessed with self-examination of pubertal development for sexual maturity and maturity offset protocol to estimate age at peak height velocity (PHV) for somatic maturity status. Stature and body mass were measured by anthropometry. Phase angle was calculated based on raw resistance and reactance values (50 kHz frequency) obtained by bioelectrical impedance with the foot-to-hand technology. Results: The multilevel regression analysis revealed that boys had significantly higher values of phase angle than girls, adjusting for age group and sexual maturity status. Overall, older and more mature adolescents had higher values of phase angle. When considering aligning variation in the phase angle by distance to estimated PHV (maturity offset), there was a higher association between the phase angle and time before and after predicted age at PHV for boys (r = 0.31, 90% CI: 0.23 to 0.39) than girls (r = 0.2, 90% CI: 0.11 to 0.28). When including body mass in the multilevel models, corresponding changes in the overall body mass mediate most of the influence of the maturity status and age group on the phase angle. Conclusion: The present study demonstrated that the variability in phase angle is related to inter-individual variation in sex, age, and maturity status, as well as differences in body size. Research with adolescents considering phase angle should use multilevel modeling with standardized parameters as default to adjust for the concurrent influence of sex, age, maturity status, and body size.

Automated Machine Learning: A Case Study of Genomic "Image-Based" Prediction in Maize Hybrids.

Machine learning methods such as multilayer perceptrons (MLP) and Convolutional Neural Networks (CNN) have emerged as promising methods for genomic prediction (GP). In this context, we assess the performance of MLP and CNN on regression and classification tasks in a case study with maize hybrids. The genomic information was provided to the MLP as a relationship matrix and to the CNN as "genomic images." In the regression task, the machine learning models were compared along with GBLUP. Under the classification task, MLP and CNN were compared. In this case, the traits (plant height and grain yield) were discretized in such a way to create balanced (moderate selection intensity) and unbalanced (extreme selection intensity) datasets for further evaluations. An automatic hyperparameter search for MLP and CNN was performed, and the best models were reported. For both task types, several metrics were calculated under a validation scheme to assess the effect of the prediction method and other variables. Overall, MLP and CNN presented competitive results to GBLUP. Also, we bring new insights on automated machine learning for genomic prediction and its implications to plant breeding.

Population-tailored mock genome enables genomic studies in species without a reference genome.

Based on molecular markers, genomic prediction enables us to speed up breeding schemes and increase the response to selection. There are several high-throughput genotyping platforms able to deliver thousands of molecular markers for genomic study purposes. However, even though its widely applied in plant breeding, species without a reference genome cannot fully benefit from genomic tools and modern breeding schemes. We used a method to assemble a population-tailored mock genome to call single-nucleotide polymorphism (SNP) markers without an available reference genome, and for the first time, we compared the results with standard genotyping platforms (array and genotyping-by-sequencing (GBS) using a reference genome) for performance in genomic prediction models. Our results indicate that using a population-tailored mock genome to call SNP delivers reliable estimates for the genomic relationship between genotypes. Furthermore, genomic prediction estimates were comparable to standard approaches, especially when considering only additive effects. However, mock genomes were slightly worse than arrays at predicting traits influenced by dominance effects, but still performed as well as standard GBS methods that use a reference genome. Nevertheless, the array-based SNP markers methods achieved the best predictive ability and reliability to estimate variance components. Overall, the mock genomes can be a worthy alternative for genomic selection studies, especially for those species where the reference genome is not available.