Designing the best breeding strategy for Coffea canephora: Genetic evaluation of pure and hybrid individuals aiming to select for productivity and disease resistance traits.

Breeding programs of the species Coffea canephora rely heavily on the significant genetic variability between and within its two varietal groups (conilon and robusta). The use of hybrid families and individuals has been less common. The objectives of this study were to evaluate parents and families from the populations of conilon, robusta, and its hybrids and to define the best breeding and selection strategies for productivity and disease resistance traits. As such, 71 conilon clones, 56 robusta clones, and 20 hybrid families were evaluated over several years for the following traits: vegetative vigor, incidence of rust and cercosporiosis, fruit ripening time, fruit size, plant height, canopy diameter, and yield per plant. Components of variance and genetic parameters were estimated via residual maximum likelihood (REML) and genotypic values were predicted via best linear unbiased prediction (BLUP). Genetic variability among parents (clones) and hybrid families was detected for most of the evaluated traits. The Mulamba-Rank index suggests potential gains up to 17% for the genotypic aggregate of traits in the hybrid population. An intrapopulation recurrent selection within the hybrid population would be the best breeding strategy because the genetic variability, narrow and broad senses heritabilities and selective accuracies for important traits were maximized in the crossed population. Besides, such strategy is simple, low cost and quicker than the concurrent reciprocal recurrent selection in the two parental populations, and this maximizes the genetic gain for unit of time.

Treasured exceptions: Association of morphoanatomical leaf traits with cup quality of Coffea arabica L. cv. "Catuaí".

The morphoanatomical characteristics of leaves were associated with altitude, hillside, and the cup quality of coffee produced in the Matas de Minas region. Although the small magnitude, there are correlations between cup quality with altitude and morpho-anatomical traits. Despite facing the differences of management inherent to 363 sampling sites, Northwestern hillside had significant lower cup quality, whereas only stomata density (SD) and thickness of the leaf epidermis in the adaxial face (AdET) showed significant differences between hillsides. Altitude, leaf mass per area (LMA) and SD, and to a lesser extent the thickness of the leaf epidermis in the abaxial face (AbET), were correlated (Spearman's correlation) with cup quality. Interestingly, AbET correlations were negative. Mantel's test significant correlations were found between coffee cup quality vs. altitude, LMA and petiole phloem area (PPhA). The spatial autocorrelation was significant only with LMA. Also, SD, to a lesser extent, was associated with cup quality. Despite the complexity of the association among the environment, plant growth and development, this is the first report to associate morpho-anatomical features of the leaf with the coffee cup traits. Even with the expectation of genotype/species vs environment interactions, and the influence of other parameters associated with post-harvest, roasting and brewing, the evaluation of LMA, SD, AdET, AbET and the thickness of the palisade parenchyma (PPT) allow a novel approach to access coffee cup quality.

Early Selection Enabled by the Implementation of Genomic Selection in Coffea arabica Breeding.

Genomic Selection (GS) has allowed the maximization of genetic gains per unit time in several annual and perennial plant species. However, no GS studies have addressed Coffea arabica, the most economically important species of the genus Coffea. Therefore, this study aimed (i) to evaluate the applicability and accuracy of GS in the prediction of the genomic estimated breeding value (GEBV); (ii) to estimate the genetic parameters; and (iii) to evaluate the time reduction of the selection cycle by GS in Arabica coffee breeding. A total of 195 Arabica coffee individuals, belonging to 13 families in generation of F2, susceptible backcross and resistant backcross, were phenotyped for 18 agronomic traits, and genotyped with 21,211 SNP molecular markers. Phenotypic data, measured in 2014, 2015, and 2016, were analyzed by mixed models. GS analyses were performed by the G-BLUP method, using the RKHS (Reproducing Kernel Hilbert Spaces) procedure, with a Bayesian algorithm. Heritabilities and selective accuracies were estimated, revealing moderate to high magnitude for most of the traits evaluated. Results of GS analyses showed the possibility of reducing the cycle time by 50%, maximizing selection gains per unit time. The effect of marker density on GS analyses was evaluated. Genomic selection proved to be promising for C. arabica breeding. The agronomic traits presented high complexity for they are controlled by several QTL and showed low genomic heritabilities, evidencing the need to incorporate genomic selection methodologies to the breeding programs of this species.

In silico identification of coffee genome expressed sequences potentially associated with resistance to diseases.

Sequences potentially associated with coffee resistance to diseases were identified by in silico analyses using the database of the Brazilian Coffee Genome Project (BCGP). Keywords corresponding to plant resistance mechanisms to pathogens identified in the literature were used as baits for data mining. Expressed sequence tags (ESTs) related to each of these keywords were identified with tools available in the BCGP bioinformatics platform. A total of 11,300 ESTs were mined. These ESTs were clustered and formed 979 EST-contigs with similarities to chitinases, kinases, cytochrome P450 and nucleotide binding site-leucine rich repeat (NBS-LRR) proteins, as well as with proteins related to disease resistance, pathogenesis, hypersensitivity response (HR) and plant defense responses to diseases. The 140 EST-contigs identified through the keyword NBS-LRR were classified according to function. This classification allowed association of the predicted products of EST-contigs with biological processes, including host defense and apoptosis, and with molecular functions such as nucleotide binding and signal transducer activity. Fisher's exact test was used to examine the significance of differences in contig expression between libraries representing the responses to biotic stress challenges and other libraries from the BCGP. This analysis revealed seven contigs highly similar to catalase, chitinase, protein with a BURP domain and unknown proteins. The involvement of these coffee proteins in plant responses to disease is discussed.

In silico identification of coffee genome expressed sequences potentially associated with resistance to diseases

Sequences potentially associated with coffee resistance to diseases were identified by in silico analyses using the database of the Brazilian Coffee Genome Project (BCGP). Keywords corresponding to plant resistance mechanisms to pathogens identified in the literature were used as baits for data mining. Expressed sequence tags (ESTs) related to each of these keywords were identified with tools available in the BCGP bioinformatics platform. A total of 11,300 ESTs were mined. These ESTs were clustered and formed 979 EST-contigs with similarities to chitinases, kinases, cytochrome P450 and nucleotide binding site-leucine rich repeat (NBS-LRR) proteins, as well as with proteins related to disease resistance, pathogenesis, hypersensitivity response (HR) and plant defense responses to diseases. The 140 EST-contigs identified through the keyword NBS-LRR were classified according to function. This classification allowed association of the predicted products of EST-contigs with biological processes, including host defense and apoptosis, and with molecular functions such as nucleotide binding and signal transducer activity. Fisher's exact test was used to examine the significance of differences in contig expression between libraries representing the responses to biotic stress challenges and other libraries from the BCGP. This analysis revealed seven contigs highly similar to catalase, chitinase, protein with a BURP domain and unknown proteins. The involvement of these coffee proteins in plant responses to disease is discussed.

Diferenças genéticas na eficiência de absorção, na translocação e na utilização de K, Ca e Mg em mudas enxertadas de cafeeiro / Genetics differences in the efficiency of absorption, translocation and use of K, Ca and Mg in grafted seedlings of coffee

O estudo da eficiência nutricional de plantas enxertadas de cafeeiro é importante para a seleção de combinações enxerto/porta-enxerto visando desenvolvimento e produção máximos. O presente trabalho teve como objetivo avaliar as diferenças genéticas na eficiência de absorção, no transporte e na utilização de Potássio, Cálcio e Magnésio em mudas enxertadas de cafeeiro. O plantio foi realizado em vasos de 20L contendo como substrato terra, areia e esterco na proporção de 3:1:1, em que as plantas permaneceram por 18 meses até a coleta do experimento. Utilizaram-se como enxertos quatro genótipos de Coffea. arabica L.: as variedades Catuaí Vermelho IAC 15 e Oeiras MG 6851 e os híbridos H419-10-3-4-4 e H514-5-5-3 do programa de melhoramento da EPAMIG/UFV. Como porta-enxerto, foram empregados cinco progênies famílias de meios-irmãos de clones de Coffea canephora Pierre cv. Conilon: "ES 21", "ES 36", "ES 26", "ES 23" e "ES 38" do programa de melhoramento de café robusta do INCAPER. Houve variação da eficiência nutricional de K, Ca e Mg das plantas de cafeeiro em função da combinação enxerto/porta-enxerto. Na maioria das vezes, as plantas enxertadas tiveram desempenho inferior ao do pé-franco quanto à eficiência de absorção, translocação e utilização do K, Ca e Mg, bem como na produção de matéria seca. As combinações da variedade Catuaí Vermelho IAC 15 com os porta-enxertos ES 26 e ES 23 foram eficientes quanto à utilização de Mg e à produção de matéria seca. A baixa eficiência de absorção de K e Mg das combinações de enxertia com a cultivar Oeiras MG 6851 podem ter contribuído para a redução de produção de matéria seca total das mesmas.

Studies on the nutritional efficiency of grafted coffee trees are important for the selection of the rootstocks/grafts combinations that aim at for a good development and maximum yield. This study aimed to evaluate the genetic differences in the efficiency of K, Ca and Mg uptake, transport and use in grafted coffee seedlings. Trees were planted in 20-L pots containing soil, sand and manure (3:1:1) to grow for 18 months, until harvest. As grafts, four genotypes of Coffea arabica L were used: varieties Catuaí Vermelho IAC 15 and Oeiras MG 6851 and hybrids H419-10-3-4-4 and H514-5-5-3, of the breeding program of EPAMIG/UFV. As rootstocks, five half-sib progenies of Coffea canephora Pierre cv. Conilon clones were used: 'ES 21', 'ES 36', 'ES 26', 'ES 23' and 'ES 38', of the robust coffee breeding program of INCAPER. The nutritional efficiency of the coffee trees regarding K, Ca and Mg varied with the graft/ rootstock combination. The performance of the grafted coffee plants was inferior to the control varieties, with regard to the nutritional efficiency and dry matter yield. Catuaí Vermelho IAC 15 combined with the rootstocks ES 26 and ES 23 was highly effective regarding Mg utilization and dry matter yield. The dry weight reduction in the cv. Oeiras MG 6851 combinations may be explained by the low potassium and magnesium uptake efficiency.

Porta-enxertos afetando o desenvolvimento de mudas de coffea arabica l / Rootstocks affecting the development of coffea arabica l. young plants

O desenvolvimento de mudas de Coffea arabica L., em função do porta-enxerto, foi avaliado em condições de campo, na fazenda Jatobá município de Paula Cândido - MG. Utilizaram-se como enxerto quatro genótipos de C. arabica L.: as variedades Catuaí Vermelho IAC 15 e Oeiras MG 6851 e as linhagens H 419-10-3-1-5 e H 514-5-5-3, e, como porta-enxerto, três genótipos de Coffea canephora Pierre et Froenher: Apoatã LC 2258, Conilon Muriaé-1, Robustão Capixaba (EMCAPA 8141) e um genótipo de C. arabica L.: Mundo Novo IAC 376-4, além da utilização de quatro pés-francos. A combinação de enxertia H419/EMCAPA teve aumento na altura da planta, no número de nós da haste principal, no número de ramos plagiotrópicos da haste principal, no diâmetro de caule, no número de nós do ramo plagiotrópico mediano e na produção quando comparada com o respectivo pé-franco. As combinações Catuaí/Apoatã, H514/Apoatã, H514/Conilon e H514/EMCAPA tiveram reduções na produção quando comparadas com os respectivos pés-francos. A enxertia em café pode influenciar o desenvolvimento das plantas, quando se compararam diferentes combinações enxerto/porta-enxerto com os respectivos pés-francos. A linhagem H 419-10-3-1-5 foi beneficiada na produção de café pelos porta-enxertos Apoatã e EMCAPA, e no crescimento apenas pelo EMCAPA.