Navegando por Autor "Caixeta, Eveline Teixeira"

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Artificial neural networks compared with Bayesian generalized linear regression for leaf rust resistance prediction in Arabica coffee
(Pesquisa Agropecuária Brasileira, 2017-03) Silva, Gabi Nunes; Nascimento, Moysés; Sant’Anna, Isabela de Castro; Cruz, Cosme Damião; Caixeta, Eveline Teixeira; Carneiro, Pedro Crescêncio Souza; Rosado, Renato Domiciano Silva; Pestana, Kátia Nogueira; Almeida, Dênia Pires de; Oliveira, Marciane da Silva
The objective of this work was to evaluate the use of artificial neural networks in comparison with Bayesian generalized linear regression to predict leaf rust resistance in Arabica coffee (Coffea arabica). This study used 245 individuals of a F2 population derived from the self-fertilization of the F1 H511-1 hybrid, resulting from a crossing between the susceptible cultivar Catuaí Amarelo IAC 64 (UFV 2148-57) and the resistant parent Híbrido de Timor (UFV 443-03). The 245 individuals were genotyped with 137 markers. Artificial neural networks and Bayesian generalized linear regression analyses were performed. The artificial neural networks were able to identify four important markers belonging to linkage groups that have been recently mapped, while the Bayesian generalized model identified only two markers belonging to these groups. Lower prediction error rates (1.60%) were observed for predicting leaf rust resistance in Arabica coffee when artificial neural networks were used instead of Bayesian generalized linear regression (2.4%). The results showed that artificial neural networks are a promising approach for predicting leaf rust resistance in Arabica coffee.
Breeding potential and genetic diversity of "Híbrido do Timor" coffee evaluated by molecular markers
(Crop Breeding and Applied Biotechnology, 2010-12) Setotaw, Tesfahun Alemu; Caixeta, Eveline Teixeira; Pena, Guilherme Ferreira; Zambolim, Eunize Maciel; Pereira, Antonio Alves; Sakiyama, Ney Sussumu
AFLP, 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.
Caracterização da resistência genética à mancha-angular e desenvolvimento de marcadores microssatélites para regiões específicas do genoma do feijoeiro
(Universidade Federal de Viçosa, 2002-04-08) Caixeta, Eveline Teixeira; Oliveira, Aluízio Borém de; http://lattes.cnpq.br/5969425230895407
A alta incidência de doenças tem sido considerada um dos principais fatores responsáveis pela baixa produtividade do feijoeiro no Brasil. Dentre as doenças que ocorrem em Minas Gerais, a mancha-angular, tem sido apontada como a mais importante da parte aérea. A grande variabilidade genética do patógeno que causa a mancha-angular (Phaeoisariopsis griseola), motiva o constante desenvolvimento de novos cultivares resistentes. Visando dar subsídios a programas de m elhoramento, foram identificadas cinco fontes de resistência à mancha-angular: México 54, AND 277, MAR-2, Cornell 49-242 e BAT 332. Em trabalhos anteriores, foram conduzidos estudos independentes de caracterização genética das quatro primeiras variedades. No presente trabalho, foi estudada a herança da resistência de BAT 332, tendo sido encontrado um gene dominante responsável por essa característica. Para auxiliar programas de melhoramento, foram identificados dois marcadores moleculares do tipo RAPD, OPAA07 950 e OPAO12 950 , ligados em fase de acoplamento a esse gene a uma distância de 5,10 e 5,83 cM, respectivamente. Posteriormente, foram conduzidos testes de alelismo entre as cinco fontes de resistência com o objetivo de entender a relação entre os genes de resistência presentes nessas fontes. Os dados obtidos sugeriram maior complexidade que a encontrada demonstrado nos que estudos Cornell de 49-242 herança possui realizados apenas um anteriormente. gene Foi dominante, denominado de Phg-3, e México 54 três genes distintos, Phg-2, Phg-5 e Phg-6. Em MAR-2 foram encontrados dois genes, um independente denominado de Phg-4 e outro uma forma alélica de um dos genes de México 54, designado de Phg-5 2 . BAT 332 possui um gene dominante, Phg-6 2 , o qual é uma forma alélica de outro gene de México 54. AND 277 possui um alelo de México 54, Phg-2 2 , um de Cornell 49-242, Phg-3 2 , e um de MAR-2, Phg-4 2 . Esses resultados são de especial importância para programas de melhoramento cujo objetivo é a piramidação de genes de resistência. Conhecendo os genes de resistência presentes nas fontes e entendendo a relação entre eles, o melhorista tem a oportunidade de escolher os genitores de seu programa de forma a obter variedade com o maior número e melhor combinação possível de genes de resistência. A maioria dos marcadores moleculares disponíveis para os programas de melhoramento do feijoeiro é do tipo RAPD. A incorporação de marcadores que revelem um maior nível de polimorfismo permite que genótipos relacionados possam ser distinguidos, cruzamentos entre indivíduos aparentados possam ser analisados e marcadores mais próximos do gene de interesse sejam identificados. Os marcadores microssatélites apresentam esse alto polimorfismo e a facilidade típica de marcadores baseados em PCR, no entanto, não têm sido utilizados em feijão pela inexistência de primers microssatélites desenvolvidos para essa espécie. Propôs-se, portanto, na terceira parte deste trabalho, o desenvolvimento desses marcadores para o feijoeiro. Foram obtidos 21 pares de primers que amplificaram bandas únicas e bem definidas, sendo que 15 apresentaram bandas polimórficas e 7 monomórficas. O número de alelos por loco variou de um a seis. A disponibilidade de marcadores moleculares co-dominantes, altamente informativos e de fácil obtenção como os microssatélites será de grande utilidade para os melhoristas e geneticistas que se dedicam ao feijoeiro.
Cross-species amplification and characterization of new microsatellite markers for the macaw palm, Acrocomia aculeata (Arecaceae)
(Plant Genetic Resources, 2016-09) Mengistu, Fekadu Gebretensay; Motoike, Sérgio Yoshimitsu; Caixeta, Eveline Teixeira; Cruz, Cosme Damião; Kuki, Kacilda Naomi
Microsatellites or simple sequence repeats (SSRs) are useful molecular markers allowing for efficient conservation and sustainable use of genetic resources of plant species. Development of SSR marker system for new species is a very expensive task and time consuming. Crossspecies amplification of microsatellite loci is considered as a cost-effective approach for developing microsatellite markers for new species. The aim of this work was to examine the transferability of some SSR markers of two Arecaceae species (Astrocaryum aculeatum and Elaeis oleifera), in Acrocomia aculeata. Out of the total markers analysed 44% of the markers successfully amplified the genomic DNA in A. aculeata, of which 26% were polymorphic detecting a range of three to eight alleles with an average of 4.5 per locus. High average percentage of polymorphic loci (P 1⁄4 71.2%) per provenance was obtained within a range of 57–100% detecting genetic variation in A. aculeata germplasm collections. The polymorphic markers detected a positive inbreeding coefficient (F . 0) per locus revealing heterozygote deficiency in the accessions that were analysed. As the cross-amplification was at family level, in which the taxonomic distance is relatively wider between the sources (A. aculeatum and E. oleifera) and the target (A. aculeata) species, the amplification success was relatively low. However, the results are promising and implicated that high cross-amplification success could be achieved at species or genus level in A. aculeata. The markers will contribute towards the domestication of the potential macaw palm through realizing various studies such as population genetics, germplasm characterization, genetic improvement and conservation.
Differential expression of molecular rust resistance components have distinctive profiles in Coffea arabica - Hemileia vastatrix interactions
(European Journal of Plant Pathology, 2017-11) Barka, Geleta Dugassa; Caixeta, Eveline Teixeira; Almeida, Robson Ferreira de; Alvarenga, Samuel Mazzinghy; Zambolim, Laércio
Countering the economic hurdle caused by coffee leaf rust disease is most appealing at this time as it has posed a major threat to coffee production around the world. Establishing differential expression profiles at different times following pathogen invasion in both innate and acquired immunities unlocks the molecular components of resistance and susceptibility. Suppression subtractive hybridization (SSH) was used to identify genes differentially over-expressed and repressed during incompatible and compatible interactions between Coffea arabica and Hemileia vastatrix. From 433 clones of expressed sequence tags (ESTs) sequenced, 352 were annotated and categorized of which the proportion of genes expressed during compatible interaction were relatively smaller. The result showed upregulation and downregulation of various genes at 12 and 24 h after pathogen inoculation in both interactions. The use of four different databases in searching for gene homology resulted in different number of similar sequences. BLASTx against EMBL-EBI (European Molecular Biology Laboratory-European Bioinformatics Institute) database being with the maximum (100%) hits for all the annotated sequences. RT-qPCR analysis of seven resistance-signaling genes showed similar expression patterns for most of the genes in both interactions, indicating these genes are involved in basal (non-specific) defense during which immune reactions are similar. Using SSH, we identified different types of resistance related genes that could be used for further studies towards resistant cultivar development. The potential role of some of the resistance related proteins found were also discussed.
Early selection enabled by the implementation of genomic selection in Coffea arabica breeding
(Frontiers in Plant Science, 2019-01) Sousa, Tiago Vieira; Caixeta, Eveline Teixeira; Alkimim, Emilly Ruas; Oliveira, Antonio Carlos Baião; Pereira, Antonio Alves; Sakiyama, Ney Sussumu; Zambolim, Laércio; Resende, Marcos Deon Vilela
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.
Ethylene responses and ACC oxidase gene expression in Lippia alba (Verbenaceae) chemotypes with varying ploidy levels
(In Vitro Cellular & Developmental Biology - Plant, 2017-06) Batista, Diego Silva; Castro, Kamila Motta de; Ribeiro, Dimas Mendes; Caixeta, Eveline Teixeira; Santos, Marcelo de Oliveira; Viccini, Lyderson Facio; Otoni, Wagner Campos
Lippia alba (Mill.) N. E. Br ex Britton & P. Wilson is a species of great economic importance due to the medicinal activity conferred by its essential oils. Ethylene (ET) is a gaseous hormone that affects several processes in plant growth and development. This hormone is synthesized through a reaction in which 1-aminocyclopropane-1-carboxylic acid (ACC) is converted to ET by the action of the enzyme ACC oxidase (ACO). The ET activity in three L. alba chemotypes (BGEN-01, triploid; BGEN-02, diploid; and BGEN-42, hexaploid) was evaluated by culturing plants in vitro in the presence of the ET precursor (ACC), scavenger mercury perchloride (MP), the inhibitors aminoethoxyvinylglycine (AVG) and silver thiosulfate (STS), and a CO2-enriched atmosphere. Leaf abscission rate, ET accumulation, and ACO gene expression (LaACO) were investigated. Leaf abscission was higher in BGEN-42, regardless of the precursor/inhibitor. ACC had the highest ET accumulation in BGEN-02 and BGEN-01, whereas BGEN-42 presented lower ET accumulation than the control. MP and AVG were effective in preventing ET production when compared to the control. LaACO was upregulated in BGEN-01 and BGEN-42 treated with ACC and in BGEN-01 treated with STS. In the CO2 enrichment experiments, LaACO expression was higher in BGEN-42 in the treatments without forced ventilation. Thus, the expression of this gene in L. alba can be altered by elevating CO2 levels and also by the addition of ACC. This is the first report of ET interactions in L. alba cultured in vitro.
Following the track of “Híbrido de Timor” origin by cytogenetic and flow cytometry approaches
(Genetic Resources and Crop Evolution, 2013-12) Clarindo, Wellington Ronildo; Carvalho, Carlos Roberto; Caixeta, Eveline Teixeira; Koehler, Andréa Dias
The supposedly first plant of the coffee cultivar “Híbrido de Timor” (HT) was found in 1927, being denoted as HT CIFC 4106. According to different researchers, this plant originated from a natural interspecific hybridation between Coffea arabica (4x = 44) and Coffea canephora (2x = 22). From HT CIFC 4106, other HT accessions were obtained and employed to establish germplasm banks in some countries. As HT has been widely used in Coffea breeding programs, this study aimed to characterize different HT accessions with regard to ploidy, nuclear DNA content and base composition. Based on these data, the ploidy of HT CIFC 4106 was determined, suggesting that this accession is an allotriploid formed from reduced reproductive cell of C. canephora and of C. arabica. All HT CIFC 4106 plants exhibited the same 2C-value, AT% and chromosome number, showing that vegetative propagation has enabled the multiplication and germplasm conservation of this cytotype since 1927. Further five analyzed HT accessions showed distinct nuclear 2C-value and AT%. Since HT CIFC 4106 has been considered the first HT, it is suggested that aneuploid reproductive cells of this HT originated the other plants. Considering that HT accessions are used in the development of C. arabica cultivars, the findings of this study are important for the design of strategies to obtain new cultivars for breeding programs. Moreover, these data represent the first step to understand the origin and genome evolution of the HT.
Fontes de resistência à mancha-angular do feijoeiro-comum no Brasil
(Revista Ceres, 2000-09) Nietsche, Silvia; Borém, Aluízio; Rocha, Renato Cipriano; Caixeta, Eveline Teixeira; Barros, Everaldo Gonçalvez de; Moreira, Maurilio Alves
The objective of this study was to evaluate the resistance of bean genotypes to different races of Phaeoisariopsis griseola present in Brazil, by studying the reaction of nine potentially resistant bean sources (MAR 1, MAR 2, MAR 3, AND 277, G 5686, BAT 332, Cornell 49-242 and Mexico 54) inoculated with 61 fungus isolates and characterized in 25 pathotypes. The first trifoliate leaf of each plant was inoculated with a 2 x 104 spores/ml suspension. Plants were maintained at 20-22 ºC and 95 % relative humidity for 48 hours. The evaluations were carried out 15 days after inoculation. The variety Mexico 54 presented & resistance reaction to 20 races thus being considered the best resistance source tested. tIhe varieties AND 277, MAR 2, Cornell 49-242, G5686 and BAT 332 were resistant to 17, 16, 12, 13 and 10 races, respectively. "Ihe Rudá variety was susceptible to most races. These results demonstrated the need to introduce more resistance genes to angular leaf spot in commercial varieties.
Herança da resistência do Híbrido de Timor UFV 443-03 à ferrugem- do- cafeeiro
(Pesquisa Agropecuária Brasileira, 2009-03) Capucho, Alexandre Sandri; Caixeta, Eveline Teixeira; Zambolim, Eunize Maciel; Zambolim, Laércio
O 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 F2, 115 plantas do retrocruzamento suscetível (RCS) e 87 plantas do retrocruzamento resistente (RCR), 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 F1 e as plantas do RCR foram resistentes. As plantas F2, quando inoculadas com a raça II, apresentaram dois padrões de segregação significativos: 15:1 e 61:3. A herança da resistência foi confirmada pela inoculação das plantas do RCS, 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.
High throughput transcriptome analysis of coffee reveals prehaustorial resistance in response to Hemileia vastatrix infection
(Plant Molecular Biology, 2017-11-01) Florez, Juan Carlos; Mofatto, Luciana Souto; Freitas-Lopes, Rejane do Livramento; Ferreira, Sávio Siqueira; Zambolim, Eunize Maciel; Carazzolle, Marcelo Falsarella; Zambolim, Laércio; Caixeta, Eveline Teixeira
Coffee rust disease, caused by the fungus Hemileia vastatrix, is one of the major diseases in coffee throughout the world. The use of resistant cultivars is considered to be the most effective control strategy for this disease. To identify candidate genes related to different mechanism defense in coffee, we present a time-course comparative gene expression profile of Caturra (susceptible) and Híbrido de Timor (HdT, resistant) in response to H. vastatrix race XXXIII infection. The main objectives were to obtain a global overview of transcriptome in both interaction, compatible and incompatible, and, specially, analyze up-regulated HdT specific genes with inducible resistant and defense signaling pathways. Using both Coffea canephora as a reference genome and de novo assembly, we obtained 43,159 transcripts. At early infection events (12 and 24 h after infection), HdT responded to the attack of H. vastatrix with a larger number of up-regulated genes than Caturra, which was related to prehaustorial resistance. The genes found in HdT at early hours were involved in receptor-like kinases, response ion fluxes, production of reactive oxygen species, protein phosphorylation, ethylene biosynthesis and callose deposition. We selected 13 up-regulated HdT-exclusive genes to validate by real-time qPCR, which most of them confirmed their higher expression in HdT than in Caturra at early stage of infection. These genes have the potential to assist the development of new coffee rust control strategies. Collectively, our results provide understanding of expression profiles in coffee—H. vastatrix interaction over a time course in susceptible and resistant coffee plants.
High-density genetic mapping for coffee leaf rust resistance
(Tree Genetics & Genomes, 2011-06-10) Loureiro, Marcelo Ehlers; Diola, Valdir; Brito, Giovani Greigh de; Caixeta, Eveline Teixeira; Maciel-Zambolim, Eunize; Sakiyama, Ney Sussumu
Coffee leaf rust caused by the fungus Hemileia vastatrix causes considerable economic losses for coffee producers. Although agrochemical products can provide sufficient disease control, the use of resistant cultivars is a safer alternative. This resistance may be constrained by one or a few genetic factors, mainly those found in material originating from interspecific hybrids. In this study, the genetic analysis of an F 2 population consisting of 224 plants derived from a crossing of Híbrido de Timor UFV 427-15 (resistant) with Catuaí Amarelo IAC 30 (susceptible) showed that a dominant gene confers the resistance of coffee to race II of H. vastatrix. From a genetic map saturated with 25 amplified fragment length polymorphism (AFLP) markers linked to the resistance gene, we developed a high-density genetic map with six sequence-characterized amplified region (SCAR) markers delimiting a chromosomal region of 9.45 cM and flanking the dominant gene at 0.7 and 0.9 cM. This is the first saturated and high-density genetic map obtained from this region containing the resistance gene. The results of this study are of great importance for the introduction of molecular markers for marker-assisted selection; they will also facilitate studies related to the cloning, structure, and function of race-specific genes involved in the resistance of coffee trees to H. vastatrix.
High-throughput targeted genotyping using next-generation sequencing applied in Coffea canephora breeding
(Euphytica, 2018-03) Alkimim, Emilly Ruas; Caixeta, Eveline Teixeira; Sousa, Tiago Vieira; Silva, Felipe Lopes da; Sakiyama, Ney Sussumu; Zambolim, Laércio
The use of molecular markers to detect polymorphism at DNA level is one of the most significant developments in molecular biology techniques. With the development of new next-generation sequencing technologies, the discovery of SNP became easier and faster, and the costs of data point were reduced. The development and use of SNP markers for coffee have provided new perspectives for the evaluation of genetic diversity and population structure via different statistical approaches. In this study, 72 Coffea canephora genotypes were analyzed to identify the SNP markers and apply them to genetic studies and selection of parents/hybrids in genetic breeding. As many as 117,450 SNP were identified using the RAPiD Genomics platform. After quality analyses, 33,485 SNP were validated for analyses of genetic diversity and population structure. Genotypes were separated based on their varietal groups, and Hybrids were differentiated using the clustering and Bayesian approach. Coffee accessions mistakenly identified in the germplasm and breeding program were detected. The Conilon varietal group presented the lowest genetic dissimilarity values, suggesting the introduction of new accessions in the germplasm bank. The highest genetic distances values were observed among genotypes of the heterotic groups (Conilon and Robusta). The markers were efficient in evaluating the genetic diversity and population structure of C. canephora. Promising crosses were selected within and between the varietal groups. Hybrids with greater genetic distances were selected, which were important for C. canephora breeding programs.
In silico identification of coffee genome expressed sequences potentially associated with resistance to diseases
(Genetics and Molecular Biology, 2010-12-01) Alvarenga, Samuel Mazzinghy; Maciel-Zambolim, Eunize; Zambolim, Laércio; Sakiyama, Ney Sussumu; Caixeta, Eveline Teixeira; Thiebaut, Flávia; Hufnagel, Bárbara
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.
Inheritance of coffee leaf rust resistance and identification of AFLP markers linked to the resistance gene
(Euphytica, 2010-03) Brito, Giovani Greigh de; Caixeta, Eveline Teixeira; Gallina, Ana Paula; Zambolim, Eunize Maciel; Zambolim, Laércio; Diola, Valdir; Loureiro, Marcelo Elhers
The most important disease of Coffea arabica is coffee leaf rust caused by the fungus Hemileia vastatrix. The purpose of this study was to characterize the inheritance of coffee resistance gene(s) to race II of this pathogen and to identify and map molecular markers linked to this trait. Different populations were used: F2 (160 plants), BCr (20), and BCs (135), derived from a cross between the resistant genotype Híbrido de Timor UFV 427-15 and the susceptible cultivar Catuaí Amarelo UFV 2143-236 (IAC 30). The segregation analysis showed that the resistance of Híbrido de Timor to race II of the H. vastatrix is conferred by a single dominant gene. The amplification of 176 AFLP (Amplified fragment length polymorphism) primer combinations using bulked segregant analysis (BSA) allowed the identification of three molecular markers linked to the resistance gene. Genetic mapping of these three markers in the F2 population indicated that they are distributed on both sides, flanking the resistance gene. The markers E.CTC/M.TTT405 and E.CGT/M.TGT300 were found linked to the resistance gene at 8.69 cM (LOD 18.91) and 25.10 cM (LOD 5.37), respectively, while E.CCT/M.TTC230 was localized on the other side of the gene, at 20.50 cM (LOD 6.15). These markers are the first rust resistance markers identified in Híbrido de Timor and can be useful for marker assisted selection in coffee breeding programs.
Inheritance study and linkage mapping of resistance loci to Hemileia vastatrix in Híbrido de Timor UFV 443-03
(Tree Genetics & Genomes, 2015-06-26) Pestana, Kátia Nogueira; Capucho, Alexandre Sandri; Caixeta, Eveline Teixeira; Almeida, Dênia Pires de; Zambolim, Eunize Maciel; Cruz, Cosme Damião; Zambolim, Laércio; Pereira, Antônio Alves; Oliveira, Antonio Carlos Baião de; Sakiyama, Ney Sussumu
Coffee leaf rust (CLR) caused by Hemileia vastatrix Berk. et Br. is one of the major Coffea arabica diseases worldwide. CLR resistance has been attributed to at least nine dominant genes, as single or in combination. We present an inheritance study and mapping loci involved in the Híbrido de Timor (HDT) UFV 443-03 resistance to race I, race II, and pathotype 001 of H. vastatrix. Molecular markers were used to ascertain the phenotypic results and to map the putative resistance loci. For all tree isolates, the inheritance study indicated that the resistance of HDT UFV 443-03 is conditioned by two independent dominant loci or by three independent loci (two dominant and one recessive). Molecular marker analyses ascertained that the resistance of HDT UFV 443-03 to race II is conditioned by at least two independent dominant loci, while the resistance to race I and pathotype 001 is conditioned by at least four independent dominant loci. Gene pyramiding might result in a cultivar with durable resistance; however, it is difficult to distinguish between plants with one or more resistance genes due to epistatic effects. Molecular markers linked to these genes were indicated for marker-assisted selection, as it is an efficient breeding alternative for CLR resistance with no such epistatic effects.
Marcadores moleculares derivados de sequências expressas do genoma café potencialmente envolvidas na resistência à ferrugem
(Pesquisa Agropecuária Brasileira, 2011-08-21) Alvarenga, Samuel Mazzinghy; Caixeta, Eveline Teixeira; Hufnagel, Bárbara; Thiebaut, Flávia; Zambolim, Eunize Maciel-; Zambolim, Laércio; Sakiyama, Ney Sussumu
O 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.
Marker-assisted selection provides arabica coffee with genes from other Coffea species targeting on multiple resistance to rust and coffee berry disease
(Molecular Breeding, 2017-01-04) Alkimim, Emilly Ruas; Caixeta, Eveline Teixeira; Sousa, Tiago Vieira; Pereira, Antônio Alves; Oliveira, Antonio Carlos Baião de; Zambolim, Laércio; Sakiyama, Ney Sussumu
Selecting superior genotypes is facilitated by marker-assisted selection (MAS), which is particularly suitable for transferring disease resistance alleles because it nullifies environmental effects and allows selection of resistant individuals in the absence of the pathogen or race, enabling preventive breeding. Molecular markers linked to two major genes (SH3 and SH?), conferring resistance to coffee rust, and those linked to the Ck-1 gene, conferring resistance to coffee berry disease (CBD), have previously been identified. These markers were validated and used in a progeny of crosses between Indian selections with Coffea arabica cultivars. Eleven resistant individuals homozygous for SH3 were identified by MAS. Of these, seven carry SH? from Híbrido de Timor and the gene introduced from Coffea liberica (SH3). SH? was characterized as derived from Coffea canephora. Thus, it was possible to identify C. arabica genotypes carrying important genes for rust resistance introgressed from other coffee species. MAS also allowed identification of sources of CBD resistance for use in preventive breeding for resistance to this serious disease. Using two validated molecular markers, two coffee plants carrying Ck-1 were identified: the UFV 328-60 genotype (F2) was resistant and homozygous based on both molecular markers but exhibited no markers related to SH3 and SH?, and the UFV 317-12 genotype (F1) was resistant and homozygous but resistant and heterozygous based on CBD-Sat207 and CBD-Sat235, respectively. Along with possessing Ck-1, the latter carries SH?. Overall, plants carrying different genes for resistance to rust and CBD were identified. These plants are important sources for gene pyramiding in breeding programs aimed at multiple and durable resistance.
Molecular diversity in Coffea canephora germplasm conserved and cultivated in Brazil
(Crop Breeding and Applied Biotechnology, 2013-12) Cruz, Cosme Damião; Souza, Flávio de França; Caixeta, Eveline Teixeira; Ferrão, Luís Felipe Ventorim; Pena, Guilherme Ferreira; Sakiyama, Ney Sussumu; Zambolim, Eunize Maciel; Zambolim, Laércio
This 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 germplasm.
Molecular diversity in Fusarium oxysporum isolates from common bean fields in Brazil
(European Journal of Plant Pathology, 2018-04-16) Silva, Lucas Fagundes; Cruz, Andre Freire; Sousa, Tiago Vieira; Nicoli, Alessandro; Paula Junior, Trazilbo Jose de; Caixeta, Eveline Teixeira; Zambolim, Laercio
The common bean (Phaseolus vulgaris L.) is widely cultivated in Brazil and is known as a very important crop for families in this country. Fusarium wilt severely harms common beans and has become a big issue for this crop. In order to assist the breeding programs that target resistance to this disease, the evaluation of genetic diversity of the pathogen and its molecular characterization are crucial. Thus, the present goal was to identify Fusarium isolates obtained from several places in Brazil using molecular tools; select molecular markers for these isolates; and analyze their diversity. All of isolates were molecularly identified as Fusarium oxysporum f. sp. phaseoli (Fop). By using seven selected SSR markers, the results of diversity obtained by the dendrogram and the Bayesian analysis formed four groups where a large diversity of this fungus was found within each state. However, the groups were more homogenous according to the collection source and the pathogenicity test. More specifically, group 2 was composed of the most virulent strains and originated from Minas Gerais State – UFV, and group 3 was mostly composed by isolates from Goias state. Group I was also more diverse in terms of location and virulence. The overall results indicated a positive correlation between Fusarium diversity and its virulence to common bean. Furthermore, the use of these markers was effective in molecular identification and in detecting polymorphism within F. oxysporum f. sp. phaseoli.