Initial performance and genetic diversity of coffee trees cultivated under contrasting altitude conditions

This work evaluated the initial performance and genetic diversity of Coffea canephora genotypes cultivated in environments at contrasting altitudes. Fourteen morphophysiological traits and seven descriptors of the genus Coffea spp. of coffee trees cultivated at altitudes of 140 m and 700 m were evaluated. The design used was Federer's augmented block in a 2 × 112 factorial scheme with six blocks. The first factor was the two environments, and the second was the 112 genotypes, with eight common treatments, being five conilon coffee clones and three arabica coffee cultivars. The data were analyzed by the method of REML/BLUP and genetic correlation method. Genetic diversity was evaluated by estimating the distance matrix, applying the Gower methodology followed by the clustering method by Tocher and UPGMA. The phenotypic means were higher in the environment at an altitude of 700 m, except for plant height, number of leaves, and canopy height (CH). Genotypic effects were significant for most traits except for leaf width, CH, unit leaf area, and total leaf area. A wide genetic diversity was verified, with distances varying from 0.037 to 0.593 for the pairs of genotypes 26 × 93 and T7 × 76, respectively. Most of the traits studied showed high genotypic correlation with the environment and expressive genetic correlation between the evaluated traits thereby demonstrating the possibility of indirect selection. There is an adaptation of conilon coffee genotypes to high altitudes and the possibility of developing a specific cultivar for the southern state of Espírito Santo.

Coffee crops adaptation to climate change in agroforestry systems with rubber trees in southern Brazil

Adaptation to climate change is a strategy for crops to cope with the scenario of rising temperatures worldwide. In the case of Coffea arabica L., the use of agroforestry systems (AFS) with woody species is a promising practice to reduce excessive heat during the day. This study aimed to 1) evaluate air temperature changes that occur in an AFS of coffee and double alleys of rubber trees (Hevea brasiliensis Müell. Arg.) and 2) carry out an analysis of future warming scenarios by comparing the cultivation of Arabic coffee in full sun and in an AFS of double alleys of rubber trees. The microclimatic variables were measured between two rows of coffee trees at 1.0 m of height from June 2016 to June 2018. The results indicate that the AFS with double alleys of rubber trees spaced 16 m apart had an average temperature reduction from 1.4 to 2.5 °C from 10h00 to 16h00. The study also simulated temperature increases of 1.7, 2.6, 3.1, and 4.8 °C from 2018 to 2099, according to scenarios predicted by the Intergovernmental Panel on Climate Change (IPCC), and the impact in coffee production in Paraná State, Brazil. Using the climatic generator PGECLIMA_R, simulations suggest a progressive reduction of traditional areas suitable for open-grown coffee in the state. Production conditions can be maintained through the AFS, since the systems attenuate mean temperatures by 1-2 °C. We conclude that the AFS of coffee and rubber trees contribute to coffee crop adaptations to a future warmer environment.

Commercial characteristics of coffee seedlings produced with different sources of phosphorus and plant growth-promoting bacteria / Características comerciais de mudas de café produzidas com diferentes fontes de fósforo e bactérias promotoras de crescimento de plantas

Considered the economic engine of many countries, the coffee culture represents an important component of the agricultural chain in Brazil. The growing values of commercialization, planting areas, and crop productivity require the acquisition of quality seedlings, which must receive adequate nutritional support through efficient fertilizers. Slow and controlled-release fertilizers, such as organominerals, gain prominence when it comes to increasing efficiency in the use of phosphorus, as well as plant growth-promoting bacteria (PGPB) with phosphate solubilizing characteristics. This study aimed to evaluate the effect of different sources of mineral and organomineral fertilizers, inoculated and non-inoculated with PGPB on the quality parameters of coffee seedlings. In general, the P sources used in the experiment positively interfered with the development of coffee seedlings. This proves that there is a need for nutritional supplementation for the good development of the seedlings. Among the sources used, the organomineral in granulated form showed better performance in coffee seedlings' growth and physiological parameters, proving to be a viable alternative to commonly used fertilizers. The addition of PGPB showed a significant advantage for seedling quality variables.

Considerado o motor econômico de muitos países, a cultura do café representa um importante componente da cadeia agrícola no Brasil. Os crescentes valores de comercialização, das áreas de plantio e da produtividade da cultura requerem aquisição de mudas de qualidade, que devem receber adequado aporte nutricional através do uso eficiente de fertilizantes. Fertilizantes de liberação lenta e controlada, a exemplo dos organominerais, ganham destaque quando se trata de aumento da eficiência no uso do fósforo, assim como as bactérias promotoras de crescimento de plantas (BPCP) com características solubilizadoras de fosfato. Esse estudo teve como objetivo avaliar o efeito de diferentes fontes de fertilizantes mineral e organomineral, inoculados e não inoculados com BPCP, sobre parâmetros de qualidade de mudas de café. De forma geral, as fontes de P utilizadas no experimento interferiram positivamente no desenvolvimento das mudas de café. Isso comprova que existe a necessidade de complementação nutricional para um bom desenvolvimento das mudas. Dentre as fontes utilizadas, o organomineral na forma granulada apresentou melhor desempenho nos parâmetros de crescimento e fisiológicos das mudas de café, mostrando ser uma alternativa viável aos fertilizantes comumente utilizados. A adição de BPCP apresentou vantagem significativa para as variáveis de qualidade das mudas.

Phosphorus sources in the growth and quality of arabica coffee seedlings produced in tubes / Fontes de fósforo no crescimento e qualidade de mudas de café arábica produzidas em tubetes

The objective of this study was to evaluate the growth and quality of arabica coffee seedlings produced in tubes under different sources of phosphorus (P). The experiment was conducted in a greenhouse in a randomized block design with ten treatments (control, Osmocote®, three doses of pelleted organomineral, three doses of mashed organomineral, MAP, coated MAP) and four replications, three plants per plot. The dose of organomineral, MAP, and MAP coated was based on the recommendation of P2O5for the formation of coffee seedlings.For Osmocote®, the manufacturer's recommendation was used depending on the amount, in dm³, of substrate. After 180 days of transplanting, the growth characteristics of the plants (leaf dry matter, stem, and roots) were evaluated, and the aerial part and root system ratio and Dickson's quality index were calculated, as well as regression equations were adjusted for the evaluated parameters. For the growth and quality of seedlings, it was observed that in fertilizations with pelleted and branched organomineral, coated MAP and Osmocote®, the highest averages were obtained for the contents of dry matter, height, diameter of the collection and quality indexes, when compared to the other sources of P2O5.The dose that provides the maximum growth and quality of coffee seedlings for the treatments with organomineral was calculated, this being equal to 6 g/dm³ of P2O5for bran and pelleted organomineral. According to the results, the sources that promoted the formation of a vigorous seedling, with an adequate supply of nutrients and a good quality standard are pelleted organonineral fertilization and MAP, reducing the risk of losses and consequently the need to discard the seedlings in the nursery.(AU)

O objetivo deste estudo foi avaliar o crescimento e a qualidade de mudas de café arábica produzidas em tubetes sob diferentes fontes de fósforo(P). O experimento foi conduzido em casa de vegetação em delineamento de blocos casualizados com dez tratamentos(controle, Osmocote®, três doses de organomineral peletizado, três doses de organomineral farelado, MAP, MAP revestido)e quatrorepetições, três plantas por parcela. A dose de organomineral, MAP e MAP revestidofoi baseada na recomendação de P2O5para a formação de mudas de café. Para Osmocote®, foi utilizada a recomendação do fabricante emfunção da quantidade, em dm³, de substrato. Após 180 dias do transplante, foram avaliadas as características de crescimento das plantas (matéria seca de folhas, caule e raízes), calculadas a razão parte aérea e sistema radicular e o índice de qualidade de Dickson, bem como ajustadas equações de regressão para os parâmetros avaliados. Para o crescimento e qualidade das mudas, observou-se que nas adubações com organomineral peletizado e farelado, MAP revestido e Osmocote®, as maiores médias para os teores de matéria seca, altura, diâmetro da coletae índices de qualidade, quando comparados as outras fontes de P2O5.Foi possível identificara dose que proporciona o máximo crescimento e qualidade de mudas de café para os tratamentos com organomineral, sendo esta igual a 6 g/dm³ de P2O5para o organomineral farelado e peletizado. De acordo com os resultados, as fontes que promoveram a formação de uma muda vigorosa, com aporte adequado de nutrientes e um bom padrão de qualidade são a adubação organomineral peletizada e MAP, reduzindo o risco de perdas e consequentemente a necessidade de descarte das mudas no viveiro.(AU)

Detection of coffee fruits on tree branches using computer vision

Coffee farmers do not have efficient tools to have sufficient and reliable information on the maturation stage of coffee fruits before harvest. In this study, we propose a computer vision system to detect and classify the Coffea arabica (L.) on tree branches in three classes: unripe (green), ripe (cherry), and overripe (dry). Based on deep learning algorithms, the computer vision model YOLO (You Only Look Once), was trained on 387 images taken from coffee branches using a smartphone. The YOLOv3 and YOLOv4, and their smaller versions (tiny), were assessed for fruit detection. The YOLOv4 and YOLOv4-tiny showed better performance when compared to YOLOv3, especially when smaller network sizes are considered. The mean average precision (mAP) for a network size of 800 × 800 pixels was equal to 81 %, 79 %, 78 %, and 77 % for YOLOv4, YOLOv4-tiny, YOLOv3, and YOLOv3-tiny, respectively. Despite the similar performance, the YOLOv4 feature extractor was more robust when images had greater object densities and for the detection of unripe fruits, which are generally more difficult to detect due to the color similarity to leaves in the background, partial occlusion by leaves and fruits, and lighting effects. This study shows the potential of computer vision systems based on deep learning to guide the decision-making of coffee farmers in more objective ways.

Influence of nitrogen fertilization in mother plants on the growth and quality of clonal seedlings of Coffea canephora 'Robusta' plants / Influência da fertilização com nitrogênio em plantas matrizes no crescimento e na qualidade de mudas clonais de plantas Coffea canephora 'Robusta'

The nutritional management of the coffee clonal garden influences the production and physiological quality and seedlings production of vegetative propagules. Thus, this study aimed to analyze the seedlings' production from clonal cuttings taken from Coffea canephora mother plants grown with increasing nitrogen mineral doses. The cuttings were taken from C. canephora var. botany Robusta, from the Embrapa Genetic Improvement Program of Rondônia. The mother plants received nitrogen fertilizer at different doses: 0 (Control); 50; 100; 150; 200; 250 and 300 kg of N per hectare divided into 4 applications, during 150 days of orthotropic stems growth (shoots). The following parameters were evaluated: Dry mass of cuttings, nutritional content of cuttings, and seedlings production, with growth analysis at 0, 48, 61, 80, 101, 122, 143, and 164 days after staking (DAS) and analysis of vegetative characteristics at 122 DAS. The nitrogen fertilization in the mother plant resulted in the variation of macronutrient accumulation in cuttings, but the order K> N> Ca> P> Mg> S was maintained, regardless of N dose. In addition, a positive correlation between nitrogen doses and dry matter accumulation, as well as the physiological quality of seedlings was identified.

O manejo nutricional do jardim clonal de cafeeiros influencia a produção e qualidade fisiológica dos propágulos vegetativos e na produção de mudas. Assim, objetivou-se analisar a produção de mudas a partir de estacas clonais retiradas de plantas matrizes de Coffea canephora cultivada com doses crescentes de nitrogênio mineral. As estacas foram retiradas de plantas matrizes de cafeeiros C. canephora var. botânica Robusta, do Programa de Melhoramento Genético da Embrapa-RO. As plantas matrizes receberam adubação nitrogenada nas doses: 0 (Controle); 50; 100; 150; 200; 250 e 300 kg de N por hectare, parceladas em quatro aplicações, durante 150 dias de crescimento das hastes ortotrópica (brotos). Os seguintes parâmetros foram avaliados: massa seca das estacas, conteúdo nutricional das estacas e a produção de mudas, com análise de crescimento, aos zero, 48, 61, 80, 101, 122, 143 e 164 dias após o estaqueamento (DAE) e a análise das características vegetativas, aos 122 DAE. A adubação nitrogenada na planta matriz resultou na variação do acúmulo de macronutrientes nas estacas, mas a ordem K > N > Ca > P > Mg > S foi mantida independente da dose de N. Além disso, foi verificado que há correlação positiva entre as doses de nitrogênio e o acúmulo de massa seca, assim como, a qualidade fisiológica das mudas.

Applying different infective structures of Beauveria bassiana to Coffea arabica infested with Hypothenemus hampei (Coleoptera: Curculionidae) under field

Coffee is the most appreciated beverage in worldwide; Brazil is the largest producer and exporter of this commodity. Organochlorine endosulfan was banned from the country in 2013 due to its teratogenic agent-related features. Since then, coffee plantations have experienced increased Hypothenemus hampei infestation rates. The aim of the current study is to assess variations in the rates of Coffea arabica fruits brocaded by H. hampei after the application of entomopathogenic fungal species Beauveria bassiana IBCB66. Experiments were carried out with 'Catuaí' and 'Mundo Novo' cultivars between 2018 and 2020, during the borer transit period. Three experiments were carried out based on the application of the aforementioned fungal species on the investigated coffee plant species, both by spraying and sprinkling, at 30-day intervals; 10 fruits were collected per face of each useful plant in each repetition. The experiment has followed a randomized blocks design with five treatments, including the control, and five repetitions, each. Beauveria bassiana Ecobass (IBCB66) wettable powder spray, at the concentration of 2 × 1013·ha­1, was used in experiments I and II. On the other hand, the mix used in experiment III was prepared with blastospores at concentration of 5 × 1012·ha­1 blastospores + 0.1% Silwet. The sprinkling process in all three experiments has used dry aerial conidia at concentration of 2 × 1013·ha­1. Collected data were subjected to analysis of variance (ANOVA), which was followed by Fisher's test at 5% probability level, in the SISVAR software. More than 35,000 fruits were assessed. In addition to variations between experiments, results have evidenced that the rate of brocaded fruits remained high.

First record of Psocodea (Psocoptera) on coffee (Coffea canephora) in the Brazilian Amazon (Rondônia state) / Primeiro registro de Psocodea ('Psocoptera') em café (Coffea canephora) em Rôndonia, na Amazônia brasileira

There is much information regarding the association of Psocoptera and coffee as stored grain pests and little is known about their presence in coffee plants. We conducted a survey in a coffee plantation of Coffea canephora in the municipality of Candeias do Jamari, Rondônia state, Brazil, where we obtained the first record of a coffee plant as a host of Psocoptera in the Brazilian Amazon region, and the first record of a representative of the family Archipsocidae (Archipsocus lenkoi) for the state of Rondônia. The psocid population was concentrated and not evenly distributed over the survey area, which indicates an irregular distribution pattern. We have not detected damage or injury to the coffee plants and therefore we cannot consider these psocids as a pest in the coffee plantation.(AU)

Há muita informação sobre a associação de Psocoptera e café como peste em grãos armazenados, mas pouco se sabe sobre sua presença nas plantas do café. Nós realizamos uma amostragem em uma plantação de café de Coffea canephora no município de Candeias do Jamari, Rondônia, onde obtivemos o primeiro registro de uma planta de café como hospedeira de Psocoptera na Amazônia brasileira e o primeiro registro de um representante da família Archipsocidae (Archipsocus lenkoi) para o estado de Rondônia. A população de psocídeos estava concentrada e não distribuída uniformemente na área de amostragem, o que indica um padrão de distribuição irregular. Não detectamos danos ou injúrias nas plantas de café e, portanto, não podemos considerar esses psocídeos como uma praga na plantação de café.(AU)

Different nitrogen levels on vegetative growth and yield of conilon coffee (Coffea canephora) / Efeitos de diferentes níveis de nitrogênio sobre o crescimento vegetativo e produtividade do café conilon (Coffea canephora)

The determination of nitrogen in plants by techniques that allow a fast diagnosis, based on plant growth characteristics, can be a useful tool for the nutritional management of coffee plants. Thus, this study evaluated growth and yield characteristics of irrigated conilon coffee in response to different nitrogen levels, resulting in the determination of the minimum N levels required to achieve the maximum yield, here called critical levels. The experiment was carried out in Colatina, Espirito Santo, Brazil, on plantations of conilon coffee, clonal variety Emcapa 8111, genotype 02. Six nitrogen levels were applied (0, 110, 220, 440, 880 and 1320 kg N ha-1) and the response in growth and yield characteristics periodically evaluated. There was a positive effect of the increasing N levels on yield, in that the N levels that provided 95% of the maximum yield (137.4 bags ha-1 and 108.5 bags ha-1) in the 2012/2013 and 2013/2014 growing seasons, respectively, were 420.7 and 543.1 kg N ha-1. There was also a positive effect of N levels on the growth characteristics and nitrogen contents, indicating their use as tools for a rapid nutritional diagnosis, with a view to optimizing the nitrogen management in Conilon coffee.

A determinação do nitrogênio nas plantas por técnicas que permitem um diagnóstico rápido, baseado nas características de crescimento das plantas, pode ser uma ferramenta útil para o manejo nutricional das plantas de café. Assim, o objetivo deste estudo foi avaliar as características de crescimento e rendimento do café conilon irrigado em resposta à diferentes níveis de nitrogênio, resultando na determinação dos níveis mínimos de N necessárias para atingir o rendimento máximo, aqui chamadas de níveis críticos. O experimento foi realizado em Colatina, Espírito Santo, Brasil, em plantações de café conilon, variedade clonal Emcapa 8111, genótipo 02. Foram aplicados seis níveis de nitrogênio (0, 110, 220, 440, 880 e 1320 kg N ha-1) e a resposta em características de crescimento e rendimento foi periodicamente avaliada. Houve um efeito positivo do aumento dos níveis de N sobre o rendimento, na medida em que os níveis de N que forneceram 95% do rendimento máximo (137,4 sacos ha-1 e 108,5 sacos ha-1) nas estações de crescimento 2012/2013 e 2013/2014, respectivamente, foram de 420,7 e 543,1 kg de N ha-1. Houve também um efeito positivo dos níveis de N sobre as características de crescimento e conteúdo de nitrogênio, indicando seu uso como ferramentas para um diagnóstico nutricional rápido, com o objetivo de otimizar o manejo de nitrogênio no café Conilon.

Bayesian modeling of the coffee tree growth curve / Modelagem bayesiana da curva de crescimento do cafeeiro

When modeling growth curves, it should be considered that longitudinal data may show residual autocorrelation, and, if this characteristic is not considered, the results and inferences may be compromised. The Bayesian approach, which considers priori information about studied phenomenon has been shown to be efficient in estimating parameters. However, as it is generally not possible to obtain marginal distributions analytically, it is necessary to use some method, such as the weighted resampling method, to generate samples of these distributions and thus obtain an approximation. Among the advantages of this method, stand out the generation of independent samples and the fact that it is not necessary to evaluate convergence. In this context, the objective of this work research was: to present the Bayesian nonlinear modeling of the coffee tree height growth, irrigated and non-irrigated (NI), considering the residual autocorrelation and the nonlinear Logistic, Brody, von Bertalanffy and Richard models. Among the results, it was found that, for NI plants, the Deviance Information Criterion (DIC) and the Criterion of density Predictive Ordered (CPO), indicated that, among the evaluated models, the Logistic model is the one that best describes the height growth of the coffee tree over time. For irrigated plants, these same criteria indicated the Brody model. Thus, the growth of the non-irrigated and irrigated coffee tree followed different growth patterns, the height of the non-irrigated coffee tree showed sigmoidal growth with maximum growth rate at 726 days after planting and the irrigated coffee tree starts its development with high growth rates that gradually decrease over time.

Na modelagem de curvas de crescimento deve-se considerar que dados longitudinais podem apresentar autocorrelação residual, sendo que, se tal característica não é considerada, os resultados e inferências podem ser comprometidos. A abordagem bayesiana, que considera informações à priori sobre o fenômeno em estudo tem se mostrado eficiente na estimação de parâmetros. No entanto, como geralmente não é possível obter as distribuições marginais de forma analítica, faz-se necessário a utilização de algum método, como o método de reamostragem ponderada, para gerar amostras dessas distribuições e assim obter uma aproximação para as mesmas. Dentre as vantagens desse método, destaca-se a geração de amostras independentes e o fato de não ser necessário avaliar convergência. Diante desse contexto, o objetivo deste trabalho foi apresentar a modelagem não linear bayesiana do crescimento em altura de plantas do cafeeiro, irrigadas e não irrigadas (NI), considerando a autocorrelação residual e os modelos não lineares Logístico, Brody, von Bertalanffy e Richards. Em vista dos resultados, verificou-se que, para as plantas NI, o DIC e CPOc, indicaram que, dentre os modelos avaliados, o modelo Logístico é o que melhor descreve o crescimento em altura do cafeeiro ao longo do tempo. E, para as plantas irrigadas, esses mesmos critérios indicaram o modelo Brody. Assim, o crescimento da planta do cafeeiro não irrigado e irrigado seguiram padrões de crescimento distintos, a altura do cafeeiro não irrigado apresentou crescimento sigmoidal com taxa máxima de crescimento aos 726 dias após o plantio, já o cafeeiro irrigado inicia seu desenvolvimento com altas taxas de crescimento que vão diminuindo aos poucos com o tempo.

Soil enzymatic activity under coffee cultivation with different water regimes associated to liming and intercropped brachiaria / Atividade enzimática de solo sob cultivo de café com diferentes regimes hídricos associados a calagem e braquiária nas entrelinhas

This research evaluated the effects of coffee cultivation with two different water regimes associated or not with liming and the presence/absence of brachiaria as intercrop on the activities of the soil enzymes ß-glucosidase, arylsulfatase and acid phosphatase. The study was carried out at the experimental farm of Embrapa Cerrados, using the cultivar IAC 144 (Coffea arabica L.), under a clayey dystrophic Cerrado Oxisol. Two water regimes (WR) were considered, WR1 with irrigation shifts throughout the year and WR3 with controlled water stress, for about 70 days, in the dry season. In each water regime, effects of lime application (with/without) and the presence/absence of brachiaria cultivated between the lines of coffee plants were evaluated. The activities of the enzymes ß-glucosidase, arylsulfatase and acid phosphatase were evaluated during the rainy and dry seasons. Liming and intercropped brachiaria positively affected the activities of the three enzymes assessed in this study at varying degrees, depending on season and/or the WR. Our findings evidenced that intercropped brachiaria in coffee rows was the factor that most positively impacted soil enzymes activities.

O objetivo desse trabalho foi avaliar os efeitos do cultivo do café sobre a atividade das enzimas do solo ß-glicosidase, arilsulfatase e fosfatase ácida em função de dois diferentes regimes hídricos associados ou não à calagem e ao cultivo de braquiária nas entrelinhas. Esse estudo foi realizado em um experimento conduzido no campo experimental do Centro de Pesquisa Agropecuária dos Cerrados, utilizando a cultivar IAC 144 (Coffea arabica L.), sob um Latossolo Vermelho distrófico argiloso. Foram considerados dois regimes hídricos (RH), RH1 com irrigação plena em turnos de rega ao longo do ano e RH3 com estresse hídrico controlado, por cerca de 70 dias, na época seca. Em cada regime hídrico foram avaliadas a aplicação ou não de calcário em cobertura e a presença ou ausência de braquiária cultivada nas entrelinhas das plantas do cafezal. As atividades das enzimas ß-glicosidase, arilsulfatase e fosfatase ácida foram avaliadas durante as estações chuvosa e seca. A calagem e a presença de braquiária nas entrelinhas tiveram efeito positivo sobre a atividade das três enzimas avaliadas nesse estudo, em graus variáveis, dependendo da época de coleta das amostras e/ou do RH. Nossos resultados evidenciam que a braquiária nas entrelinhas do café foi o fator de maior impacto positivo sobre a atividade enzimática do solo.

Receptor-Like Kinase (RLK) as a candidate gene conferring resistance to Hemileia vastatrix in coffee

The biotrophic fungus Hemileia vastatrix causes coffee leaf rust (CLR), one of the most devastating diseases in Coffea arabica. Coffee, like other plants, has developed effective mechanisms to recognize and respond to infections caused by pathogens. Plant resistance gene analogs (RGAs) have been identified in certain plants as candidates for resistance (R) genes or membrane receptors that activate the R genes. The RGAs identified in different plants possess conserved domains that play specific roles in the fight against pathogens. Despite the importance of RGAs, in coffee plants these genes and other molecular mechanisms of disease resistance are still unknown. This study aimed to sequence and characterize candidate genes from coffee plants with the potential for involvement in resistance to H. vastatrix . Sequencing was performed based on a library of bacterial artificial chromosomes (BAC) of the coffee clone Híbrido de Timor (HdT) CIFC 832/2 and screened using a functional marker. Two RGAs, HdT_LRR_RLK1 and HdT_LRR_RLK2, containing the motif of leucine-rich repeat-like kinase (LRR-RLK) were identified. Based on the presence or absence of the HdT_LRR_RLK2 RGA in a number of differential coffee clones containing different combinations of the rust resistance gene, these RGAs did not correspond to any resistance gene already characterized (SH1-9). These genes were also analyzed using qPCR and demonstrated a major expression peak at 24 h after inoculation in both the compatible and incompatible interactions between coffee and H. vastatrix . These results are valuable information for breeding programs aimed at developing CLR-resistant cultivars, in addition to enabling a better understanding of the interactions between coffee and H. vastatrix .(AU)

Receptor-Like Kinase (RLK) as a candidate gene conferring resistance to Hemileia vastatrix in coffee

The biotrophic fungus Hemileia vastatrix causes coffee leaf rust (CLR), one of the most devastating diseases in Coffea arabica. Coffee, like other plants, has developed effective mechanisms to recognize and respond to infections caused by pathogens. Plant resistance gene analogs (RGAs) have been identified in certain plants as candidates for resistance (R) genes or membrane receptors that activate the R genes. The RGAs identified in different plants possess conserved domains that play specific roles in the fight against pathogens. Despite the importance of RGAs, in coffee plants these genes and other molecular mechanisms of disease resistance are still unknown. This study aimed to sequence and characterize candidate genes from coffee plants with the potential for involvement in resistance to H. vastatrix . Sequencing was performed based on a library of bacterial artificial chromosomes (BAC) of the coffee clone Híbrido de Timor (HdT) CIFC 832/2 and screened using a functional marker. Two RGAs, HdT_LRR_RLK1 and HdT_LRR_RLK2, containing the motif of leucine-rich repeat-like kinase (LRR-RLK) were identified. Based on the presence or absence of the HdT_LRR_RLK2 RGA in a number of differential coffee clones containing different combinations of the rust resistance gene, these RGAs did not correspond to any resistance gene already characterized (SH1-9). These genes were also analyzed using qPCR and demonstrated a major expression peak at 24 h after inoculation in both the compatible and incompatible interactions between coffee and H. vastatrix . These results are valuable information for breeding programs aimed at developing CLR-resistant cultivars, in addition to enabling a better understanding of the interactions between coffee and H. vastatrix .

Genetic divergence based on leaf vegetative and anatomical traits of Coffea canephora clones / Divergência genética com base em características vegetativas e anatômicas foliares de clones de Coffea canephora

Knowledge of the expression of traits associated with drought tolerance is important to mitigate impacts on coffee production in a climate change scenario. This study aimed to understand the genetic divergence between Coffea canephora genotypes grown in the Western Amazon based on leaf vegetative and anatomical traits. For this, fifteen high-performance genotypes were evaluated in a randomized block design with five replications of one plant per plot to analyze three leaf vegetative traits (leaf area index, root volume, and total dry mass) and five leaf anatomical traits (polar and equatorial diameter, density and number of stomata, and stomatal area). The data were interpreted using analysis of variance and the Scott-Knott mean cluster test (p ≤ 0.05). The Tocher optimization method and principal component analysis with reference points were used to quantify the genetic divergence. Tocher clustering separated the fifteen clones into five groups, and the scatter in the plane into three groups. Stomatal density was the trait that most contributed to the dissimilarity between genotypes with the potential to be used in future studies for the selection of water deficit-tolerant genotypes. The BRS 3213 genotype showed the greatest genetic dissimilarity and composed a group isolated from the other genotypes in terms of anatomical characteristics. Hybrids 12 and 15 have leaf anatomical traits with higher drought tolerance potential.

O conhecimento da expressão de características associadas a tolerância a seca é importante para mitigar os impactos na produção cafeeira em um cenário de mudanças climáticas. Objetivou-se com o presente trabalho entender a divergência de natureza genética entre genótipos de Coffea canephora cultivados na Amazônia Ocidental, com base em características vegetativas e anatômicas foliares. Para isso, quinze genótipos foram avaliados em delineamento de blocos casualizados com cinco repetições de uma planta por parcela, para análise de três características vegetativas (área foliar, volume de raiz, massa seca total) e cinco características anatômicas foliares (diâmetro polar e equatorial; densidade e número de estômatose área estomática). Os dados foram interpretados utilizando análise de variância e o teste de Scott-Knott (p ≤ 0,05). Para quantificar a divergência genética foi interpretado o agrupamento estimado pelo método de otimização de Tocher e a dispersão no plano obtida utilizando a técnica de componentes principais. O agrupamento de Tocher separou os 15 clones em cinco grupos, e a dispersão no plano em três grupos. A densidade estomática foi a característica que mais contribuiu para a dissimilaridade entre os genótipos com potencial para ser utilizada em estudos futuros de seleção de genótipos tolerantes ao déficit hídrico. O genótipo BRS 3213 apresentou maior dissimilaridade genética, constituindo um grupo isolado dos demais genótipos quanto as características anatômicas. Os Híbridos 12 e 15 apresentam características anatômicas foliares com maior potencial de tolerância a seca.

Genetic divergence based on leaf vegetative and anatomical traits of Coffea canephora clones / Divergência genética com base em características vegetativas e anatômicas foliares de clones de Coffea canephora

Knowledge of the expression of traits associated with drought tolerance is important to mitigate impacts on coffee production in a climate change scenario. This study aimed to understand the genetic divergence between Coffea canephora genotypes grown in the Western Amazon based on leaf vegetative and anatomical traits. For this, fifteen high-performance genotypes were evaluated in a randomized block design with five replications of one plant per plot to analyze three leaf vegetative traits (leaf area index, root volume, and total dry mass) and five leaf anatomical traits (polar and equatorial diameter, density and number of stomata, and stomatal area). The data were interpreted using analysis of variance and the Scott-Knott mean cluster test (p ≤ 0.05). The Tocher optimization method and principal component analysis with reference points were used to quantify the genetic divergence. Tocher clustering separated the fifteen clones into five groups, and the scatter in the plane into three groups. Stomatal density was the trait that most contributed to the dissimilarity between genotypes with the potential to be used in future studies for the selection of water deficit-tolerant genotypes. The BRS 3213 genotype showed the greatest genetic dissimilarity and composed a group isolated from the other genotypes in terms of anatomical characteristics. Hybrids 12 and 15 have leaf anatomical traits with higher drought tolerance potential.(AU)

O conhecimento da expressão de características associadas a tolerância a seca é importante para mitigar os impactos na produção cafeeira em um cenário de mudanças climáticas. Objetivou-se com o presente trabalho entender a divergência de natureza genética entre genótipos de Coffea canephora cultivados na Amazônia Ocidental, com base em características vegetativas e anatômicas foliares. Para isso, quinze genótipos foram avaliados em delineamento de blocos casualizados com cinco repetições de uma planta por parcela, para análise de três características vegetativas (área foliar, volume de raiz, massa seca total) e cinco características anatômicas foliares (diâmetro polar e equatorial; densidade e número de estômatose área estomática). Os dados foram interpretados utilizando análise de variância e o teste de Scott-Knott (p ≤ 0,05). Para quantificar a divergência genética foi interpretado o agrupamento estimado pelo método de otimização de Tocher e a dispersão no plano obtida utilizando a técnica de componentes principais. O agrupamento de Tocher separou os 15 clones em cinco grupos, e a dispersão no plano em três grupos. A densidade estomática foi a característica que mais contribuiu para a dissimilaridade entre os genótipos com potencial para ser utilizada em estudos futuros de seleção de genótipos tolerantes ao déficit hídrico. O genótipo BRS 3213 apresentou maior dissimilaridade genética, constituindo um grupo isolado dos demais genótipos quanto as características anatômicas. Os Híbridos 12 e 15 apresentam características anatômicas foliares com maior potencial de tolerância a seca.(AU)

Genomic prediction of leaf rust resistance to Arabica coffee using machine learning algorithms

Genomic selection (GS) emphasizes the simultaneous prediction of the genetic effects of thousands of scattered markers over the genome. Several statistical methodologies have been used in GS for the prediction of genetic merit. In general, such methodologies require certain assumptions about the data, such as the normality of the distribution of phenotypic values. To circumvent the non-normality of phenotypic values, the literature suggests the use of Bayesian Generalized Linear Regression (GBLASSO). Another alternative is the models based on machine learning, represented by methodologies such as Artificial Neural Networks (ANN), Decision Trees (DT) and related possible refinements such as Bagging, Random Forest and Boosting. This study aimed to use DT and its refinements for predicting resistance to orange rust in Arabica coffee. Additionally, DT and its refinements were used to identify the importance of markers related to the characteristic of interest. The results were compared with those from GBLASSO and ANN. Data on coffee rust resistance of 245 Arabica coffee plants genotyped for 137 markers were used. The DT refinements presented equal or inferior values of Apparent Error Rate compared to those obtained by DT, GBLASSO, and ANN. Moreover, DT refinements were able to identify important markers for the characteristic of interest. Out of 14 of the most important markers analyzed in each methodology, 9.3 markers on average were in regions of quantitative trait loci (QTLs) related to resistance to disease listed in the literature.

Genomic prediction of leaf rust resistance to Arabica coffee using machine learning algorithms

Genomic selection (GS) emphasizes the simultaneous prediction of the genetic effects of thousands of scattered markers over the genome. Several statistical methodologies have been used in GS for the prediction of genetic merit. In general, such methodologies require certain assumptions about the data, such as the normality of the distribution of phenotypic values. To circumvent the non-normality of phenotypic values, the literature suggests the use of Bayesian Generalized Linear Regression (GBLASSO). Another alternative is the models based on machine learning, represented by methodologies such as Artificial Neural Networks (ANN), Decision Trees (DT) and related possible refinements such as Bagging, Random Forest and Boosting. This study aimed to use DT and its refinements for predicting resistance to orange rust in Arabica coffee. Additionally, DT and its refinements were used to identify the importance of markers related to the characteristic of interest. The results were compared with those from GBLASSO and ANN. Data on coffee rust resistance of 245 Arabica coffee plants genotyped for 137 markers were used. The DT refinements presented equal or inferior values of Apparent Error Rate compared to those obtained by DT, GBLASSO, and ANN. Moreover, DT refinements were able to identify important markers for the characteristic of interest. Out of 14 of the most important markers analyzed in each methodology, 9.3 markers on average were in regions of quantitative trait loci (QTLs) related to resistance to disease listed in the literature.(AU)

Coffea arabica L: History, phenology and climatic aptitude of the state of São Paulo, Brazil

ABSTRACT The genus Coffea belongs to the Rubiaceae family and includes two species with optimum economic performances, Coffea arabica and Coffea canephora. The state of São Paulo is one of the states that produce the species C. arabica in Brazil. Arabica coffee has been of great importance to São Paulo, providing relevant contributions to the historical, political, architectural, gastronomic, touristic, artistic, agricultural, industrial and social sectors since its introduction into the state in the nineteenth century. The agricultural sector includes crops produced by both small farmers and by highly technological agricultural groups. Coffea arabica plants present six phenological phases, all sensitive to changes in temperature and rainfall. In the reproductive phases, the species requires short days, low temperatures and no rainfall, followed by the rainy season. However, the phenological phases of the coffee plants can be harmed or even inhibited by dry or rainy seasons that are too long or too short. In the state of São Paulo, the municipalities of Garça and Franca show optimal coffee productivity, whereas those of Adamantina and Registro are low, and the agricultural aptitudes of these four municipalities show strong relationships with their geographical distributions in the state. Garça and Franca are situated in areas where the predominant dry and rainy seasons favor the occurrence of the phenological phases of arabica coffee plants, whereas Adamantina and Registro are located in areas with long dry and rainy seasons, respectively, characteristics that harm the development of the reproductive phenological phases of this culture.

Parasitism of Meloidogyne exigua races 1 and 2 in coffee plants derived from Timor Hybrid / Parasitismo de Meloidogyne exigua raças 1 e 2 em cafeeiros derivados do Híbrido de Timor

To investigate the degree of parasitism of two populations of Meloidogyne exigua, the gall index (GI) and the reproduction factor (RF) of M. exigua races 1 (Est E2) and 2 (Est E1) were analyzed in 47 progenies on F3:4 or F4:5 generation derived from the crossing between Coffea arabica cv. Catuaí Amarelo and Timor Hybrid. C. canephora cv. Apoatã IAC 2258 and C. arabica cv. Catuaí Vermelho IAC 144 were used as resistance and susceptibility checks, respectively. The genotypes that were classified as resistant or susceptible by RF were similarly classified by GI, showing a close relationship between both methodologies. The data also indicated no differences in virulence between the nematode populations, since the progenies showed similar resistance reactions to the M. exigua races 1 and 2. According to GI from the 47 mother plants evaluated, 27 progenies (57.4%) were classified as resistant to M. exigua races 1 and 2, with GI ranging from 0.0 to 1.4 and 20 progenies (42.6%) were susceptible with GI from 2.6 to 4.4. These results showed that most of the evaluated germplasm was very promising in relation to the development of new Arabica coffee cultivars with resistance to M. exigua.(AU)

Com o objetivo de investigar o grau de parasitismo de duas populações de Meloidogyne exigua, o índice de galhas (IG) e o fator de reprodução (FR) de M. exigua raças 1 (Est E2) e 2 (Est E1) foram analisados em 47 progênies na geração F3:4 ou F4:5, derivadas do cruzamento entre Coffea arabica cv. Catuaí Amarelo e Híbrido de Timor. Plantas de C. canephora cv. Apoatã IAC 2258 e C. arabica cv. Catuaí Vermelho IAC 144 foram usadas como padrão de resistência e de suscetibilidade, respectivamente. Os genótipos que foram classificados como resistentes ou suscetíveis pelo FR foram similarmente classificados pelo IG, mostrando uma estreita relação entre as duas metodologias para a avaliação da resistência. Os dados também indicaram que não houve diferenças quanto à virulência entre as duas populações do nematoide, uma vez que as progênies mostraram similar reação de resistência a M. exigua raça 1 e 2. De acordo com o IG, das 47 plantas-mãe avaliadas, 27 progenies (57,4%) foram classificadas como resistentes a M. exigua raças 1 e 2, com IG variando de 0,0 a 1,4 e 20 progenies (42,6%) foram suscetíveis, com IG variando de 2,6 a 4,4. Esses resultados mostraram que a maioria dos germoplasmas avaliados foi muito promissora em relação ao desenvolvimento de novas cultivares de café Arábica com resistência a M. exigua.(AU)

Coffea arabica L: History, phenology and climatic aptitude of the state of São Paulo, Brazil

The genus Coffea belongs to the Rubiaceae family and includes two species with optimum economic performances, Coffea arabica and Coffea canephora. The state of São Paulo is one of the states that produce the species C. arabica in Brazil. Arabica coffee has been of great importance to São Paulo, providing relevant contributions to the historical, political, architectural, gastronomic, touristic, artistic, agricultural, industrial and social sectors since its introduction into the state in the nineteenth century. The agricultural sector includes crops produced by both small farmers and by highly technological agricultural groups. Coffea arabica plants present six phenological phases, all sensitive to changes in temperature and rainfall. In the reproductive phases, the species requires short days, low temperatures and no rainfall, followed by the rainy season. However, the phenological phases of the coffee plants can be harmed or even inhibited by dry or rainy seasons that are too long or too short. In the state of São Paulo, the municipalities of Garça and Franca show optimal coffee productivity, whereas those of Adamantina and Registro are low, and the agricultural aptitudes of these four municipalities show strong relationships with their geographical distributions in the state. Garça and Franca are situated in areas where the predominant dry and rainy seasons favor the occurrence of the phenological phases of arabica coffee plants, whereas Adamantina and Registro are located in areas with long dry and rainy seasons, respectively, characteristics that harm the development of the reproductive phenological phases of this culture.