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Genomic selection has been proposed as the standard method to predict breeding values in animal and plant breeding. Although some crops have benefited from this methodology, studies in Coffea are still emerging. To date, there have been no studies describing how well genomic prediction models work across populations and environments for different complex traits in coffee. Considering that predictive models are based on biological and statistical assumptions, it is expected that their performance vary depending on how well these assumptions align with the true genetic architecture of the phenotype. To investigate this, we used data from two recurrent selection populations of Coffea canephora, evaluated in two locations, and single nucleotide polymorphisms identified by Genotyping-by-Sequencing. In particular, we evaluated the performance of 13 statistical approaches to predict three important traits in the coffee—production of coffee beans, leaf rust incidence and yield of green beans. Analyses were performed for predictions within-environment, across locations and across populations to assess the reliability of genomic selection. Overall, differences in the prediction accuracy of the competing models were small, although the Bayesian methods showed a modest improvement over other methods, at the cost of more computation time. As expected, predictive accuracy for within-environment analysis, on average, were higher than predictions across locations and across populations. Our results support the potential of genomic selection to reshape traditional plant breeding schemes. In practice, we expect to increase the genetic gain per unit of time by reducing the length cycle of recurrent selection in coffee.

Genomic selection (GS) has been studied in several crops to increase the rates of genetic gain and reduce the length of breeding cycles. Despite its relevance, there are only a modest number of reports applied to the genus Coffea . Effective implementation depends on the ability to consider genomic models, which correctly represent breeding scenario in which the species are inserted. Coffee experimentation, in general, is represented by evaluations in multiple locations and harvests to understand the interaction and predict the performance of untested genotypes. Therefore, the main objective of this study was to investigate GS models suitable for use in Coffea canephora . An expansion of traditional GBLUP was considered and genomic analysis was performed using a genotyping-by-sequencing (GBS) approach, showed good potential to be used in coffee breeding programs. Interactions were modeled using the multiplicative mixed model theory, which is commonly used in multi-environment trials (MET) analysis in perennial crops. The effectiveness of the method used was compared with other genetic models in terms of goodness-of-fit statistics and prediction accuracy. Different scenarios that mimic coffee breeding were used in the cross-validation process. The method used had the lowest AIC and BIC values and, consequently, the best fit. In terms of predictive ability, the incorporation of the MET modeling showed higher accuracy (on average 10–17% higher) and lower prediction errors than traditional GBLUP. The results may be used as basis for additional studies into the genus Coffea and can be expanded for similar perennial crops.

This study aimed to assess and compare the behavior of superior genotypes of Coffea canephora in terms of fruiting capacity using directed hybridizations in a full diallel design with reciprocals. Hybridizations were performed using 12 possible combinations between genotypes 02, 03, 23 and 83 from the Incaper breeding program. High estimates of the genotypic coefficient of determination in terms of the total number of pinheads per cross (TNP) and fruit set (FS) indicated variability of genetic nature. FS averaged 52,27 %, ranging from 31,32 % to 82,09 %, with the higher rates relating to clone 23 as the male parent. Differences were found between reciprocal crosses in the combinations with genotype 23, which emerged as the donor plant with the best fruiting rate, but poor receiving ability. Clone 83 prevailed as the best receiving plant and the least effective donor. In the comparison of these two genotypes, antagonism was observed in their behavior when they were used as pollen-donor plants (male parents) and pollen-receiver plants (female parents), highlighting their possible maternal effect. Crosses involving clones 02 and 03 showed no differences when used reciprocally. The estimates of genotypic correlations were negative for the four associations involving the FS characteristic, being of greater magnitude with TNP. Este trabajo tuvo como objetivo evaluar y comparar la eficiencia en la producción de frutos entre cruces recíprocos en Coffea canephora con el uso de hibridaciones controladas en un dialelo completo con diseño recíproco. Las hibridaciones se realizaron involucrando los genotipos 02, 03, 23 y 83 del programa de mejoramiento Incaper. Las estimaciones altas del coeficiente de determinación genotípica para el número total de frutos iniciados por cruzamiento (TNP) y la proporción de frutos (FS) indicaron una variabilidad de naturaleza genética. La FS promedio fue de 52,27 %, con un rango de 31,32 % a 82,09 %, siendo mayor con el clon 23 como progenitor masculino. Se encontraron diferencias entre cruces recíprocos en combinaciones con el genotipo 23, que se destacó como la planta donante con la mejor tasa en la producción de frutos, pero con habilidad receptora deficiente. El clon 83 se destacó como la mejor planta receptora y la peor donante. En la comparación de estos dos genotipos (23 y 83) se observó antagonismo en su comportamiento al ser utilizados como plantas donadoras de polen (progenitores masculinos) y plantas receptoras de polen (progenitores femeninos), evidenciando un posible efecto maternal. Los cruces entre los clones 02 y 03 no mostraron diferencias cuando se usaron recíprocamente. Las estimaciones de las correlaciones genotípicas fueron negativas para las asociaciones que involucraron la característica FS, siendo de mayor magnitud con TNP.

Recurrent intrapopulation selection is a key approach for the plant breeding of Coffea canephora, enabling the development of progenies superior to their parents while preserving genetic variability. This study was conducted in Espírito Santo, a major Conilon coffee production hub in Brazil, across two environments with contrasting soil and climatic conditions. This study to evaluated the agronomic performance, selection gains, and genetic divergence of 56 hybrid progenies from a late-maturing population, along with six parental plants. Genetic parameter estimates confirmed the presence of genetic variability and selection potential among the genotypes. Using Mulamba and Mock and Additive selection indices, 16 promising progenies were identified for the development of new cultivars. The strategy proved effective in recommending high-yielding genotypes adapted to each environment, highlighting its importance for sustainable cultivation under diverse edaphoclimatic conditions. RESUMO: A seleção intrapopulacional recorrente é uma abordagem fundamental para o melhoramento genético de Coffea canephora, permitindo o desenvolvimento de progênies superiores aos seus pais, preservando a variabilidade genética. Este estudo foi conduzido no Espírito Santo, um importante polo produtor de café Conilon no Brasil, em dois ambientes com condições edafoclimáticas contrastantes. O objetivo foi avaliar o desempenho agronômico, os ganhos de seleção e a divergência genética de 56 progênies híbridas de uma população de maturação tardia, juntamente com seis plantas parentais. As estimativas dos parâmetros genéticos confirmaram a presença de variabilidade genética e potencial de seleção entre os genótipos. Utilizando os índices de seleção Mulamba e Mock e Additive, 16 progênies promissoras foram identificadas para o desenvolvimento de novas cultivares. A estratégia se mostrou eficaz na recomendação de genótipos de alta produtividade adaptados a cada ambiente, destacando sua importância para o cultivo sustentável sob diversas condições edafoclimáticas.

The state of Espírito Santo is the major producer of Coffea canephora in Brazil. Knowledge of genetic reserves is fundamental to plant breeding. Therefore, the present study characterized and analyzed the genetic diversity of 600 C. canephora accessions from the germplasm bank of Incaper based on 38 traits evaluated in 24-30-month-old plants. Further, the predominant descriptors or traits were identified, and high phenotypic variability was determined. Genetic distances for the grouped (Gower), quantitative, and qualitative datasets were 0.48, 0.61, and 0.92, respectively, with accessions 76 (Conilon) and 407 (Robusta) being the most divergent ones at Incaper. In clustering using the Tocher optimization method, 30 groups were formed, with three accessions introduced from Epamig’s Robusta collection being the most dissimilar ones. Graphical dispersion analysis using the principal coordinate method revealed the predominance of three groups formed by the Robusta, Conilon, and hybrid Robusta × Conilon genotypes.

PurposeThe purpose of this paper is to evaluate the contents of bioactive compounds and/or that of interest for the brew quality (trigonelline, caffeine, total chlorogenic acids and melanoidins), acidity and antioxidant activity (AA) of roasted coffee brews produced with Coffea canephora.Design/methodology/approachCoffee samples corresponded to three cultivars – Diamante ES8112, ES8122 “Jequitibá,” and Centenária ES8132 – with different fruit-ripening seasons (early, medium and late, respectively). The study evaluated five genotypes from each cultivar and coffees were cultivated in two sites, a total of 30 samples.FindingsThe average contents on the coffee brews varied from 1,176 to 1,452 µg mL−1 for caffeine; from 206 to 413 µg mL−1 for trigonelline; from 528 to 942 µg mL−1 for total chlorogenic acids; from 6.8 to 7.8 mg mL−1 for melanoidins; showing total titratable acidity between 1.15 and 1.79 mL of NaOH 0.1 mol L−1 by 20 mL of the brew. AA varied from 6.78 to 8.80 mg of TROLOX mL−1, correlating positively with the contents of caffeine, total chlorogenic acids, melanoidins. Fruit-ripening seasons had no effect on coffee brew composition and AA.Originality/valueThe results presented provide not only a unique analysis of coffee brew from genotypes developed to improve the good agricultural practice and brew quality, but also relevant information that can be extended for research in coffee composition and for the coffee industry.

The role of abscisic acid (ABA) in drought tolerance of Coffea canephora is unknown. To determine whether ABA is associated with drought tolerance and if the use of tolerant rootstocks could increase ABA and drought tolerance, we performed reciprocal grafting experiments between clones with contrasting tolerance to drought (clone 109, sensitive; and clone 120, tolerant). Plants were grown in large (120 L) pots in a greenhouse and subjected to drought stress by withholding irrigation. The non-grafted 120 plants and graft treatments with 120 as a rootstock showed a slower reduction of predawn leaf water potential (Ψpd) and a lower negative carbon isotopic composition ratio compared with the other grafting combinations in response to drought. The same 120 graft treatments also showed higher leaf ABA concentrations, lower levels of electrolyte leakage, and lower activities of ascorbate peroxidase and catalase under moderate (Ψpd = − 1.0 or − 1.5 MPa) and severe (Ψpd = − 3.0 MPa) drought. Root ABA concentrations were higher in plants with the 120 rootstocks regardless of watering regime. The 120 shoots could also contribute to drought tolerance because treatment with 120/109 rootstock/scion combination showed postponed dehydration, higher leaf ABA concentration, and lower leaf electrolyte leakage compared with the sensitive clone. We conclude that both the shoot and root systems of the tolerant clone can increase the concentrations of ABA in leaves in response to drought. This further suggests that ABA is associated with a delayed onset of severe water deficit and decreased oxidative damage in C. canephora.

Coffee outturn can be defined as the ratio between the harvested coffee and its respective processed grains. This character is greatly influenced by genotypic and environmental effects, and in breeding programs your analysis is costly and time-consuming. In this sense, the use of an outturn index to estimate coffee yield on experimental plots is a desirable measure aiming at reducing resources and time in postharvest evaluations. Thus, the present study aimed to evaluate the accuracy of the use of an outturn index equal to 4.0, in the estimation of Conilon coffee grains production. This index indicates that four kilograms of harvested fruit would be needed to obtain one kilogram of processed grains. Based on the average of 157 genotypes conducted in three trials and four harvests, we evaluated the relationship between harvested fruits and processed grains (FcBe), the observed (OGY), and the estimated grain yield per plant (EGY) based on FcBe equal to 4.0 (an outturn index). Descriptive statistics, adequation test for EGY, and the coincidence of occurrence of genotypes observations relating to the top 20% of all observations of OGY and EGY. In the estimation of grain yield in Conilon, the use of FcBe equal to 4.0 showed high precision in the average of the analyzed trials. However, further studies should be conducted to elucidate the effects of climate variables on the yield of Conilon coffee, especially in atypical crop years. Thus, the use of an outturn index becomes interesting in cases where the number of genotypes to be evaluated is very large and a screening of the promising ones is desirable.

The purpose of this study was to assess the growth of conilon coffee tree plantlets that were propagated by grafting and cutting. The experiment was conducted at the plantlet production site of Incaper’s Experimental Farm in the city of Marilândia, Espírito Santo State. For grafting, plantlets derived from the seed propagation of Coffea canephora cv. Robusta Tropical (ENCAPER 8151) were used as rootstocks, and six clones of cv. Conilon Vitória (INCAPER 8142) were used as the grafts. The cutting was performed with six clones that were used for grafting. The experimental design consisted of randomized blocks of twelve treatments with five repetitions composed of twelve plantlets. On the hundred and fifth day, the averages of the variables were assessed and compared by the Scheffé test at a probability of 5%. The grafted plantlets were superior for almost all of the characteristics assessed, which suggests that it is possible to propagate conilon coffee trees.

In the northern Minas region, the dry-warm climate predisposes coffee plants to the occurrence of leaf miners, mites, cercosporiosis, and leaf scald. Aiming for the development of a cultivar adapted to these conditions, Coffea canephora Pierre ex A. Froehner clones were selected through genetic parameters under an irrigated system, without agrochemicals. Eighteen agronomic traits were evaluated. The survival rate, number of nodes per plagiotropic branch, leaf miner infestation and cercosporiosis incidence were chosen as characteristics for selection of ‘Vitória Incaper 8142’, once they have shown superiority of the genetic parameters. The survival rate variable was used to rank the EMCAPA 8141 Robustão Capixaba clones. Clones V2, V4, V6, V13, RC7, and RC9 were selected as more tolerant to pests and diseases and can provide genetic improvements in conilon breeding program for region. The genetic dissimilarity identified between clones allowed suitable clone combinations to be proposed for use in future crosses.