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URI permanente desta comunidadehttps://thoth.dti.ufv.br/handle/123456789/3352
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Resultados da Pesquisa
Item Partial map of Coffea arabica L. and recovery of the recurrent parent in backcross progenies(Crop Breeding and Applied Biotechnology, 2007-06-30) Oliveira, Antonio Carlos Baião de; Sakiyama, Ney Sussumu; Caixeta, Eveline Teixeira; Zambolim, Eunize Maciel; Rufino, Raphael José Nascif; Zambolim, LaércioA 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. Seventeen markers were not linked, while 117 formed 11 linkage groups, covering a genome distance of 803.2 cM. The maximum distance between adjacent markers was 26.9 cM, and only seven intervals exceeded 20 cM. The markers were further used for assisted selection of the plants closest to the recurrent parent, to accelerate the introgression of rust resistance genes in the coffee breeding program. Three BC1 plants resistant to coffee leaf rust and with high genetic similarity to ?Catuaí? were selected and integrated in the following backcross cycles.Item In silico identification of coffee genome expressed sequences potentially associated with resistance to diseases(Sociedade Brasileira de Genética, 2010) Alvarenga, Samuel Mazzinghy; Caixeta, Eveline Teixeira; Hufnagel, Bárbara; Thiebaut, Flávia; Maciel-Zambolim, Eunize; Zambolim, Laércio; Sakiyama, Ney SussumuSequences 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.Item Receptor-Like Kinase (RLK) as a candidate gene conferring resistance to Hemileia vastatrix in coffee(Escola Superior de Agricultura "Luiz de Queiroz", 2021) Almeida, Dênia Pires de; Castro, Isabel Samila Lima; Mendes, Tiago Antônio de Oliveira; Alves, Danúbia Rodrigues; Barka, Geleta Dugassa; Barreiros, Pedro Ricardo Rossi Marques; Zambolim, Laércio; Sakiyama, Ney Sussumu; Caixeta, Eveline TeixeiraThe 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.Item Genomic prediction of leaf rust resistance to Arabica coffee using machine learning algorithms(Escola Superior de Agricultura "Luiz de Queiroz", 2021) Sousa, Ithalo Coelho de; Nascimento, Moysés; Silva, Gabi Nunes; Nascimento, Ana Carolina Campana; Cruz, Cosme Damião; Silva, Fabyano Fonseca e; Almeida, Dênia Pires de; Pestana, Kátia Nogueira; Azevedo, Camila Ferreira; Zambolim, Laércio; Caixeta, Eveline TeixeiraGenomic 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.Item Molecular characterization of arabica and conilon coffee plants genotypes by ssr and issr markers(Instituto de Tecnologia do Paraná - Tecpar, 2014-09) Motta, Ludymila Brandão; Soares, Taís Cristina Bastos; Ferrão, Maria Amélia Gava; Caixeta, Eveline Teixeira; Lorenzoni, Rodrigo Monte; Souza Neto, José Dias deThe molecular characterization of ten genotypes of the Coffea arabica plants and of seven genotypes of C. canephora having interesting features for coffee breeding programs was carried to select the parents for breeding. A total of 40 SSR and 29 ISSR primers were used. The primers generated a total of 331 (307 polymorphic and 24 monomorphic) bands. Analysis of genetic diversity presented dissimilarity intervals ranging from 0.22 to 0.44 between the Conilon genotypes, from 0.02 to 0.28 between the Arabica genotypes, and from 0.49 to 0.60 between the genotypes of the two species in the joint analysis. Four groups were formed: I = genotypes of C. arabica, II = four progenies of C. canephora, Conilon group, and one non defined C. canephora (Conilon or Robusta), III = one progeny of un-defined C. canephora (Conilon or Robusta) and IV = one progeny of C. canephora of Robusta group. The grouping formed was consistent with the origins of each group. High stabilities of the bifurcations were found by bootstrap analysis. The use of molecular markers of the SSR and ISSR types in the diversity study was efficient in distinguishing genotypes between and within C. arabica and C. canephora.Item Triple plagiotropic branch in coffee: a new promising mutant?(Crop Breeding and Applied Biotechnology, 2017-10) Sakiyama, Ney Sussumu; Picoli, Edgard Augusto de Toledo; Oliveira, Antonio Carlos Baião de; Caixeta, Eveline Teixeira; Zambolim, Laércio; Martinez, Hermínia Emília Prieto; Pereira, Antonio AlvesCoffee tree is a shrub with dimorphic branches. The orthotropic stem grows vertically with two near-horizontal plagiotropic branches, per node, in opposite phyllotaxy. The consecutive nodes of the orthotropic stem are organ- ized in parastichies. We report here mutant plants of Coffea arabica with triple plagiotropic branch, resulted from the whorled phyllotaxy of the orthotropic stem. In mutant plants three plagiotropic branches in the same node are sepa- rated by angles of approximately 120 o , while in normal plants two plagiotropic branches in the same node are separated by angles of approximately 180 o . In mutant plants the angles of the parastichies increase approximately 50 o clock- wise between consecutive nodes, while in normal plants the angles increase approximately 87 o . The plant architecture is changed. The triple plagiotropic branch is a putative mutant with potential to be explored in coffee breeding programs. The hypotheses for the origin of the mutation and the research perspectives are discussed.Item Molecular diversity in Coffea canephora germplasm conserved and cultivated in Brazil(Crop Breeding and Applied Biotechnology, 2013-12) Souza, Flávio de França; Caixeta, Eveline Teixeira; Ferrão, Luís Felipe Ventorim; Pena, Guilherme Ferreira; Sakiyama, Ney Sussumu; Zambolim, Eunize Maciel; Zambolim, Laércio; Cruz, Cosme DamiãoThis work aimed to characterize accessions that represent the C. canephora germplasm conserved and cultivated in Brazil. A total of 130 accessions from germplasm banks of IAC (São Paulo), UFV (Minas Gerais) and also collected in plantations of the State of Espírito Santo and Rondônia were evaluated with a set of 20 new microsatellite primers. Multivariate methods were used to estimate the relationship among the accessions. High level of polymorphism and two major diversity clusters were identified. First cluster was composed by the accessions conserved in the IAC and UFV collections and the second was formed by accessions collected in areas under cultivation. Accessions from Espírito Santo and Rondônia were clear separated, composing two subclusters. Despite the great polymorphism found in Brazilian plantations, the diversity may be increased, because a new threshold in the genetic gains is expected on breeding programs with the intensification of the use of conserved germplasmItem Breeding potential and genetic diversity of “Híbrido do Timor” coffee evaluated by molecular markers(Crop Breeding and Applied Biotechnology, 2010-06-20) Setotaw, Tesfahun Alemu; Caixeta, Eveline Teixeira; Pena, Guilherme Ferreira; Zambolim, Eunize Maciel; Pereira, Antonio Alves; Sakiyama, Ney SussumuAFLP, RAPD and SSR molecular markers were used to study the genetic diversity and genetic structure of the Híbrido de Timor germplasm. The principal coordinate analysis, UPGMA cluster analysis based on genetic dissimilarity of Jaccard, Bayesian model-based cluster analysis, percentage of polymorphic loci, Shannon’s information index and Nei gene diversity were employed to assess the genetic diversity. The analyses demonstrated a high genetic diversity among Híbrido de Timor accessions. UPGMA and Bayesian cluster analyses grouped the accessions into three clusters. The genetic structure of Híbrido de Timor is reported. The management of Híbrido de Timor germplasm variability and its potential use in breeding programs are discussed.Item Herança da resistência do Híbrido de Timor UFV 443-03 à ferrugem-do-cafeeiro(Empresa Brasileira de Pesquisa Agropecuária - Embrapa, 2009-03) Capucho, Alexandre Sandri; Caixeta, Eveline Teixeira; Zambolim, Eunize Maciel; Zambolim, LaércioO objetivo deste trabalho foi caracterizar a herança da resistência do Híbrido de Timor UFV 443-03 à ferrugem-do-cafeeiro (Hemileia vastatrix). Para isso, a raça II e o patótipo 001 de ferrugem foram inoculados em 246 plantas da população F 2 , 115 plantas do retrocruzamento suscetível (RC S ) e 87 plantas do retrocruzamento resistente (RC R ), originadas do cruzamento entre o genótipo suscetível cv. Catuaí Amarelo IAC 64 e a fonte de resistência Híbrido de Timor UFV 443-03. Para ambos os inóculos, a cv. Catuaí Amarelo IAC 64 foi suscetível, enquanto o Híbrido de Timor UFV 443-03, a planta representante da geração F 1 e as plantas do RC R foram resistentes. As plantas F 2 , quando inoculadas com a raça II, apresentaram dois padrões de segregação signifi cativos: 15:1 e 61:3. A herança da resistência foi confi rmada pela inoculação das plantas do RC S , que segregaram na proporção de 3:1, padrão esperado para herança condicionada por dois genes. A hipótese de segregação 7:1 para três genes foi rejeitada. Resultados semelhantes foram obtidos para o patótipo 001. Dois genes dominantes e independentes conferem a resistência genética do Híbrido de Timor UFV 443-03 à raça II e ao patótipo 001 de H. vastatrix.Item Marcadores moleculares derivados de sequências expressas do genoma café potencialmente envolvidas na resistência à ferrugem(Empresa Brasileira de Pesquisa Agropecuária - Embrapa, 2011-08) Alvarenga, Samuel Mazzinghy; Caixeta, Eveline Teixeira; Hufnagel, Bárbara; Thiebaut, Flávia; Maciel‑Zambolim, Eunize; Zambolim, Laércio; Sakiyama, Ney SussumuO objetivo deste trabalho foi identificar marcadores moleculares relacionados à resistência do cafeeiro (Coffea arabica) à ferrugem (Hemileia vastatrix). Foram identificadas sequências de DNA potencialmente envolvidas na resistência do cafeeiro a doenças, por meio de análise “in silico”, a partir das informações geradas pelo Projeto Brasileiro do Genoma Café. A partir das sequências mineradas, foram desenhados 59 pares de iniciadores para amplificá‐las. Os 59 iniciadores foram testados em 12 cafeeiros resistentes e 12 susceptíveis a H. vastatrix. Vinte e sete iniciadores resultaram em bandas únicas e bem definidas, enquanto um deles amplificou fragmento de DNA em todos os cafeeiros resistentes, mas não nos suscetíveis. Esse marcador molecular polimórfico amplificou uma região do DNA que corresponde a uma janela aberta de leitura parcial do genoma de C. arabica que codifica uma proteína de resistência a doenças. O marcador CARF 005 é capaz de diferenciar os cafeeiros analisados em resistentes e susceptíveis a H. vastatrix.