Abstract: Enviromics is the field of applied data science that integrates databases of environmental factors into biostatistics and quantitative genetics. It can leverage plant ecophysiology knowledge to bridge the gaps about environment interactions with systems biology (genes, transcripts, proteins, and metabolites), which also boosts the ability to understand and model the phenotypic plasticity of the main agronomic traits. Recently, the plant breeding community has experienced reduced costs for acquiring environmental sensors to be installed in the field trials while increasing the reliability and resolution of the remote sensing techniques. The combination of those two factors has started the spring of enviromics-aided breeding in recent years. However, the use of environmental information in plant breeding is not a novelty approach developed a few years ago, but a core of efforts originated in the last 60 years, yet some basic ideas traced back to early 20th century attempts to establish a relationship between phenotypic and environmental variation. This review highlights the main concepts surrounding the construction of the “modern enviromics science”, tracing back to its origins in the last decades. Finally, we present how this field has helped integrate different data sources in prediction-based models or build one framework.

ABSTRACT New apps have changed the traditional way of learning and teaching; they are also applied as a quickly executed and effective method in agriculture. Soil-app is a web application with a friendly click-point interface built through packages lodged in R software. The app is an advanced model of an open-source platform to support teaching and learning activities in soil analyses and fertilizer recommendations. Soil-app includes soil test interpretation, soil amendment calculations (lime and gypsum), the fertilizer rate for the most important crops in Brazil, an NPK blend calculator, and NPK blend evaluation. It also includes experimental statistical analysis as applied to soil science. Soil-app is a user-friendly and high-performance tool, garnering fast adoption by both students and professionals. It is available for network use through the following link: http://www.genetica.esalq.usp.br/alogamas/R.html

RESUMO O estado do Paraná está entre os principais produtores de soja não só do Brasil, mas do Mundo. Contudo, apresenta variação edafoclimática considerável ao longo de sua área. Isso é uma das principais causas da interação genótipos por ambientes, dificultando o processo seletivo bem como a recomendação de cultivares no estado. Diante disso, objetivou-se com esse estudo: (i) identificar ambiente(s) que possibilite(m) representar as condições edafoclimáticas do estado do Paraná, visando facilitar o processo de seleção e recomendação de cultivares em futuros programas de melhoramento e (ii) identificar linhagens de soja estáveis e adaptadas a essas condições. Para isso, foram usados dados de ensaios no ano agrícola de 2013/2014 conduzidos com 24 linhagens de soja em 18 localidades distintas. Observou-se diferenças genotípicas entre as linhagens com um nível de acurácia de 0,93. Apesar das diferenças ambientais, foi possível explicar aproximadamente 70% da variação global dos dados com os três primeiros componentes principais. Com base das dispersões gráficas (biplots), constatou-se que a localidade de Record-PR foi a mais discriminante e representativa, enquanto que Iporã-PR propiciou menores produtividades de grãos entre as linhagens avaliadas. No geral, as linhagens 5, 9, 23 e 24 apresentaram boa adaptabilidade e estabilidade bem como elevadas produtividade de grãos.

ABSTRACT The state of Paraná is among the main producers of soybeans not only in Brazil, but in the World. However, it presents considerable edaphoclimatic variation throughout its area. This is one of the main causes genotype-by-environment interactions, hindering the selective process as well as the recommendation of cultivars in the state. Therefore, the objective of this study was: (i) to identify the environment that make it possible to represent the conditions of the state of Paraná, in order to facilitate the selection and recommendation of cultivars in future breeding programs; (2) to identify soybean inbres lines stable and adapted to state of Paraná. For this, data from trials in the agricultural year of 2013/2014 conducted with 24 soybeansinbred lines in 18 locations. Genotypic differences were observed with a level of accuracy of 0.93. Despite the environmental differences, it was possible to explain approximately 70% of the global variation of the data with the first three main components. Based on the biplots, it was verified that the locality of Record-PR was the most discriminant and representative, whereas Iporã-PR provided lower. In general, inbred lines 5, 9, 23 and 24 showed good adaptability and stability as well as high grain yield.

ABSTRACT The evaluation of segregating populations in plant breeding programs is an onerous and time-consuming process. Early identification of populations with genetic potential can be done by m + a methodology. However, the possibility of a modification in the traditional methodology in order to make it more efficient, that is, faster and cheaper, was envisaged. Thus, the objective of this study was to compare the genetic gains obtained by both methodologies, the traditional one and the proposed modification. For this, ten segregating bean-cowpea populations were evaluated at two distinct levels of homozygous F3:4 and F3:5. Genetic values were predicted by two different statistical genetic models. This was possible due to the methodology proposed here to present a much shorter execution time than the traditional methodology. Thus, with a shorter evaluation time, the breeding program manager can plan the evaluation of a larger number of populations in a short time.

ABSTRACT: Despite important biotic stresses to common bean, Anthracnose (ANT) and Angular Leaf Spot (ALS) can cause losses of up to 80 % and occur in more than 60 countries around the world. Genetic resistance is the most sustainable strategy to manage these diseases. Thus, we aimed to (1) identify new SNP markers associated with ALS and ANT resistance loci in elite common bean lines, and (2) provide a functional characterization of the DNA sequences containing the identified SNP markers. We evaluated 60 inbred lines, under field conditions, which represent the elite germplasm developed by the Embrapa common bean breeding program across 22 years, in terms of severity of the ALS and ANT. The lines were genotyped with 5,398 SNPs. Then, a Mixed Linear Model was run to determine the SNP-trait associations. We observed two-significant marker-trait associations reacting to ANT, both located on chromosome Pv-02. These markers explained 25 % of the phenotypic variation. For ALS, only one significant marker-trait association was observed, which is located in chromosome Pv-10 and explained 19 % of the phenotypic variation. These markers, along with others already used, will be useful to add or keep ANT and ALS resistance loci identified in this work in the new carioca and black seeded cultivars.

Resumo: O objetivo deste trabalho foi examinar a possibilidade de usar componentes de produção e caracteres reprodutivos, fisiológicos e de raiz na seleção precoce para eficiência de uso de nitrogênio (EUN) em milho. Foram avaliadas 64 linhagens em dois regimes de adubação nitrogenada: ideal e baixo. As avaliações foram feitas em três estádios fenológicos: oito folhas completamente expandidas, florescimento masculino e maturação fisiológica. É possível selecionar linhagens superiores quanto à EUN, mas os componentes de produção não tiveram comportamento diferencial sob os diferentes níveis de nitrogênio avaliados. Os caracteres radiculares, reprodutivos e fisiológicos não se mostraram confiáveis para seleção precoce de linhagens de milho com elevada EUN. De forma semelhante, os estádios de oito folhas e de florescimento masculino não se mostraram promissores para esse propósito, uma vez que, para a estimação da EUN, deve-se levar em consideração a produção de grãos. Entretanto, a seleção indireta para EUN pode ser feita via número de espigas ou com o uso de índice de seleção que considere número e peso de espigas.

Abstract: The objective of this work was to examine the possibility of using yield components and reproductive, physiological, and root traits in early selection for nitrogen use efficiency (NUE) in corn. Sixty-four inbred lines were evaluated under two nitrogen fertilization levels: ideal and low. The evaluations were performed at three phenological stages: eight fully-expanded leaves, tasseling stage, and physiological maturity. It is possible to select superior lines for NUE, but the yield components did not show differential behavior under the different nitrogen levels evaluated. Root, reproductive, and physiological traits are not promising for early selection of corn lines with high NUE. Likewise, the eight-leaves and tasseling stages were not promising for this purpose, since NUE should be estimated taking grain yield into account. However, indirect selection for NUE can be performed via number of ears or using the selection index considering number and weight of ears.

Abstract In order to successfully achieve the final goal of genotype selection in plant breeding programs, many aspects must be considered and carefully thought regarding cost, time, and efficiency. Thus, we have developed the Be-Breeder application to perform main biometric and statistical analyses using mixed and multivariate models. Implemented using the Shiny R package, this is one the first online platforms proposed in this context. Be-Breeder is available at http://www.genetica.esalq.usp.br/alogamas/R.html.

ABSTRACT Maize plants can be N-use efficient or N-stress tolerant. The first have high yields in favorable environments but is drastically affected under stress conditions; whereas the second show satisfactory yields in stressful environments but only moderate ones under optimal conditions. In this context, our aim was to assess the possibility of selecting tropical maize lines that are simultaneously N-stress tolerant and N-use efficient and check for differences between simultaneous selection statistical methods. Sixty-four tropical maize lines were evaluated for Nitrogen Agronomic Efficiency (NAE) and Low Nitrogen Tolerance (LNTI) response indices and two per se selection indices, Low Nitrogen Agronomic Efficiency (LNAE) and Harmonic Mean of Relative Performance (HMRP). We performed eight selection scenarios: LNAE; HMRP; Additive index; Mulamba-Mock index; and Independent culling levels. The last three was predicted by REML/BLUP single-trait and multi-trait using genotypic values of NAE and LNTI. The REML/BLUP multi-trait analysis was superior to the single-trait analysis due to high unfavorable correlation between NAE and LNTI. However, the accuracy and genotypic determination coefficient of NAE and LNTI were too low. Thus, neither single- nor multi-trait analysis achieved a good result for simultaneous selection nor N-use efficiency nor N-stress tolerance. LNAE obtained satisfactorily accurate values and genotypic determination coefficient, but its performance in selection gain was worse than HMRP, particularly in terms of N-use efficiency. Therefore, because of the superior performance in accuracy, genotypic determination coefficient and selection, HMRP was considered the best simultaneous selection methodology of the scenarios tested for N-use efficiency and N-stress tolerance.

RESUMO O Brasil apresenta uma demanda anual de mais de 2,83 milhões de toneladas de fertilizantes fosfatados. Parte disto se deve a baixa eficiência no uso do fósforo (EUP) pelas plantas, especialmente nos atuais cultivares de milho. Assim, objetivou-se foi elaborar índices que permitam a seleção acurada de genótipos de milho eficientes no uso de P para condições de baixa e alta disponibilidade deste nutriente. O experimento foi conduzido em casa de vegetação (20º45'14"S; 42º52'53"W), na Universidade Federal de Viçosa, em outubro de 2010. Foram avaliadas 39 combinações híbridas experimentais e 14 linhagens de milho, divergentes para a eficiência no uso de P, em duas condições de disponibilidade deste nutriente. Foi realizada a análise de importância relativa dos caracteres estudados, estimada por meio do método dos componentes principais, a análise de fatores e confecção dos índices de seleção. Para obtenção de genótipos responsivos a alta disponibilidade de fósforo é recomendado o índice ISAP = 0,3985 MRS + 0,3099 MPS + 0,5567 CRLAT + 0,2340 EAbP - 0,1139 SER. Para obtenção de genótipos tolerantes a baixa disponibilidade deste nutriente é sugerido o índice ISBP = 0,3548 MRS + 0,3996 CRLAT + 0,3344 MSP + 0,0041 PA/SR - 0,1019 SER.

ABSTRACT Brazil generates an annual demand for more than 2.83 million tons of phosphate fertilizers. Part of this is due to low P use efficiency (PUE) by plants, particularly in current maize cultivars. Thus, the aim of this study was to create indexes that allow accurate selection of maize genotypes with high PUE under conditions of either low or high P availability. The experiment was conducted in a greenhouse (20º45'14"S; 42º52'53"W) at the Universidade Federal de Viçosa in October 2010. We evaluated 39 experimental hybrid combinations and 14 maize inbred lines with divergent PUE under two conditions of P availability. The relative importance of the traits studied was analyzed and estimated by principal component analysis, factor analysis, and establishment of selection indexes. To obtain genotypes responsive to high P availability, the index SIHP (selection index for high phosphorus) = 0.3985 RDM + 0.3099 SDM + 0.5567 RLLAT + 0.2340 PUEb - 0.1139 SRS is recommended. To obtain genotypes tolerant to low P availability, the index SILP (selection index for low phosphorus) = 0.3548 RDM + 0.3996 RLLAT + 0.3344 SDM + 0.0041 SH/RS - 0.1019 SRS is suggested.

Abstract Be-Breeder is an application directed toward genetic breeding of plants, developed through the Shiny package of the R software, which allows different phenotype and molecular (marker) analysis to be undertaken. The section for analysis of molecular data of the Be-Breeder application makes it possible to achieve quality control of genotyping data, to obtain genomic kinship matrices, and to analyze genome selection, genome association, and genetic diversity in a simple manner on line. This application is available for use in a network through the site of the Allogamous Plant Breeding Laboratory of ESALQ-USP (http://www.genetica.esalq.usp.br/alogamas/R.html).

RESUMO O nitrogênio é indispensável à manutenção da vida no planeta, sendo o mais importante nutriente para a obtenção de elevadas produções agrícolas. No entanto, a sua utilização ocasiona a liberação de óxido nitroso, com potencial de aquecimento global 296 vezes maior que a molécula de CO2, tornando-se um grande desafio a redução de seu uso na agricultura. O objetivo desta pesquisa foi identificar linhagens de milho-pipoca eficientes e responsivas no uso de nitrogênio e que apresentem um elevada capacidade de expansão. Para isto, avaliaram-se 29 linhagens da Coleção de Germoplasma da Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF) em dois níveis contrastantes de nitrogênio (baixo e ideal) em dois locais representativos do Norte e Noroeste do Estado do Rio de Janeiro, Brasil, arranjadas no delineamento em blocos casualizados com três repetições. Estas linhagens foram discriminadas em relação a eficiência no uso do nitrogênio pela técnica multivariada GGE Biplot. A acurácia seletiva foi próxima de 1, revelando que os genótipos foram suficientes contrastantes para proporcionar sucesso em procedimentos seletivos. Os dois primeiros componentes principais (CP) retiveram 93,82% da variação total, sendo que o CP1 expressou relação de informação (IR) não impactada por ruídos. L77 foi a linhagem mais instável, enquanto P7, P2, P6, P3, P5, P4, P9, P10, P8, P9, L70, L74 e L55 foram eficientes e responsivas. Recomenda-se o método GGE Biplot na identificação fidedigna de linhagens de milho-pipoca eficientes e responsivas ao uso do nitrogênio.

ABSTRACT Nitrogen is essential for sustaining life on the planet, and it is the most important nutrient for obtaining high agricultural production. However, their use leads to the release of nitrous oxide with a global warming potential 296 times higher than the CO2 molecule, making it a challenge to reduce their use in agriculture. The objective of this research was to identify efficient popcorn inbred lines and responsive nitrogen use and exhibit a good expansion volume. For this, 29 inbred lines from the Germplasm Collection of Darcy Ribeiro North Fluminense State University (UENF) were evaluated at two contrasting levels of nitrogen availability (low and ideal) at two representative locations in the north and northwest of the state of Rio de Janeiro, Brazil, arranged in a randomized block design with three replicates. These inbred lines were discriminated against efficient use of nitrogen by multivariate GGE Biplot. Selective accuracy was close to 1, showing that the genotypes were enough to provide contrasting success in selection procedures. The first two main components (PC) retained 93.82% of the total variation, and PC1 furnished an information ratio (IR) that was unaffected by noise. L77 was the most unstable line, while P7, P2, P6, P3, P5, P4, P9, P10, P8, P9, L70, L74, and L55 were efficient and responsive. The GGE biplot method is recommended for the reliable identification of popcorn lines that are efficient and responsive to the use of nitrogen.

Abstract The Be-Breeder application is an on-line tool constructed through the R software for the purpose of assisting in some of the main genetic and statistical analyses related to the area of plant breeding. In addition, Be-Breeder provides a section called "Learning", which in a simple click-point manner allows explanation of theories related to the effect of inbreeding, population structure, qualitative and quantitative traits, heterosis, population size, effect of selection, and composition of hybrids. Be-Breeder is available for network use on the website of the Allogamous Plant Breeding Laboratory (Laboratório de Melhoramento de Plantas Alógamas) of ESALQ-USP through the link: http://www.genetica.esalq.usp.br/alogamas/R.html.

Vários trabalhos de avaliação de eficiência no uso de nitrogênio (EUN) já foram feitos utilizando estádios precoces. Contudo, não há relatos científicos sobre o estádio ideal e, neste, quais caracteres que apresentam maior correlação com a EUN. Assim, o objetivo foi identificar os estádios fenológicos e os caracteres secundários que maximizam a acurácia na seleção precoce e indireta para a EUN em milho. Para isso, foram avaliadas três linhagens endogâmicas de milho em delineamento inteiramente casualizado, com cinco repetições, em esquema fatorial triplo (linhagens x níveis de N x estádio fenológico), em duas doses contrastantes de nitrogênio - baixo e alto nitrogênio. As plantas foram avaliadas em cinco estádios fenológicos sendo eles: nove (V9) e 14 folhas completamente desenvolvidas (V14), pendoamento (VT), florescimento (R1) e maturidade fisiológica (R6). Foram avaliados os caracteres: eficiência na utilização, na absorção, no uso e na translocação de nitrogênio, atividade da nitrato redutase e da glutamina sintetase, comprimento de raiz lateral e axial, área de raiz específica, teor de clorofila, número de folhas, altura de planta, diâmetro de colmo, teor de fósforo e potássio. Considerando os ganhos diretos e indiretos estimados, conclui-se que as atividades da glutamina sintetase, nos estádios V9 e V14, permitem a seleção precoce e indireta para eficiência no uso de nitrogênio em milho, nas condições de baixa e alta disponibilidade de N, respectivamente.

Several studies to evaluate nitrogen use efficiency (NUE) have been carried out using early growth stages. However, there are no scientific reports on the ideal stage for evaluation and on which characteristics have the highest correlation with the NUE at that stage. The aim therefore was to identify the phenological stages and secondary characteristics which maximize accuracy in early indirect selection for NUE in maize. To do this, three endogamic maize strains were evaluated in a completely randomised design with five replications, in a triple factorial scheme (strains x N levels x phenological stage), at two contrasting nitrogen levels: low and high nitrogen. The plants were evaluated at five growth stages: stage nine (V9), with 14 fully-developed leaves (V14), tasseling (VT), flowering (R1) and physiological maturity (R6). The following characteristics were evaluated: efficiency in the usage, absorption, use and translocation of nitrogen; activity of nitrate reductase and glutamine synthetase; length of the lateral and axial roots; specific root area; chlorophyll content; number of leaves; plant height; stem diameter; and the levels of phosphorus and potassium. Considering the estimated direct and indirect gains, it can be concluded that the activities of glutamine synthetase at the V9 and V14 stages permit early indirect selection for nitrogen use efficiency in maize under conditions of low and high N availability respectively.

Objetivou-se com este trabalho comparar o sistema de produção de milho, recomendado nos anos 40, com o atualmente empregado. Para isso, utilizou-se como base o artigo publicado por Antônio Secundino de São José, na Revista Ceres, em 1944, comparando-se as práticas agrícolas recomendadas para a cultura do milho na época com as atualmente empregadas. Naquela época, não havia preocupação direta com os aspectos conservacionistas de solo e água. Todavia, iniciava-se o processo de elevação da produtividade de grãos, com base no uso de mais insumos, todos obtidos na propriedade, como o esterco bovino, e de obtenção das próprias sementes. A cultura do milho era tratada de maneira individualizada, sem os conceitos de integração de lavoura, pecuária e conservação de solo e água. Atualmente, muitos conceitos recomendados há 70 anos ainda são utilizados na agricultura orgânica e familiar. Por outro lado, no cultivo em grande escala da cultura do milho utilizam-se os mais variados insumos, como fertilizantes sintéticos, herbicidas, inseticidas, sementes de híbridos (com ou sem eventos transgênicos), aplicação de fungicidas, plantio e colheita mecanizados. Conclui-se que nos últimos 70 anos ocorreram muitas mudanças no sistema de produção de milho e que estas mudanças foram fundamentais para que a produtividade aumentasse 3,79 vezes no período analisado. Todo o sistema de produção foi modificado em relação aos fatores de construção e proteção da produtividade, que por sua vez, deram suporte para que o Brasil chegasse a posição de terceiro maior produtor e exportador de milho do mundo, saltando de 5,6 milhões de toneladas em 1944 para 81,5 milhões de toneladas em 2013.

The objective of this work was to compare the maize production system recommended in the decade of 1940 with the system currently employed in Brazil. We used the paper published by Antônio Secundino de São José at Revista Ceres in 1944 to compare the agricultural practices used at that time with the ones currently employed. In the 40's, we found no direct concern with aspects of soil and water conservation. However, the process of raising grain yield based on the use of more on-farm inputs , such as manure and seeds, was initiated at that time. The maize crop was treated as a sole enterprise without the concepts of integrating crop-livestock and soil and water conservation. Currently, many concepts recommended 70 years ago are still on use in the organic and smallholder farming systems. On the other hand, the large-scale maize cultivation have used a large number of varied inputs such as synthetic fertilizers, herbicides, insecticides, fungicides, hybrid seeds (transgenic or not), planting and harvesting machinery. We conclude from the literature reviewed that in the last 70 years many chances have occurred in maize production system which were essential for the productivity to have increased 3.79 times in the period analyzed. The entire production system was modified in relation to the construction and protection of productivity, which in turn, gave support to Brazil to become the third-largest world producer and exporter of maize, increasing from 5.6 million tons in 1944 to 81.5 million tons in 2013.

As limitações do N no cultivo do milho relacionam-se ao fato de a eficiência da adubação nitrogenada no milho não ultrapassar os 50%, principalmente devido aos processos de perda por volatilização, desnitrificação ou lixiviação no solo. Nesse contexto, torna-se importante o desenvolvimento de cultivares eficientes no uso de N (EUN). Assim, o objetivo foi elaborar índices que permitissem a seleção acurada de genótipos de milho eficientes no uso de nitrogênio para as condições de alta e baixa disponibilidade desse nutriente. O experimento foi conduzido em casa de vegetação na Universidade Federal de Viçosa (20º45'14''S; 42º52'53''W) durante o mês de outubro de 2010. Foram avaliadas 39 combinações híbridas experimentais e 14 linhagens de milho divergentes para a eficiência no uso de N em duas condições de disponibilidade desse nutriente. Foram realizadas a análise de importância relativa dos caracteres estudados, estimada por meio do método dos componentes principais, a análise de fatores e a confecção dos índices de seleção. A seleção indireta e precoce para genótipos de milho tropical pode ser realizada por meio dos índices I AN = 0,022 MPS + 0,35 PASR + 0,35 CR AXI + 0,35 EUN, para ambientes de alta disponibilidade de nitrogênio, e I BN = -0,06 PSAR + 0,35 AS AXI + 0,35 CR AXI + 0,39 MPS, para condições de baixa disponibilidade de nitrogênio.

Nitrogen (N) limitation in maize crops is related to the fact that the efficiency of nitrogen fertilization in maize does not exceed 50%, primarily due to volatilization, denitrification and soil leaching. Therefore, the development of new nitrogen use efficient (NUE) cultivars is necessary. The aim of the present study was to develop indices for the accurate selection of NUE maize genotypes for use in conditions of both high and low N availability. The experiment was conducted in a greenhouse (20º45'14"S; 42º52'53"W) at the Federal University of Viçosa during October 2010. A total of 39 experimental hybrid combinations and 14 maize lines differing in NUE were evaluated under two N availability conditions. We determined the relative importance of the studied characters using principal component analysis, factor analysis and by developing efficient selection indices. We conclude that indirect and early selection of tropical maize genotypes can be performed using the indices I HN = 0.022 SDM + 0.35 RSDM + 0.35 RL A + 0.35 NUE for high N availability environments and I LN = -0.06 RSDM + 0.35 RSA A + 0.35 RL A + 0.39 SDM for low N availability environments.