Do feature selection methods for selecting environmental covariables enhance genomic prediction accuracy?

Genomic selection (GS) is transforming plant and animal breeding, but its practical implementation for complex traits and multi-environmental trials remains challenging. To address this issue, this study investigates the integration of environmental information with genotypic information in GS. The study proposes the use of two feature selection methods (Pearson's correlation and Boruta) for the integration of environmental information. Results indicate that the simple incorporation of environmental covariates may increase or decrease prediction accuracy depending on the case. However, optimal incorporation of environmental covariates using feature selection significantly improves prediction accuracy in four out of six datasets between 14.25% and 218.71% under a leave one environment out cross validation scenario in terms of Normalized Root Mean Squared Error, but not relevant gain was observed in terms of Pearson´s correlation. In two datasets where environmental covariates are unrelated to the response variable, feature selection is unable to enhance prediction accuracy. Therefore, the study provides empirical evidence supporting the use of feature selection to improve the prediction power of GS.

Genotype-by-environment interactions for starch, mineral, and agronomic traits in pearl millet hybrids evaluated across five locations in West Africa.

Introduction: Pearl millet is a staple cereal grown in the harshest environments of arid and semi-arid regions of Asia and sub-Saharan Africa. It is the primary source of calories for millions of people in these regions because it has better adaptation to harsh environmental conditions and better nutritional traits than many other cereals. By screening the pearl millet inbred germplasm association panel (PMiGAP), we earlier reported the best genotypes with the highest concentration of slowly digestible and resistant starch in their grains. Methods: In the current study, we tested these 20 top-performing pearl millet hybrids, identified based on starch data, in a randomised block design with three replications at five locations in West Africa, viz. Sadore and Konni (Niger), Bambey (Senegal), Kano (Nigeria), and Bawku (Ghana). Phenotypic variability was assessed for agronomic traits and mineral traits (Fe and Zn). Results and discussion: Analysis of variance demonstrated significant genotypic, environmental, and GEI effects among five testing environments for agronomic traits (days to 50% flowering, panicle length, and grain yield), starch traits (rapidly digestible starch, slowly digestible starch, resistant starch, and total starch), and mineral trait (iron and zinc). Starch traits, such as rapidly digestible starch (RDS) and slowly digestible starch (SDS), showed nonsignificant genotypic and environmental interactions but high heritability, indicating the lower environmental influence on these traits in the genotype × testing environments. Genotype stability and mean performance across all the traits were estimated by calculating the multi-trait stability index (MTSI), which showed that genotypes G3 (ICMX207070), G8 (ICMX207160), and G13 (ICMX207184) were the best performing and most stable among the five test environments.

Varietal evaluation of hybrid maize in the summer and winter seasons in terai region of Nepal.

Comparing hybrid maize to open-pollinated varieties, the former is widely recognized for its higher producing capacity. However, the production potential of hybrids varies depending on the region and the season. In order to find the high yielding stable genotypes throughout both settings, this experiment was carried out in the summer of 2021 and the winter of 2021-2022, using a Randomized Complete Block Design with 11 genotypes and 3 replications. The tallest genotypes among those evaluated were CP 808 and G-25 in the winter and summer, respectively. Both P3553 in the winter and CP 808 in the summer reported earlier days to anthesis. Grain yield showed a substantial and positive links with cob characteristics and a negative correlation with reproductive traits, according to correlation analysis. When compared to the yield of both seasons, P3355 and Bisco gold 941 showed highest yield in both environments. Thus, genotypes P3355 and Bisco gold 941 are recommended for cultivation in study area over other available hybrids in the market.

Partial Least Squares Enhances Genomic Prediction of New Environments.

In plant breeding, the need to improve the prediction of future seasons or new locations and/or environments, also denoted as "leave one environment out," is of paramount importance to increase the genetic gain in breeding programs and contribute to food and nutrition security worldwide. Genomic selection (GS) has the potential to increase the accuracy of future seasons or new locations because it is a predictive methodology. However, most statistical machine learning methods used for the task of predicting a new environment or season struggle to produce moderate or high prediction accuracies. For this reason, in this study we explore the use of the partial least squares (PLS) regression methodology for this specific task, and we benchmark its performance with the Bayesian Genomic Best Linear Unbiased Predictor (GBLUP) method. The benchmarking process was done with 14 real datasets. We found that in all datasets the PLS method outperformed the popular GBLUP method by margins between 0% (in the Indica data) and 228.28% (in the Disease data) across traits, environments, and types of predictors. Our results show great empirical evidence of the power of the PLS methodology for the prediction of future seasons or new environments.

Characterization, costs, cues and future perspectives of phenotypic plasticity.

BACKGROUND: Plastic responses of plants to the environment are ubiquitous. Phenotypic plasticity occurs in many forms and at many biological scales, and its adaptive value depends on the specific environment and interactions with other plant traits and organisms. Even though plasticity is the norm rather than the exception, its complex nature has been a challenge in characterizing the expression of plasticity, its adaptive value for fitness and the environmental cues that regulate its expression. SCOPE: This review discusses the characterization and costs of plasticity and approaches, considerations, and promising research directions in studying plasticity. Phenotypic plasticity is genetically controlled and heritable; however, little is known about how organisms perceive, interpret and respond to environmental cues, and the genes and pathways associated with plasticity. Not every genotype is plastic for every trait, and plasticity is not infinite, suggesting trade-offs, costs and limits to expression of plasticity. The timing, specificity and duration of plasticity are critical to their adaptive value for plant fitness. CONCLUSIONS: There are many research opportunities to advance our understanding of plant phenotypic plasticity. New methodology and technological breakthroughs enable the study of phenotypic responses across biological scales and in multiple environments. Understanding the mechanisms of plasticity and how the expression of specific phenotypes influences fitness in many environmental ranges would benefit many areas of plant science ranging from basic research to applied breeding for crop improvement.

Genomic Prediction of Grain Yield in a Barley MAGIC Population Modeling Genotype per Environment Interaction.

Multi-parent Advanced Generation Inter-crosses (MAGIC) lines have mosaic genomes that are generated shuffling the genetic material of the founder parents following pre-defined crossing schemes. In cereal crops, these experimental populations have been extensively used to investigate the genetic bases of several traits and dissect the genetic bases of epistasis. In plants, genomic prediction models are usually fitted using either diverse panels of mostly unrelated accessions or individuals of biparental families and several empirical analyses have been conducted to evaluate the predictive ability of models fitted to these populations using different traits. In this paper, we constructed, genotyped and evaluated a barley MAGIC population of 352 individuals developed with a diverse set of eight founder parents showing contrasting phenotypes for grain yield. We combined phenotypic and genotypic information of this MAGIC population to fit several genomic prediction models which were cross-validated to conduct empirical analyses aimed at examining the predictive ability of these models varying the sizes of training populations. Moreover, several methods to optimize the composition of the training population were also applied to this MAGIC population and cross-validated to estimate the resulting predictive ability. Finally, extensive phenotypic data generated in field trials organized across an ample range of water regimes and climatic conditions in the Mediterranean were used to fit and cross-validate multi-environment genomic prediction models including G×E interaction, using both genomic best linear unbiased prediction and reproducing kernel Hilbert space along with a non-linear Gaussian Kernel. Overall, our empirical analyses showed that genomic prediction models trained with a limited number of MAGIC lines can be used to predict grain yield with values of predictive ability that vary from 0.25 to 0.60 and that beyond QTL mapping and analysis of epistatic effects, MAGIC population might be used to successfully fit genomic prediction models. We concluded that for grain yield, the single-environment genomic prediction models examined in this study are equivalent in terms of predictive ability while, in general, multi-environment models that explicitly split marker effects in main and environmental-specific effects outperform simpler multi-environment models.

Combined selection for adaptability, genotypic stability and cowpea yield from mixed models / Seleção combinada para adaptabilidade, estabilidade genotípica e produtividade de feijão-caupi a partir de modelos mistos

ABSTRACT: The potential expression of crop productivity is a constant challenge for plant breeders in the face of oscillations in environmental variables, making selection difficult and increasing the operational and methodological costs in obtaining the ideal cultivar for a determined region. The objective of the research was to investigate the effects of genotype x environment interaction in the selection of cowpea lines with high grain yield, adaptability, and genotypic stability simultaneously, in environments of the Northwest region of Rio de Janeiro State, using mixed models (Maximum Restricted Likelihood - REML/Best Linear Unbiased Prediction - BLUP). 27 cowpea genotypes were evaluated in six environments by combining location (Cambuci-RJ and Bom Jesus do Itabapoana-RJ) and year (2016, 2017 and 2018). A randomized block design with four replications was performed. The genetic parameters were estimated via the REML/BLUP procedure, and the selection was based on the harmonic mean method of the relative performance of the genetic values (HMRPGV). A meaningful difference was observed for environment and genotype x environment interaction. The residual variance and the variance of the genotype x environment interaction formed the most significant fractions of the phenotypic variance. Lines 4 (Bico-de-ouro 1-5-24), 6 (Pingo-de-Ouro 1-5-4), 5 (Pingo-de-Ouro 1-5-26), and 9 (Pingo-de-Ouro 1-5-8), stood out as superior in terms of stability and adaptability and grain yield by HMRPGV. Commercial cultivars 13 (BRS-Tumucumaque) and 26 (BRS-Itaim) had high grain yield, adaptability, and specific stability in the evaluated edaphoclimatic conditions.

RESUMO: A expressão potencial da produtividade das culturas constitui um desafio constante aos criadores de plantas frente às oscilações das variáveis ambientais, dificultando a seleção e onerando os custos operacionais e metodológicos na obtenção da cultivar ideal para determinada região. O objetivo do trabalho foi investigar os efeitos da interação genótipos x ambientes na seleção de linhagens de feijão-caupi com alta produtividade de grãos, adaptabilidade e estabilidade genotípica simultaneamente, em ambientes da região Noroeste do estado do Rio de Janeiro, usando modelos mistos (Máximo Verosimilhança Restrita - REML/Melhor Predição Linear não Viesado - BLUP). Avaliou-se 27 genótipos de feijão-caupi em seis ambientes pela combinação de local (Cambuci-RJ e Bom Jesus do Itabapoana-RJ) e ano (2016, 2017 e 2018). Foi utilizado o delineamento em blocos casualizados com quatro repetições. Os parâmetros genéticos foram estimados via procedimento REML/BLUP, e a seleção baseou-se no método da média harmônica do desempenho relativo dos valores genéticos (HMRPGV). Observou-se diferença significativa para ambiente e interação genótipo x ambiente. A variância residual e a variância da interação genótipo x ambiente formaram as maiores frações da variância fenotípica. As linhagens 4 (Bico-de-ouro 1-5-24), 6 (Pingo-de-ouro 1-5-4), 5 (Pingo-de-ouro 1-5-26) e 9 (Pingo-de-ouro 1-5-8) foram classificadas como superiores quanto a estabilidade e adaptabilidade e rendimento de grãos pelo critério da HMRPGV. As cultivares comerciais 13 (BRS-Tumucumaque) e 26 (BRS-Itaim) reuniram elevada produtividade de grãos, adaptabilidade e estabilidade específica nas condições edafoclimáticas avaliadas.

Effect of sowing time and density for vegetative and reproductive traits of genotypes of maize landrace in an agroecological system / Efeito de época e densidade de semeadura nas características vegetativas e reprodutivas em genótipos de variedades crioulas de milho em sistema de base agroecológica

ABSTRACT: Family farmers preserve the tradition of cultivating maize landrace varieties because these plants have characteristics that hybrids lack. The greatest challenge in conserving in situ on-farm genetic diversity is avoiding gene flow and genetic introgression of transgenes to landrace varieties. Thus, farmers are obliged to change sowing times to guarantee temporal isolation since most farms are small, making spatial isolation impossible. The objective of the present work was to evaluate the behavior of maize landrace varieties submitted to different sowing times and densities in an agroecological system. The test was conducted in sub-sub-divided plots, where the main plot was represented by the sowing time, the sub-plot by the genotype, and the sub-sub-plot by the density, with three replications, for two consecutive years. The results demonstrate the effect of sowing time and density on the characteristics evaluated. In western Santa Catarina, the best time to sow seeds of maize landrace varieties in an agroecological system is in September, which is when the varieties expressed the greatest potential at densities from 45,000 to 50,000 pl.ha-1 , but it will not avoid transgene contamination.

RESUMO: Famílias camponesas preservaram a tradição do cultivo das variedades crioulas de milho estimuladas por características que os híbridos não apresentam. Sendo, o maior desafio para a conservação da diversidade genética in situ on farm evitar o fluxo gênico e a introgressão genética de trangenes nas variedades crioulas. Nesse sentido, os agricultores são obrigados a alterar épocas de semeadura para garantir isolamento temporal uma vez que a maioria das áreas é pequena inviabilizando o isolamento no espaço. O objetivo do presente trabalho foi avaliar o comportamento de variedades crioulas de milho em sistema de base agroecológica submetidas às diferentes épocas e densidades de semeadura. No ensaio conduzido em parcelas sub-sub-divididas, a parcela principal foi representada pela época, a sub-parcela pelo genótipo e a sub-sub-parcela pela densidade, com três repetições, por dois anos consecutivos. Os resultados demostraram efeito de época e densidade de semeadura nas características avaliadas. É possível indicar que a época mais adequada para semeadura de variedades crioulas de milho em sistema de base agroecológica é em setembro para o oeste de Santa Catarina, sendo que para essa época as variedades expressaram maior potencial de produtividade de grãos na faixa de densidade de 45000 a 50000 pl.ha-1 , mas não impedirá a contaminação por transgene.

Adaptability and stability of early carioca beans by mixed models / Adaptabilidade e estabilidade de feijão carioca precoce via modelos mistos

The genotype x environment interaction represents one of the major selection challenges due to the difficulty in identifying effectively superior genotypes. The present study aimed at estimating genetic parameters and selecting genotypes of early Carioca beans by analyzing simultaneous attributes, including yield, adaptability, and stability. In the agricultural year of 2015 and 2016, three trials were conducted, using a randomized block design, with three repetitions each, in the Agreste and Sertao regions of Pernambuco State. The genetic parameters were estimated using the mixed model procedure, and the selection was based on the harmonic mean of the relative performance of genetic values (MHPRVG, abbreviation in Portuguese) method. The environments influenced the phenotypic expression of the bean genotypes during both years, setting a specific adaptation. The mean heritability of the genotypes regarding yield exhibited low magnitude values in the trials of 2015 (5.78%) and 2016 (13.77%), indicating costly conditions for the selection of the improved genotypes. Genotype CNFC 15856 was selected, considering the genetic gain predicted for yield, by the average and specific performance in the three environments, and by the simultaneous attributes of yield, adaptability, and stability. The MHPRVG method enables the optimized selection of genotypes considering yield, stability, and adaptability; therefore, it should be included in the recommended selective criteria for agronomically superior genotypes in commercial plantations.

A interação genótipos x ambientes representa um dos maiores desafios da seleção por dificultar a identificação de genótipos efetivamente superiores. O objetivo desta pesquisa foi estimar os parâmetros genéticos e, pelos atributos simultâneos de produtividade, adaptabilidade e estabilidade, selecionar genótipos de feijão carioca precoce. No ano agrícola de 2015 e 2016, foram conduzidos três ensaios sob o delineamento de blocos casualizados com três repetições no Agreste e Sertão de Pernambuco. Os parâmetros genéticos foram estimados pelo procedimento de modelos mistos, e a seleção baseou-se no método da média harmônica do desempenho relativo dos valores genéticos. Os ambientes influenciaram na expressão fenotípica dos genótipos de feijão nos dois anos, configurando adaptação específica. A herdabilidade média dos genótipos para produtividade apresentou valores de baixa magnitude nos ensaios de 2015 (5,78%) e 2016 (13,77%), indicando condições dispendiosas para seleção dos genótipos melhorados. O genótipo CNFC 15856 foi selecionado considerando o ganho genético predito para produtividade pelo desempenho médio e específico nos três ambientes e pelos atributos simultâneos de produtividade, adaptabilidade e estabilidade. O método MHPRVG proporciona seleção otimizada de genótipos quanto à produtividade, à estabilidade e à adaptabilidade e, portanto, deve fazer parte dos critérios seletivos de recomendação de genótipos agronomicamente superiores para plantios comerciais.

Genotype-by-environment interaction in coast redwood outside natural distribution - search for environmental cues.

BACKGROUND: Effective matching of genotypes and environments is required for the species to reach optimal productivity and act effectively for carbon sequestration. A common garden experiment across five different environments was undertaken to assess genotype x environment interaction (GxE) of coast redwood in order to understand the performance of genotypes across environments. RESULTS: The quantitative genetic analysis discovered no GxE between investigated environments for diameter at breast height (DBH). However, no genetic component was detected at one environment possibly due to stressful conditions. The implementation of universal response function allowed for the identification of important environmental factors affecting species productivity. Additionally, this approach enabled us to predict the performance of species across the New Zealand environmental conditions. CONCLUSIONS: In combination with quantitative genetic analysis which identified genetically superior material, the URF model can directly identify the optimal geographical regions to maximize productivity. However, the finding of ideally uncorrelated climatic variables for species with narrow ecological amplitude is rather challenging, which complicates construction of informative URF model. This, along with a small number of tested environments, tended to overfit a prediction model which resulted in extreme predictions in untested environments.

Combined selection in beans for cycle, plant architecture and grain yield / Seleção combinada em feijão para ciclo, arquitetura de planta e produtividade de grãos

The selection of common bean cultivars for high agronomic performance can be difficulty by genotype x environment interaction. The objectives of this work were to evaluate if common bean cultivars differ for cycle, plant architecture and grain yield in different growing seasons, and to select early, upright and highly grain yield common bean cultivars, by the use of selection index. For this, five experiments were conducted in the randomized blocks design, with three replicates. A total of 26 common bean cultivars were evaluated and the multiplicative index was used to select superior cultivars. A significant cultivar x season interaction for flowering, cycle, insertion of the first pod, insertion of the last pod, number of pods per plant and grain yield was observed. The common bean cultivars have early or semiearly cycle in rainy season and upright plant architecture. The cultivars Macanudo, BRS Campeiro, IAPAR 81, and IPR Juriti presented high grain yield in most growing seasons. The four superior common bean cultivars selected by the multiplicative index were BRS Campeiro, Macanudo, IPR Juriti, and Guapo Brilhante. The cultivars BRS Campeiro, Macanudo, and IPR Juriti presents earliness, upright plant architecture, and high grain yield and will be selected for the breeding program.

A seleção de cultivares de feijão com alto desempenho agronômico pode ser dificultada pela ocorrência de interação genótipo x ambiente. Os objetivos desse trabalho foram avaliar se cultivares de feijão diferem para ciclo, arquitetura de planta e produtividade de grãos em diferentes épocas de cultivo e selecionar cultivares de feijão precoces, eretas e altamente produtivas pelo uso de índice de seleção. Para tanto, cinco experimentos foram conduzidos em delineamento de blocos ao acaso, com três repetições. Um total de 26 cultivares de feijão foram avaliadas e o índice multiplicativo foi usado para selecionar cultivares superiores. Interação cultivar x época de cultivo significativa foi constatada para a floração, ciclo, inserção da primeira vagem, inserção da última vagem, número de vagens por planta e produtividade de grãos. As cultivares de feijão avaliadas possuem ciclo precoce ou semiprecoce no cultivo de safra e arquitetura de planta ereta. As cultivares Macanudo, BRS Campeiro, IAPAR 81 e IPR Juriti apresentaram alta produtividade de grãos na maioria das épocas avaliadas. As quatro melhores cultivares de feijão selecionadas pelo índice multiplicativo foram BRS Campeiro, Macanudo, IPR Juriti e Guapo Brilhante. As cultivares BRS Campeiro, Macanudo e IPR Juriti apresentam precocidade, arquitetura de planta ereta e alta produtividade de grãos, portanto serão selecionadas pelo programa de melhoramento.

Dissecting Key Adaptation Traits in the Polyploid Perennial Medicago sativa Using GBS-SNP Mapping.

Understanding key adaptation traits is crucial to developing new cultivars with broad adaptations. The main objective of this research is to understand the genetic basis of winter hardiness (WH) and fall dormancy (FD) in alfalfa and the association between the two traits. QTL analysis was conducted in a pseudo-testcross F1 population developed from two cultivars contrasting in FD (3010 with FD = 2 and CW 1010 with FD = 10). The mapping population was evaluated in three replications at two locations (Watkinsville and Blairsville, GA). FD levels showed low to moderate correlations with WH (0.22-0.57). Assessing dormancy in winter is more reliable than in the fall in southern regions with warm winters. The mapping population was genotyped using Genotyping-by-sequencing (GBS). Single dose allele SNPs (SDA) were used for constructing linkage maps. The parental map (CW 1010) consisted of 32 linkage groups spanning 2127.5 cM with 1377 markers and an average marker density of 1.5 cM/SNP. The maternal map (3010) had 32 linkage groups spanning 2788.4 cM with 1837 SDA SNPs with an average marker density of 1.5 cM/SNP. Forty-five significant (P < 0.05) QTLs for FD and 35 QTLs for WH were detected on both male and female linkage maps. More than 75% (22/28) of the dormancy QTL detected from the 3010 parent did not share genomic regions with WH QTLs and more than 70% (12/17) dormancy QTLs detected from CW 1010 parent were localized in different genomic regions than WH QTLs. These results suggest that the two traits have independent inheritance and therefore can be improved separately in breeding programs.

Genetic divergence of strawberry cultivars under different managements / Divergência genética de cultivares de morango em diferentes manejos

Developing strawberry cultivars that can be grown on a large scale, it is necessary to gather desirable characteristics such as: tolerance to Tetranychus urticae, high fruit yield and wide adaptability to several cropping managements. Therefore, our objective was to study the genetic diversity among 13 strawberry cultivars under different managements and to recommend promising crosses to obtain segreganting populations with high fruit yield and T. urticae tolerance. Trial was performed under field conditions at the Centro Regional de Desenvolvimento Rural Centro Serrano of the Instituto Capixaba for Technical Assistance and Rural Extension (Incaper), Domingos Martins-ES. We evaluated strawberry cultivars Albion, Aleluia, Aromas, Camarosa, Camino Real, Campinas, Diamante, Dover, Festival, Seascape, Toyonoka, Tudla, and Ventana, cultivated in three cropping managements: open field, low tunnel and high tunnel. Experimental design was randomized complete blocks with three replications. Variables evaluated were: number of two-spotted spider mite/cm2 on the leaf (NTSSM), total number of fruits (TNF), number of commercial fruits (NCF) and fruit yield (YIE, t/ha). We applied the generalized Mahalanobis distance and Tocher's optimization method to study the genetic diversity among cultivars in each management, and the relative contribution of traits to genetic diversity was evaluated according to the criterion described by Singh (1981). For the low tunnel and high tunnel environments, the crosses Aleluia x Camarosa, Aleluia x Aromas and Aleluia x Festival are the most promising to generate segregating populations with a higher possibility to appearance transgressive individuals, while for the open field cultivation system, we recommend the cross among Aleluia x Toynoka. The variables that most contributed for genetic dissimilarity were total number of fruits, fruit yield and number of commercial fruits for the environments open field, low tunnel and high tunnel, respectively.

´Para desenvolver cultivares de morango que podem ser cultivados em larga escala é necessário reunir características desejáveis como: tolerância ao Tetranychus urticae, alta produtividade de frutos e ampla adaptabilidade a diversos sistemas de cultivo. Portanto, o objetivo do trabalho foi estuda a diversidade genética entre 13 cultivares de morango sob diferentes manejos e recomendar cruzamentos promissores para obtenção de populações segregantes com alta produtividade de frutos e tolerantes ao T. urticae. O experimento foi conduzido sob condições de campo no Centro Regional de Desenvolvimento Rural Centro Serrano do Instituto Capixaba de Assistência Técnica e Extenção Rural (Incaper), Domingos Martins-ES, no mês de outubro (primavera). Foram avaliadas as cultivares Albion, Aleluia, Aromas, Camarosa, Camino Real, Campinas, Diamante, Dover, Festival, Seascape, Toyonoka, Tudla e Ventana, cultivadas em três sistemas de cultivo: campo aberto, túnel baixo e túnel alto. O delineamento experimental utilizado foi blocos casualizados com três repetições. As variáveis avaliadas foram: número de ácaro/cm² na folha (NTSSM), número total de frutos (TNF), número de frutos comerciais (NCF) e produtividade de frutos (YIE, t/ha). Foram empregadas a distância generalizada de Mahalanobis e o método de otimização de Tocher para o estudo da diversidade genética entre os cultivares em cada manejo, e a contribuição relativa dos caracteres para a diversidade genética foi avaliada segundo o critério de Singh (1981). Para os manejos túnel baixo e túnel alto, os cruzamentos entre os cultivares Aleluia x Camarosa, Aleluia x Aromas e Aleluia x Festival são os mais promissores para gerar populações segregantes com alta possibilidade de aparecimento de indivíduos transgressivos, enquanto que para o campo aberto recomenda-se o cruzamento entre os cultivares Aleluia x Toynoka. As variáveis que mais contribuíram para a dissimilaridade genética foram o número total de frutos, produtividade e número de frutos comerciais para os ambientes campo aberto, túnel baixo e túnel alto, respectivamente.

Number of experiments for adaptability and stability analysis in maize by Lin and Binns method / Número de experimentos para a análise de adaptabilidade e estabilidade em milho pelo métodode Lin e Binns

ABSTRACT: The objective of this study was to determine the necessary number of experiments to analyze the adaptability and stability of maize cultivars (Zea mays L.) using the Lin and Binns method. Grain yield data extracted from 63 maize cultivar trials were used. Trials were divided in six groups of experiments, according to the cycle (early and super early) and the agricultural year (2002/2003, 2003/2004, and 2004/2005). In each group, from the set of all experiments (reference file) new data files were formed by combinations in groups of 2, 3, 4, ..., n-1 experiments, with a total of 10,683 files. For each file, the estimation of the adaptability and stability parameter (Pi) of the Lin and Binns method was calculated. To verify the degree of association of the estimates of Pi obtained with the combinations of experiments and with all the experiments (reference), Spearman correlation coefficient (r) was used. Number of experiments giving values of r≥0.80 in 100% of the combinations was considered sufficient. Seven experiments sufficed for the analysis of adaptability and stability of maize cultivars by the method of Lin and Binns.

RESUMO: O objetivo deste trabalho foi determinar o número necessário de experimentos para a análise de adaptabilidade e estabilidade de cultivares de milho (Zea mays L.) por meio do método de Lin e Binns. Foram usados os dados de produtividade de grãos de 63 ensaios de competição de cultivares de milho. Os ensaios foram divididos em seis grupos de experimentos, conforme o ciclo (precoce e superprecoce) e o ano agrícola (2002/2003, 2003/2004 e 2004/2005). Em cada grupo, a partir do conjunto de todos os experimentos (arquivo referência), formaram-se novos arquivos de dados por meio de combinações em grupos de 2, 3, 4, ..., n-1 experimentos do grupo, totalizando 10.683 arquivos. Para cada arquivo foi calculada a estimativa do parâmetro de adaptabilidade e estabilidade (Pi) do método de Lin e Binns. Para verificar o grau de associação das estimativas de Pi obtidas com as combinações de experimentos e com todos os experimentos (referência), foi utilizado o coeficiente de correlação de Spearman (r). Considerou-se como suficiente o número de experimentos que proporciona valores de r≥0,80 em 100% das combinações. Sete experimentos foram suficientes para a análise de adaptabilidade e estabilidade de cultivares de milho por meio do método de Lin e Binns.

Genomic prediction accuracies in space and time for height and wood density of Douglas-fir using exome capture as the genotyping platform.

BACKGROUND: Genomic selection (GS) can offer unprecedented gains, in terms of cost efficiency and generation turnover, to forest tree selective breeding; especially for late expressing and low heritability traits. Here, we used: 1) exome capture as a genotyping platform for 1372 Douglas-fir trees representing 37 full-sib families growing on three sites in British Columbia, Canada and 2) height growth and wood density (EBVs), and deregressed estimated breeding values (DEBVs) as phenotypes. Representing models with (EBVs) and without (DEBVs) pedigree structure. Ridge regression best linear unbiased predictor (RR-BLUP) and generalized ridge regression (GRR) were used to assess their predictive accuracies over space (within site, cross-sites, multi-site, and multi-site to single site) and time (age-age/ trait-trait). RESULTS: The RR-BLUP and GRR models produced similar predictive accuracies across the studied traits. Within-site GS prediction accuracies with models trained on EBVs were high (RR-BLUP: 0.79-0.91 and GRR: 0.80-0.91), and were generally similar to the multi-site (RR-BLUP: 0.83-0.91, GRR: 0.83-0.91) and multi-site to single-site predictive accuracies (RR-BLUP: 0.79-0.92, GRR: 0.79-0.92). Cross-site predictions were surprisingly high, with predictive accuracies within a similar range (RR-BLUP: 0.79-0.92, GRR: 0.78-0.91). Height at 12 years was deemed the earliest acceptable age at which accurate predictions can be made concerning future height (age-age) and wood density (trait-trait). Using DEBVs reduced the accuracies of all cross-validation procedures dramatically, indicating that the models were tracking pedigree (family means), rather than marker-QTL LD. CONCLUSIONS: While GS models' prediction accuracies were high, the main driving force was the pedigree tracking rather than LD. It is likely that many more markers are needed to increase the chance of capturing the LD between causal genes and markers.

Selection of cowpea genotypes for Mato Grosso do Sul viaGGE Biplot and linear regression / Seleção de genótipos de feijão-caupi para Mato Grosso do Sul via GGEe Biplot e regressão linear

The aim of this study was to investigate the association between GGE Biplot and Eberhart and Russell methodologies and to select cowpea genotypes that meet both high grain yield, adaptability and stability for Mato Grosso do Sul environments. The trials were carried out from February to July of 2010, 2011 and 2012 in the municipalities of Dourados, Aquidauana and Chapadão do Sul. The trials in Chapadão do Sul were conducted only in the years 2010 and 2011, totaling eight environments. After detecting significant GE interaction, adaptability and phenotypic stability of cowpea genotypes were analyzed by GGE Biplot and linear regression methods. Eberhart and Russell and GGE biplot methodologies discriminate differently the best cowpea genotypes and it can be used in a complementary way. MNCO1-649F-2-11 and MNCO2-675-4-9 genotypes are the closest to the ideal in terms of high grain yield and phenotypic stability, being so suitable for cultivation in the state of Mato Grosso do Sul.

O objetivo deste trabalho foi verificar a associação entre as metodologias de Eberhart & Russel e GGE Biplot e selecionar genótipos de feijão-caupi que reúnam simultaneamente alta produtividade de grãos, adaptabilidade e estabilidade aos ambientes de Mato Grosso do Sul. Os experimentos foram realizados no período de fevereiro a julho de 2010, 2011 e 2012, nos municípios de Dourados, Aquidauana e Chapadão do Sul. Os experimentos em Chapadão do Sul foram realizados apenas nos anos de 2010 e 2011, totalizando oito ambientes. Após detectar interação da GE significativa, a adaptabilidade e estabilidade fenotípica dos genótipos de feijão-caupi foi analisada pelos métodos GGE Biplot e regressão linear. As metodologias de Eberhart & Russell e GGE biplot discriminam de forma distinta os melhores genótipos de feijão-caupi e podem ser usadas de forma complementar. Os genótipos MNCO1-649F-2-11 e MNCO2-675-4-9 são indicados para o cultivo no Estado de Mato Grosso do Sul, pois aliam alta produtividade de grãos e estabilidade fenotípica.

Parametric and non-parametric analysis for determining the adaptability and stability of soybean genotypes in three sowing periods / Análises paramétricas e não paramétricas para determinação da adaptabilidade e estabilidade de genótipos de soja em três épocas de semeadura

The use of different evaluation methods of adaptability and stability in a breeding program is essential to obtain more accurate results of the lines that have been studied. The purpose of this research is to study the adaptability and stability of 25 soybean lines derived from the soybean breeding program, and for that, it was used parametric and non-parametric analysis at the Federal University of Uberlandia. The experiment was set up in randomized complete block design with three replications in three sowing periods (November 2006, November 2007 and November 2008) and conducted in Campo Alegre de Goias, Brazil. Thirty soybean genotypes were evaluated, including 25 late-cycle lines and five cultivars (BRS/MG Garantia, UFUS Impacta, UFUS Xavante UFUS Milionária and M-Soy 8914) as controls). Grain productivity was determined for each block. The average yield was 3104.201 kg ha-1. Adaptability and stability were determined using Eberhart and Russel (1966), Lin and Binns (1988) modified by Carneiro (1998) and Centroide (ROCHA, 2005) methods. The UFUS 6 and UFUS 21 lines and the UFUS Impacta and UFUS Xavante cultivars stood out because they had the highest average grain yield, highest adaptability and stability regardless of evaluation method.

A utilização de diferentes métodos para avaliação da adaptabilidade e estabilidade em um programa de melhoramento genético é essencial para a obtenção de resultados mais precisos das linhagens estudadas. O objetivo deste trabalho foi estudar a adaptabilidade e a estabilidade de 25 linhagens de soja oriundas do Programa de Melhoramento de Soja da Universidade Federal de Uberlândia através dos métodos paramétricos e não paramétricos. O experimento foi conduzido em delineamento de blocos completos casualizados, com três repetições, em três épocas de semeadura, em novembro de 2006, novembro de 2007 e novembro de 2008, no município de Campo Alegre de Goiás-GO. Avaliaram-se 30 genótipos de soja, sendo 25 linhagens de ciclo tardio e cinco cultivares como testemunhas (BRS/MG Garantia, UFUS Impacta, UFUS Xavante, UFUS Milionária e M-Soy 8914). Em cada parcela, foi determinada a produtividade de grãos. A média da produtividade foi de 3104,201 kg ha-1. Para o estudo sobre adaptabilidade e estabilidade utilizaram-se os métodos de Eberhart e Russel (1966), Lin e Binns (1988) modificado por Carneiro (1998) e Centroide (ROCHA, 2005). As linhagens UFUS 6, UFUS 21 e as cultivares UFUS Impacta e UFUS Xavante se destacaram por apresentarem elevadas médias de produtividade de grãos, ampla adaptação e alta estabilidade por todos os métodos estudados

Modelos de norma de reação para estudo das características de qualidade da carne de codornas de corte em função das razões (metionina + cistina): lisina da dieta / Reaction norm models for the study of meat quality of european quail in function of (methionine + cysteine): lysine diet ratio

Objetivou-se avaliar a sensibilidade dos valores genéticos para características de qualidade da carne em codornas de corte alimentadas com dietas contendo diferentes relações de (metionina + cistina): lisina, do nascimento aos 21 dias de idade, por meio de modelos de normas de reação. Utilizaram-se 9011 informações de qualidade de carne referentes a 1400 progênies de 80 reprodutores e 160 matrizes de duas linhas (LF1 e LF2). Para o ajuste dos modelos de regressão aleatória, foi usado o programa WOMBAT, considerando-se nas análises homogeneidade de variância residual. As codornas foram alimentadas do nascimento aos 21 dias de idade com dietas contendo as relações 0,61; 0,66; 0,71; 0,76 e 0,81 de (metionina + cistina): lisina, mantendo os níveis de proteína bruta de 26,12% e de energia em 2900 kcal EM/kg da dieta. Dos 22 aos 35 dias de idade, todas as codornas foram alimentadas com dieta contendo 22% de proteína bruta e 3050 kcal EM/kg da dieta. As estimativas da variância genética e da herdabilidade foram influenciadas pelo gradiente ambiental e pela linha, com mudanças nessas estimativas com o aumento do gradiente ambiental. Os valores genéticos das características de qualidade de carne referentes a cada uma das linhas se alteraram com o aumento das relações de aminoácidos das dietas em razão das mudanças no ordenamento dos valores genéticos, evidenciando a existência da interação genótipo x nível de relação dos aminoácidos da dieta para características de qualidade de carne. Predições de valores genéticos de características de qualidade de carne com base em determinada relação de (metionina + cistina): lisina da dieta não são válidas para outras relações desses aminoácidos.

This study aimed to evaluate the sensitivity of breeding values for meat quality traits of European quails fed different (methionine + cystine): lysine ratio diets from hatch to 21 days of age, using reaction norm models. A total of 9011 meat quality records from 1400 progenies of 80 sires and 160 dams from two lines (LF1 and LF2) were used in the analyses considering homogeneity of residual variance. The quails from hatch to 21 days of age were fed diets containing 0.61, 0.66, 0.71, 0.76 and 0.81 (methionine + cystine): lysine ratios, 26.12% of crude protein and 2900 ME/kcal of diet. From 22 to 35 days of age all quail were fed a diet containing 22% of crude protein and 3050 kcal ME/kg of diet. The random regression model analyses was performed using the WOMBAT program considering homogeneity of residual variance. Genetic variance and heritability estimates were affected by the environment gradient of diet and line, increasing these estimates with the increase of the (methionine + cystine): lysine ratio of the diet. The breeding values changed with the increase of the environment gradient of the diet with changes in the rank of genetic breeding values characterizing the existence of genotype by environment interaction for meat quality traits. Predictions of meat quality trait breeding values based on a given (methionine + cystine): lysine ratio are not valid for other levels of the amino acid ratio.

Adaptabilidade e estabilidade de genótipos eretos de amendoim cultivados nas regiões Nordeste e Centro-Oeste / Comparison of adaptability and stability estimates in upright peanut genotypes cultivated in Northeast and Midwest regions

O presente trabalho teve por objetivo estimar a estabilidade e a adaptabilidade de oito genótipos de amendoim ereto e comparar os modelos de análise de EBERHART & RUSSELL (1966), WRICKE (1965) e LIN & BINNS (1988), baseando-se em dados de produtividade de vagens e sementes. Os genótipos de amendoim foram avaliados em 14 ambientes situados nas Regiões Nordeste e Centro-Oeste, durante os anos de 2006 a 2011, sob o delineamento de blocos ao acaso com cinco repetições. Verificou-se que, entre os três métodos estudados, os de EBERHART & RUSSELL(1966) e LIN & BINNS (1988) geraram informações concordantes para estimativas de adaptação e estabilidade de produção de vagens e sementes, baseando-se nas condições deste estudo. Os genótipos L7 Bege e BRS 151 L7 foram os mais produtivos, com adaptabilidade específica a ambientes favoráveis, enquanto que CNPA 280 revelou adaptabilidade ampla e alta estabilidade fenotípica.

This study aimed to estimate the stability and adaptability parameters in upright-peanut genotypes, based on pod and seed yield, through EBERHART & RUSSELL (1966), WRICKE (1965) and LIN & BINNS (1988) methodologies. The genotypes were evaluated in 14 environments located in Northeast and Midwest regions, during 2006 to 2011, in a randomized blocks design, with five replications. EBERHART & RUSSELL (1966) and LIN & BINNS (1988) methodologies revealed similar results, identifying genotypes with high adaptability and stability to pod and seed yield. The BRS 151 L7 and L7 Bege were the most productive, revealing specific adaptability to favorable environment, while CNPA 280 AM revealed broad adaptability and high phenotypical stability.

Adaptabilidade e estabilidade de genótipos de café no cultivo orgânico em Minas Gerais / Adaptability and stability of coffee genotypes in the organic cultivation in Minas Gerais, Brazil

Este trabalho teve como objetivo comparar a adaptabilidade e estabilidade de cultivares de café quanto à média de produtividade anual e de biênios, pelo método de EBERHART & RUSSEL (1996), e selecionar cultivares de café para o cultivo orgânico em Minas Gerais. Os experimentos foram conduzidos em três locais, em delineamento de blocos casualizados com trinta genótipos e três repetições. Uma análise se baseou na produtividade média anual de quatro colheitas (2005/2006, 2006/2007, 2007/2008 e 2008/2009) com o total de doze ambientes. A outra análise considerou a média de dois biênios (2005/2006 e 2006/2007; 2007/2008 e 2008/2009) com o total de seis ambientes. A análise em que se considerou a média da produtividade do biênio apresentou redução expressiva do coeficiente de variação ambiental. Por isso, foi possível identificar mais cultivares com adaptabilidade e estabilidade para o cultivo orgânico. Conclui-se que a análise de adaptabilidade e estabilidade com base na produtividade de biênio é mais segura para a seleção de cultivares. Considerando essa premissa, as cultivares 'Catucaí Vermelho 36/6', 'Catuaí Vermelho IAC 15' e 'Siriema 842' são indicadas somente para os ambientes favoráveis. As cultivares 'Sabiá 708', 'IBC Palma 1', 'Catucaí Amarelo 24/137', 'Oeiras MG 6851' e as linhagens H518 e H514 são indicadas para o cultivo orgânico em locais com ambientes similares aos avaliados em Minas Gerais.

The aim of this research was to compare the stability and adaptability of coffee cultivars in relation to the average annual yield and to the biannual yield by the method of EBERHART & RUSSELL (1996), and select coffee cultivars for organic cultivation in Minas Gerais. The experiments were conducted at three sites in randomized block design with thirty genotypes and three replications. An analysis was based on the annual average yield of four crops (2005/2006, 2006/2007, 2007/2008 and 2008/2009) resulting in twelve environments. The other analysis considered the average of two biannual (2005/2006 and 2006/2007; 2007/2008 and 2008/2009) with a total of six environments. The analysis in which was considered that average biannual yield enabled a significant reduction in the coefficient of environmental variation. Thus, it was possible to identify cultivars with more adaptability and stability to organic cultivation. It was concluded that the analysis of stability and adaptability based on the biannual yield is more precise for selecting cultivars. Considering this premise the cultivars 'Catucaí Vermelho 36/6', 'Catuaí Vermelho IAC 15' and 'Siriema 842' are promising only for favorable environments. The cultivars 'Sabia 708', 'IBC Palma 1', 'Catucaí Amarelo 24/137', 'Oeiras MG 6851' and the lines H518 and H514, stood out in organic farming in similar environments like the locations evaluated in Minas Gerais.