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

Partial map of Coffea arabica L. and recovery of the recurrent parent in backcross progenies

A partial map of Coffea arabica L. was constructed based on a backcross population and RAPD markers.From a total of 178 markers evaluated, only 134 that segregated 1:1 (P>0.05) were used to develop the map. Seventeenmarkers were not linked, while 117 formed 11 linkage groups, covering a genome distance of 803.2 cM. The maximumdistance between adjacent markers was 26.9 cM, and only seven intervals exceeded 20 cM. The markers were further used forassisted selection of the plants closest to the recurrent parent, to accelerate the introgression of rust resistance genes in thecoffee breeding program. Three BC1 plants resistant to coffee leaf rust and with high genetic similarity to Catuaí wereselected and integrated in the following backcross cycles

Assessment of coconut tree genetic divergence by compound sample RAPD marker analysis

ABSTRACT The coconut tree (Cocos nucifera L.) is a tropical species widely cultivated throughout the world, which is found in all intertropical regions. The species shows wide phenotypic variability, which, however, is little understood at the genetic level. This study of the variability among the various coconut tree populations is important to increase the efficiency of the development of superior cultivars adapted to different ecological conditions. It also helps the selection of divergent progenies that can maximize heterosis in hybridizations. Genetic divergence among 19 coconut tree populations available in the BAG -Coco at EMBRAPA/CPATC was estimated by RAPD. Leaf samples from 21 plants of each cultivar were squashed together (compound samples) in liquid nitrogen and the DNA extracted using the modified Doyle and Doyle (1990) protocol. Samples of these DNA were amplified with 24 primers of the OPERON Technologies series. One hundred and twenty-seven polymorphic and 61 monomorphic loci were obtained. Six different clusters, possibly heterotic groups, were formed by the Tocher optimized clustering analysis which used the matrix of the complement of the Jaccard index. Group 1 included the dwarf group cultivars. Giant accessions, abbreviated to GBR (Brazilian Giant), formed group 2, except GBRPF, which together with West African Giant (GOA) formed group 4. The most distant accession was the Tonga Giant cultivar (GTG) that did not group with the others and presents potential for hybridization with the six cultivars in the dwarf group cultivars and with the five in the GBR group. Group 3 consisted of GRL, GPY and GRT and Group 5 of GML and GVT. The dendrogram obtained by the nearest neighbor method was in line with the clustering obtained by the Tocher optimization method. The markers used permitted identification of each one of the populations showing that they were genetically different (absence of duplicity). The use of compound samples was effective to investigate the interpopulational genetic diversity. However, to understand the intrapopulation genetic variability, individual sampling should be used

Diferenciação entre linhagens do café Catimor derivadas do híbrido HW 26-5, com base em Marcadores RAPD

Em trabalho anterior sobre Coffea arabica L., 23 progênies de Catimor, gerações F6 e F7, dependentes do hibrido CIFC HW 26-5, e uma linhagem de Catuaí Vermelho foram avaliadas com descritores morfológicos. Comparando-se com os dadas de genealogia, os descritores morfológicos nab foram eficientes para diferenciar as linhagens, exceto quando descritores de herdabilidade acima de 80% foram considerados. No presente trabalho, procurouse distinguir as mesmas 23 progênies de Catimor em geração F6 e F7 empregando-se marcadores RAPD. As distâncias genéticas entre as progênies foram estimadas com base em 14 logos polimórficos. Dadas de agrupamento com base em distâncias genéticas, obtidas a partir de marcadores RAPD, foram coerentes com os dados de genealogia destas progênies, mostrando que estes marcadoresforam eficientes gora diferenciar as descendências de Catimor derivadas da híbrido CIFC HW 26-5.A In a previous report on Cofiea ambica L., a Catuai Vermelho line and 23 Catimor lines (generation F6 and F7, derived from CIFC HW 26-5 hybrid) were evaluated by means of morphological descriptors. These were not efficient in grouping the lines according to their genealogic data, except when descriptors with high heritability (>80%) were considered. The same lines are now evaluated with random amplified polymorphic DNA (RAPD) markers. Genetic distances were estimated based on 14 polymorphic loci. Grouping analysis based on the genetic distances obtained with RAPD markers was in accordance with the genealogic data of these lines, showing that these, markers were efficient in differentiating among descendants of Catimor lines derived from CIFC HW 26-5 hybrid

Qualidade de café nos estádios cereja e verde-cana via condutividade elétrica

A maturação é um fator muito importante para a qualidade do café (Coffea arabica L.). Contribuições significativas para a melhoria da qualidade são atribuídas ao preparo do café por via úmida. O teste de condutividade elétrica é um indicador indireto de danos causados às membranas e paredes celulares que podem ser relacionados à qualidade de bebida. O objetivo deste trabalho foi estimar através do teste de condutividade elétrica o potencial de qualidade do café colhido nos estádios cereja e verde-cana quando preparados por via úmida e determinar o melhor período de embebição. Os grãos em pergaminho foram secos até atingir umidade de 10,5 a 11% e posteriormente beneficiados, e padronizados quanto a defeitos e peneira. A condutividade elétrica do exsudato foi aferida após os períodos de embebição de 3,5 e 5 horas. O experimento foi montado no esquema fatorial 7x2 (7 lotes de café e dois níveis de maturação: cereja e verde-cana), em DIC com quatro repetições. As médias foram comparadas pelo teste F e Scott-Knott a 5%. Grãos verde-cana apresentam maior condutividade elétrica que grãos cereja, porém, de modo geral, todos os resultados situaram-se em níveis baixos, indicando boa integridade das membranas e potencial para bebida de qualidade

Qualidade de café nos estádios cereja e verde-cana via condutividade elétrica

A maturação é um fator muito importante para a qualidade do café (Coffea arabica L.). Contribuições significativas para a melhoria da qualidade são atribuídas ao preparo do café por via úmida. O teste de condutividade elétrica é um indicador indireto de danos causados às membranas e paredes celulares que podem ser relacionados à qualidade de bebida. O objetivo deste trabalho foi estimar através do teste de condutividade elétrica o potencial de qualidade do café colhido nos estádios cereja e verde-cana quando preparados por via úmida e determinar o melhor período de embebição. Os grãos em pergaminho foram secos até atingir umidade de 10,5 a 11% e posteriormente beneficiados, e padronizados quanto a defeitos e peneira. A condutividade elétrica do exsudato foi aferida após os períodos de embebição de 3,5 e 5 horas. O experimento foi montado no esquema fatorial 7x2 (7 lotes de café e dois níveis de maturação: cereja e verde- cana), em DIC com quatro repetições. As médias foram comparadas pelo teste F e Scott-Knott a 5%. Grãos verde-cana apresentam maior condutividade elétrica que grãos cereja, porém, de modo geral, todos os resultados situaram-se em níveis baixos, indicando boa integridade das membranas e potencial para bebida de qualidade.Maturation is a very important factor for the quality of coffee (Coffea arabica L.). Significant contributions to quality improvement are attributed to the preparation of coffee by wet processing. The electrical conductivity test is an indirect indicator of damage to the membranes and cell wall that may be related to the coffee beverage quality. The objective of this study was to estimate through the electrical conductivity test the potential quality of the coffee harvested in the green stage sugarcane when prepared by wet processing and also to determine the period of soaking. The beans in parchment were dried until moisture from 10.5 to 11% and subsequently benefited, and standardized for defects and sieve. The electrical conductivity of exudate was measured after soaking periods of 3.5 and 5 hours. The experiment was conducted in a 7x2 factorial arrangement (seven lots of coffee and two levels of maturity: cherry and green cane), in CRD with four replications. The means were compared by F test and by the criterion of Scott-Knott at 5%. Grains green sugarcane have higher electrical conductivity than grains cherry, however, in general, all results stood at low levels, indicating good membrane integrity and potential for quality beverage

Avaliação de híbridos F1 de café (coffee arabica l.) e respectivos progenitores com marcadores RAPD

Foi utilizado neste estudo uma população do programa de melhoramento do cafeeiro do Departamento de Fitopatologia da Universidade Federal de Viçosa descendente de cruzamentos entre linhagens de Catual (Vermelho e Amarelo) e seleções do Hibiido de Timor. Um estudo com marcadores RAPD foi realizado para avaliação de híbridos F1 de café e respectivos progenitores. Analisaram-se 51 genélipos (10 progenitores Catual, 12 progenitores Híbrido de Timor e 29 hibridos F1). Para a certificação da natureza hibrida die 12 híbridos F1 estudados, a análise RAPD também foi utilizada. No estudo da diversidade genética., realizaram-se 15? reações, com 86 primers, tendo 53,5% deles apresentado polimorfismo, totalizando l08 bandas polimórficas, com média de 2,35 bandas polimórficaslprimer. Dentre os primers que apresentaram maior número de bandas polimórficas estão: OPA-8, OPC4O, OPA5 e OPA-10. Com um limite die dissimilaridade genética de 54%, o Híbrido de Timor UFV 427-I S permaneceu no grupo dos cultivares Catual. Dos 12 genõ tipos mais produtivos na geração F/, I I tiveram sua natureza híbrida confirmada. Marcadores RAPD foram eficientes na avaliação de diversidade genética em C. arabica e na certificação da natureza híbrida de materiais gentticos obtidas porcruzamentos artificiais.I'hisstudyusedapopulationownedbythecoã'eebreedingprogramofthePlant Pathology Department of the Federal University of Viçosa, descendem of crossings between ancestries of Catuaí with red and yellow benies and Timor Hybrid selections. RAPD markers were used to evaluate the Fl coffee hybrids and their respective progenitors. To study the genetic diversity, 51 genotypes were analyzed (10 Catuai ancestors, 12 Timor Hybrid ancestors and 29 hybrids Fl). To detamine the hybrid nature of the 12 Fl genotypes, the RAPD analysis was used In the study of genetic diversity, a total of 157 reactions, with 86 primers were carried out, with 535% of them presenting polimorphic bands, totalizing 108 with an average of 2.35 polimorphic bands/primer. The primers presenting the greatest number of polimorphic bands were: OPA-8, OPC-10, OPA-S and OPA-10. Limited to a genetic distance of 54%, the Timor Hybrid UFV 427-15 remained in the group of Catuai. Eleven of the twelve more productive genotypes in the generation Fl confirmed their hybrid nature. RAPD markers were eiiicient to evaluate the genetic diversity in C. arabica, and to certify the hybrid condition of the genetic materials obtained by artificial crosses