Adaptability and stability analyses of plants using random regression models.

The evaluation of cultivars using multi-environment trials (MET) is an important step in plant breeding programs. One of the objectives of these evaluations is to understand the genotype by environment interaction (GEI). A method of determining the effect of GEI on the performance of cultivars is based on studies of adaptability and stability. Initial studies were based on linear regression; however, these methodologies have limitations, mainly in trials with genetic or statistical unbalanced, heterogeneity of residual variances, and genetic covariance. An alternative would be the use of random regression models (RRM), in which the behavior of the genotypes is characterized as a reaction norm using longitudinal data or repeated measurements and information regarding a covariance function. The objective of this work was the application of RRM in the study of the behavior of common bean cultivars using a MET, based on Legendre polynomials and genotype-ideotype distances. We used a set of 13 trials, which were classified as unfavorable or favorable environments. The results revealed that RRM enables the prediction of the genotypic values of cultivars in environments where they were not evaluated with high accuracy values, thereby circumventing the unbalanced of the experiments. From these values, it was possible to measure the genotypic adaptability according to ideotypes, according to their reaction norms. In addition, the stability of the cultivars can be interpreted as variation in the behavior of the ideotype. The use of ideotypes based on real data allowed a better comparison of the performance of cultivars across environments. The use of RRM in plant breeding is a good alternative to understand the behavior of cultivars in a MET, especially when we want to quantify the adaptability and stability of genotypes.

Selecting common bean breeding populations via mixe d models / Seleção de populações segregantes de feijão comum por meio de modelos mistos

Choosing breeding populations in a common bean (Phaseolus vulgaris L.) breeding program via recurrent selection is a crucial step since it maximizes the effort to find superior inbred lines. The application of the mixed models methodology (REML/BLUP) in predicting breeding values has shown good results in animal and perennial crops breeding programs. Conversely, studies on the application of this methodology to annual crops are still scarce. The present work aimed to use the REML/BLUP methodology to select breeding populations of a common bean breeding program via recurrent selection. Thirty-five F3populations were evaluated. Individual plants data were assessed for grain yield and hypocotyl diameter, and the genetic potential of the population was estimated via the mixed models and the Jinks and Pooni's methodologies. A selection index was applied to the selection among and within population, considering both characters simultaneously, using the population and individual BLUP means. REML/BLUP has shown to be afeasible methodology to predict and select the potential of breeding populations, considering more than one character. Selecting individual plants within population provides positive genetic gain estimates for both characters. BLUP breeding values are fundamental to the choice of the number of populations and single plants to be conducted in a common bean breeding program via recurrent selection.

Na cultura do feijoeiro (Phaseolus vulgaris L.), a escolha de populações segregantes em programas de melhoramento conduzidos por seleção recorrente é etapa crucial, uma vez que se aumenta a chance de extrair linhagens superiores. A aplicação da metodologia de modelos mistos (REML/BLUP) na predição de valores genéticos tem mostrado bons resultados em programas de melhoramento animal e de culturas perenes, enquanto que em culturas anuais, sua utilização ainda necessita resultados adicionais. O objetivo deste estudo foi utilizar a metodologia REML/BLUP na seleção de populações segregantes em um programa de melhoramento de feijoeiro por seleção recorrente. Trinta e cinco populações F3 foram avaliadas por meio de dados individuais de plantas quanto aos caracteres rendimento de grãos e diâmetro do hipocótilo. Os potenciais genéticos das populações foram estimados por meio da metodologia de modelos mistos e da metodologia de Jinks e Pooni. Um índice de seleção foi utilizado a fim de selecionar entre e dentro depopulações para ambos os caracteres simultaneamente, por meio do BLUP de populações e de indivíduo. A metodologia de modelos mistos mostrou-se viável para predizer o potencial de populações segregantes, bem como para selecionar tais populações, considerando mais de um caráter ao mesmo tempo. A seleção de plantas individuais permite estimativas de ganho genético positivas para ambos os caracteres. Os valores genéticos preditos são de grande importância em um programa de melhoramento por seleção recorrente, pois permiteescolher o número de populações e plantas individuais dentro de populações

Analysis of the adaptability of black bean cultivars by means of quantile regression / Análise da adaptabilidade de cultivares de feijão preto por meio de regressão quantílica

ABSTRACT: The aim of this study was to use quantile regression (QR) to characterize the effect of the adaptability parameter throughout the distribution of the productivity variable on black bean cultivars launched by different national research institutes (research centers) over the last 50 years. For this purpose, 40 cultivars developed by Brazilian genetic improvement programs between 1959 and 2013 were used. Initially, QR models were adjusted considering three quantiles (τ = 0.2, 0.5 and 0.8). Subsequently, with the confidence intervals, quantile models τ = 0.2 and 0.8 (QR0.2 and QR0.8) showed differences regarding the parameter of adaptability and average productivity. Finally, by grouping the cultivars into one of the two groups defined from QR0.2 and QR0.8, it was reported that the younger cultivars were associated to the quantile τ = 0.8, i.e., those with higher yields and more responsive conditions indicating that genetic improvement over the last 50 years resulted in an increase in both the productivity and the adaptability of cultivars.

RESUMO: Neste estudo objetivou-se utilizar a regressão quantílica (RQ) para caracterizar o efeito do parâmetro de adaptabilidade ao longo de toda a distribuição da variável produtividade em cultivares de feijão preto lançadas por diferentes instituições nacionais de pesquisa nos últimos 50 anos. Para tanto utilizou-se 40 cultivares desenvolvidas pelos programas brasileiros de melhoramento genético entre os anos de 1959 a 2013. Inicialmente foram ajustados modelos de RQ considerando três quantis (τ=0,2, 0,5, 0,8). Posteriormente, com os intervalos de confiança verificou-se que os modelos quantílicos τ=0,2 e 0,8 (RQ0,2 e RQ0,8) apresentaram diferenças quanto ao parâmetro de adaptabilidade e produtividade média. Finalmente, por meio do agrupamento das cultivares em um dos dois grupos definidos a partir de RQ0,2 e RQ0,8, constatou-se que as cultivares mais novas foram associadas ao quantil τ = 0,8, ou seja, aquelas com maiores produtividades e mais responsivas as condições ambientais indicando que o melhoramento ao longo dos últimos 50 anos possibilitou o incremento tanto na produtividade quanto na adaptabilidade das cultivares.

Genome prediction accuracy of common bean via Bayesian models / Acurácia de predição genômica em feijoeiro-comum via modelos Bayesianos

ABSTRACT: We aimed to apply genomic information based on SNP (single nucleotide polymorphism) markers for the genetic evaluation of the traits "stay-green" (SG), plant architecture (PA), grain aspect (GA) and grain yield (GY) in common bean through Bayesian models. These models were compared in terms of prediction accuracy and ability for heritability estimation for each one of the mentioned traits. A total of 80 cultivars were genotyped for 377 SNP markers, whose effects were estimated by five different Bayesian models: Bayes A (BA), B (BB), C (BC), LASSO (BL) e Ridge regression (BRR). Although, prediction accuracies calculated by means of cross-validation have been similar within each trait, the BB model stood out for the trait SG, whereas the BRR was indicated for the remaining traits. The heritability estimates for the traits SG, PA, GA and GY were 0.61, 0.28, 0.32 and 0.29, respectively. In summary, the Bayesian methods applied here were effective and ease to be implemented. The used SNP markers can help in the early selection of promising genotypes, since incorporating genomic information increase the prediction accuracy of the estimated genetic merit.

RESUMO: Objetivou-se incorporar informações genômicas de marcadores SNP ("single nucleotide polymorphism") na avaliação genética das características "stay-green" (SG), arquitetura de planta (AP), aspecto de grãos (AG) e produtividade de grãos (PG) em feijoeiro-comum via modelos Bayesianos. Estes modelos foram comparados quanto a acurácia de predição e habilidade de estimação da herdabilidade para cada característica. Utilizaram-se informações de 80 cultivares genotipadas para 377 marcadores SNP, cujos efeitos de substituição alélica foram estimados por meio de cinco diferentes modelos Bayesianos: Bayes A (BA), B (BB), C (BC), LASSO (BL) e regressão "ridge" (BRR). Embora as acurácias de predição calculadas por meio de análise de validação cruzada tenham sido similares dentro de cada característica, o modelo BB se destacou para a característica SG, enquanto o modelo BRR foi indicado para as demais. As herdabilidades estimadas para SG, AP, AG e PG foram, respectivamente, 0,61, 0,28, 0,32 e 0,29. Em resumo, os métodos contemplados mostraram-se efetivos e de fácil implementação. O conjunto de marcadores utilizado pode auxiliar na seleção precoce de genótipos promissores, uma vez que a incorporação de informações genômicas aumenta a acurácia de predição do mérito genético estimado.

Phenotypic and molecular characterization of sweet sorghum accessions for bioenergy production.

Sweet sorghum [Sorghum bicolor (L.) Moench] is a type of cultivated sorghum characterized by the accumulation of high levels of sugar in the stems and high biomass accumulation, making this crop an important feedstock for bioenergy production. Sweet sorghum breeding programs that focus on bioenergy have two main goals: to improve quantity and quality of sugars in the juicy stem and to increase fresh biomass productivity. Genetic diversity studies are very important for the success of a breeding program, especially in the early stages, where understanding the genetic relationship between accessions is essential to identify superior parents for the development of improved breeding lines. The objectives of this study were: to perform phenotypic and molecular characterization of 100 sweet sorghum accessions from the germplasm bank of the Embrapa Maize and Sorghum breeding program; to examine the relationship between the phenotypic and the molecular diversity matrices; and to infer about the population structure in the sweet sorghum accessions. Morphological and agro-industrial traits related to sugar and biomass production were used for phenotypic characterization, and single nucleotide polymorphisms (SNPs) were used for molecular diversity analysis. Both phenotypic and molecular characterizations revealed the existence of considerable genetic diversity among the 100 sweet sorghum accessions. The correlation between the phenotypic and the molecular diversity matrices was low (0.35), which is in agreement with the inconsistencies observed between the clusters formed by the phenotypic and the molecular diversity analyses. Furthermore, the clusters obtained by the molecular diversity analysis were more consistent with the genealogy and the historic background of the sweet sorghum accessions than the clusters obtained through the phenotypic diversity analysis. The low correlation observed between the molecular and the phenotypic diversity matrices highlights the complementarity between the molecular and the phenotypic characterization to assist a breeding program.

Adaptabilidade e estabilidade e a produtividade de grãos em cultivares de feijão preto recomendadas no Brasil nas últimas cinco décadas / Adaptability and stability and grain yield of black common bean cultivars used in Brazil in the last five decades

RESUMO:O objetivo deste trabalho foi estudar os parâmetros de adaptabilidade e estabilidade fenotípica e avaliar o incremento na produtividade de grãos em genótipos de feijão preto, desenvolvidos pelos programas brasileiros de melhoramento genético entre os anos de 1960 a 2013. Os experimentos foram realizados considerando 38 cultivares e duas linhagens em quatro ambientes (Coimbra e Viçosa nas safras da seca e de inverno de 2013), usando um delineamento em blocos casualizados com três repetições. Os resultados evidenciaram incremento efetivo na produtividade de grãos, proporcionado pela recomendação de novas cultivares pelos programas de melhoramento de feijão do Brasil nas últimas cinco décadas. Além disso, a análise da interação GxA indicou que as cultivares recomendadas após o ano de 2005 foram as que apresentaram conjuntamente altas produtividades de grãos, ampla adaptabilidade e alta previsibilidade de comportamento.

ABSTRACT:The objective of this research was to study the parameters of adaptability and phenotypic stability and estimate the increase in grain yield in black common bean genotypes developed by brazilian breeding programs between the years 1960-2013. The experiments were carried out considering 38 cultivars and two lines in four different environments (Coimbra and Viçosa cities, and dry and winter seasons of 2013 year) by using a randomized block design with three replications. Results showed an effective increasing of the grain yield provided by the recommendation of new cultivars from different Brazilian breeding programs in the past five decades. In addition, the GxE analysis interaction indicated that cultivars recommended after the year 2005 were those with high average grain yield, wide adaptability and high predictability.

Estabelecimento inicial de espécies de braquiária em consórcio com feijoeiro-comum, sob doses reduzidas de fluazifop-p-butyl / Initial establishment of brachiaria species in consortium with bean under reduced rates of fluazifop-p-butyl

Objetivando avaliar o estabelecimento inicial de duas espécies de braquiária em consórcio com o feijoeiro-comum, em função de doses reduzidas de fluazifop-p-butyl, foi conduzido experimento em diferentes épocas de semeadura. Os tratamentos foram dispostos em esquema fatorial, envolvendo duas espécies de braquiária (Brachiaria brizantha e B. decumbens) consorciadas com o feijoeiro-comum, e seis doses de fluazifop-p-butyl (0; 7,81; 15,62; 31,25; 62,50 e 125,00 g ha-1), além do monocultivo da braquiária. O delineamento experimental foi o de blocos casualizados, com quatro repetições. Os resultados obtidos permitiram concluir que na safra das águas a B. brizantha apresenta maior produção de biomassa em monocultivo do que em consórcio, sem o uso do fluazifop-p-butyl, enquanto a B. decumbens apresenta produção equivalente nas duas situações. Entretanto, na safra da seca, ambas as espécies de braquiária apresentam maiores produções em monocultivo do que em consórcio. Na safra da seca a utilização de doses a partir de 15,62 g ha-1 do herbicida causa prejuízo para o estabelecimento da pastagem até os 30 dias após a colheita do feijão, entretanto, com exceção da B. decumbens submetida a dose total do herbicida, a produção de biomassa da forrageira aos 150 dias após a colheita do feijão não é afetada pela aplicação do herbicida, em consórcio com o feijoeiro-comum. Na safra das águas pode-se aplicar até 125,00 ou 62,50 g ha-1 do herbicida no consórcio da B. brizantha ou B. decumbens com o feijoeiro-comum, respectivamente, alcançando produção satisfatória de biomassa aos 60 dias após a colheita do feijão.

In order to evaluate the initial establishment of two species of Brachiaria in consortium with common bean, due to reduced rates of fluazifop-p-butyl experiment was carried out at different planting dates. The treatments were arranged in a factorial design, involving two species (Brachiaria brizantha and B. decumbens) intercropped with common bean, and six doses of fluazifop-p-butyl (0; 7,81; 15,62; 31,25; 62,50 and 125,00 g ha-1), and the monoculture of Brachiaria. The experimental design was a randomized complete block with four replications. The results showed that in the rainy season B. brizantha presented higher biomass in monoculture than in intercropping without the use of fluazifop-p-butyl, while B.decumbens presents equivalent production in both situations. In the season of drought, both species have higher yields in monoculture than in the consortium. In the dry season using doses from 15,62 g ha-1 of the herbicide causes damage to the establishment of the pasture until 30 days after the bean harvest, however, with the exception of B. decumbens subjected to a total dose of the herbicide, biomass production of forage for 150 days after the bean harvest is not affected by herbicide application, in consort with the beans. In the rainy season can be applied up 125,00 or 62,50 g ha-1 of the herbicide in the consortium of B.brizantha or B. decumbens with common bean, respectively, achieving satisfactory production of biomass at 60 days after the bean harvest.

Efeito da época de semeadura de Brachiaria decumbens e de dessecantes em pré-colheita sobre o rendimento de grãos do feijoeiro e a biomassa forrageira em cultivo consorciado / Effect of sowing dates of Brachiaria decumbens and desiccant in pre-harvest on the yield of grain bean and forage biomass in intercropped system

Com o objetivo de avaliar a época de semeadura e os efeitos da dessecação da Brachiaria decumbens em consórcio com duas cultivares de feijão (Phaseolus vulgaris L.), foi conduzido um experimento, em Coimbra, MG, em esquema fatorial envolvendo cultivares de feijão (Ouro Vermelho e VC3), duas épocas de semeadura da braquiária (simultânea e na capina do feijão), três tipos de dessecação (sem dessecação, Carfentrazone-ethil e Paraquat), mais dois tratamentos adicionais: os monocultivos do feijão e da braquiária, em DBC com quatro repetições. O feijoeiro foi plantado com semeadora mecanizada, no espaçamento de 0,50 m entre linhas. A braquiária foi semeada com semeadora manual, sempre nas entrelinhas do feijoeiro. Foram avaliados o estande final de plantas e o rendimento de grãos do feijão e a biomassa seca da parte aérea da braquiária, aos 15 e aos 60 dias após a colheita do feijão. Concluiu-se que a cultivar Ouro Vermelho é mais indicada para o consórcio com B. decumbens na safra das águas que a VC3. O retardamento da semeadura da braquiária proporciona maior rendimento de grãos do feijão, mas prejudica a produção de biomassa seca da forrageira. A dessecação na pré-colheita não influencia a produtividade do feijoeiro, mas, quando é realizada com paraquat, prejudica a produção de biomassa seca da forrageira.

In order to evaluate different sowing dates and the effect of desiccation on Brachiaria decumbens intercropped with two beans cultivars (Phaseolus vulgaris L.), an experiment was conducted in Coimbra, MG in a factorial design involving two bean cultivars (Ouro Vermelho and VC3), two sowing dates (simultaneous and during bean weeding), three desiccation types (without desiccation, Carfentrazone-ethyl and Paraquat), plus two additional plantings of monoculture bean and brachiaria in DBC with four replications. The beans were seeded by mechanized planting with 0.50 m spacing between the rows. Brachiaria was sown by manual planting between the bean rows. We evaluated the final stand and grain yield of the beans, and the dry biomass of the brachiaria shoots, at 15 and 60 days after the bean harvest. It was concluded that the cultivar Ouro Vermelho was most suitable for intercropping with B. decumbens in the rainy season. Sowing brachiaria after weeding the beans increased the grain yield of the beans, but hindered the production of dry biomass in the brachiaria shoots. Pre-harvest desiccation does not influence the grain yield, but when performed with Paraquat it again hinders the production of dry biomass in brachiaria shoots.

Performance of common bean families after different generations under natural selection

A segregant bulk population derived from a single cross between the Carioca MG cultivar and the ESAL 686 line was used to investigate whether the action of natural selection in the direction required by the breeders and the delaying line extraction would increase the chance of obtaining families with greater grain yield. The populations were advanced from F2 to F24 and obtained families F2, F8 and F24 from the plants. These families and their parents were assessed for grain yield (kg/ha) in Lavras-MG in three sowing seasons (July 2001, November 2001 and March 2002) in an 18 x 18 lattice design with two replications in the first sowing and three in the other two. The largest mean yield, regardless of sowing season, was among the families derived from the F24 plants. The frequency of superior families increased when line extraction was delayed to more advanced generations.