Identificação de variantes somaclonais em bananeiras 'Prata Anã', utilizando técnicas moleculares e citogenéticas / Identification of somaclonal variants in 'Prata Anã' banana using molecular and cytogenetic techniques

Variação somaclonal é uma variação fenotípica de origem genética, ou seja, uma variação cromossômica que se torna herdável nas gerações seguintes, ou epigenética, que é uma variação transitória devido ao estresse fisiológico que o material sofre, quando submetido ao cultivo in vitro. Um problema específico envolvendo a variação somaclonal em bananeiras 'Prata Anã' foi observado em Andradas, Minas Gerais, em plantas oriundas de micropropagação. A maior dificuldade na separação dos indivíduos normais e variantes é que os caracteres morfológicos, que são inerentes a este tipo de variação, só se tornam evidentes quando a planta está adulta, o que impossibilita a eliminação dos indivíduos variantes ainda em viveiro. Com o objetivo de identificar, ainda em viveiro aqueles indivíduos variantes somaclonais, técnicas moleculares (RAPD e SSR) e citogenéticas (contagem cromossômica e citometria de fluxo) foram utilizadas. Cento e três primers RAPD, 11 combinações de dois primers RAPD, e 33 pares de primers SSR foram utilizados na tentativa de se encontrar marcadores polimórficos capazes de distinguir os indivíduos normais dos variantes, além de distinguir bananeiras 'Prata Anã' de 'Prata'. O primer OPW-08 gerou um fragmento polimórfico que distinguiu uma planta variante de todas as demais, provando que a variação não ocorre de maneira uniforme no genoma dos indivíduos variantes e que não há um retorno à cultivar Prata. As análises com marcadores SSR e a contagem cromossômica não possibilitaram a distinção dos indivíduos variantes, nem a separação das cultivares Prata e Prata Anã. As análises de citometria de fluxo evidenciaram a grande instabilidade cromossômica das bananeiras, porém elas não foram eficientes na identificação de variantes somaclonais.

Somaclonal variation is a phenotypical variation of genetic origin, that is, a chromosomal variation that becomes inheritable in the generations to follow, or of epigenetic origin, in this case being a transitory variation due to the physiological stress suffered when the material is submitted to in vitro cultivation. A specific problem involving somaclonal variation in 'Prata Anã' banana was observed in Andradas, Minas Gerais, in plants originated from tissue culture. The main difficulty in the distinction between the normal and variant plants is the fact that the morphological characters that allow the separation of these two types are only visible and distinguishable when the plants are in their adult phase, which makes it impossible to eliminate the variant seedlings at the nursery stage. For the early distinction of the variants, molecular (RAPD - Random Amplified Polymorphic DNA and SSR - Simple Sequence Repeat) and cytogenetic (chromosome counting and flow cytometry) techniques were used. In the attempt to find polymorphic markers that distinguished the normal plants from the variants as well as the Prata cultivar from the Prata Anã cultivar, 103 RAPD primers, 11 combinations of two RAPD primers, and 33 pairs of SSR primers were used. Primer OPW-08 generated a polymorphic fragment that distinguished a variant from all of the other plants, proving that the variation does not occur uniformly in the genome of all variants, and that there is no return to Prata cultivar. Analyses with SSR markers and chromosome counting were not efficient in separating normal plants from variants or 'Prata' from 'Prata Anã'. Flow cytometry analyses showed an evident instability in the banana genome in terms of number of chromosomes, however, they were not efficient in identifying the somaclonal variants.

Padrões eletroforéticos das proteínas de reserva em grãos de sorgo com presença e ausência de tanino / Electrophoretic patterns of grain storage proteins of sorghum with presence and absence of tannin

Muitos métodos para determinar a presença de taninos são descritos na literatura, mas nenhum deles é universalmente aceito como ideal ou utilizado de forma unânime. Alguns métodos colorimétricos não diferenciam taninos de outros compostos fenólicos, outros utilizam substâncias que não são adequadas como padrão. Métodos que utilizam a capacidade dos taninos de precipitar as proteínas podem causar resultados divergentes devido às diferenças na conformação dessas moléculas. Assim, objetivou-se, neste estudo, identificar a presença de taninos em 10 híbridos de sorgo através da análise de padrões proteicos obtidos por eletroforese. O método colorimétrico Azul da Prússia foi utilizado para quantificar os taninos nas amostras. A precipitação das proteínas pelos taninos permitiu identificar os genótipos de sorgo com tanino através dos padrões proteicos das frações albuminas, globulinas e prolaminas. A análise eletroforética das prolaminas mostrou que as bandas produzidas pelo polipeptídeo kafirina, podem ser utilizadas na identificação de sorgo sem tanino no grão.

Several methods are described on the literature to determine the presence of tannin, however none of them is universally accepted as the ideal or even are used in a unanimous way. Some colorimetric methods do not differentiate tannins from others phenolic compounds, others use substances which are not appropriate to use as standard. Methods that use the capacity of tannins to precipitate proteins may end up with divergent results due to differences on the molecule conformation. Thus, the objective of this study was to identify the presence of tannin in 10 hybrids of sorghum throughout analysis of pattern proteins obtained by electrophoresis. The colored method Prussian Blue was used to quantify tannins on the samples. The protein precipitation by tannins permitted to identify the sorghum genotypes with grain tannin through protein standards of fractions of albumin, globulin and prolamins. The electrophoresis analysis of the prolamins showed that the bands produced by the kafirin polypeptide may be used in sorghum identification without the presence of tannin in grain.

Bacterial and fungal communities in bulk soil and rhizospheres of aluminum-tolerant and aluminum-sensitive maize (Zea mays L.) lines cultivated in unlimed and limed Cerrado soil.

Liming of acidic soils can prevent aluminum toxicity and improve crop production. Some maize lines show aluminum (Al) tolerance, and exudation of organic acids by roots has been considered to represent an important mechanism involved in the tolerance. However, there is no information about the impact of liming on the structures of bacterial and fungal communities in Cerrado soil, nor if there are differences between the microbial communities from the rhizospheres of Al-tolerant and Al-sensitive maize lines. This study evaluated the effects of liming on the structure of bacterial and fungal communities in bulk soil and rhizospheres of Al-sensitive and Al-tolerant maize (Zea mays L.) lines cultivated in Cerrado soil by PCR-DGGE, 30 and 90 days after sowing. Bacterial fingerprints revealed that the bacterial communities from rhizospheres were more affected by aluminum stress in soil than by the maize line (Al-sensitive or Al-tolerant). Differences in bacterial communities were also observed over time (30 and 90 days after sowing), and these occurred mainly in the Actinobacteria. Conversely, fungal communities from the rhizosphere were weakly affected either by liming or by the rhizosphere, as observed from the DGGE profiles. Furthermore, only a few differences were observed in the DGGE profiles of the fungal populations during plant development when compared with bacterial communities. Cloning and sequencing of 16S rRNA gene fragments obtained from dominant DGGE bands detected in the bacterial profiles of the Cerrado bulk soil revealed that Actinomycetales and Rhizobiales were among the dominant ribotypes.

Diversity of nifH gene pools in the rhizosphere of two cultivars of sorghum (Sorghum bicolor) treated with contrasting levels of nitrogen fertilizer.

The diversity of nitrogen-fixing bacteria was assessed in the rhizospheres of two cultivars of sorghum (IS 5322-C and IPA 1011) sown in Cerrado soil amended with two levels of nitrogen fertilizer (12 and 120 kg ha(-1)). The nifH gene was amplified directly from DNA extracted from the rhizospheres, and the PCR products cloned and sequenced. Four clone libraries were generated from the nifH fragments and 245 sequences were obtained. Most of the clones (57%) were closely related to nifH genes of uncultured bacteria. NifH clones affiliated with Azohydromonas spp., Ideonella sp., Rhizobium etli and Bradyrhizobium sp. were found in all libraries. Sequences affiliated with Delftia tsuruhatensis were found in the rhizosphere of both cultivars sown with high levels of nitrogen, while clones affiliated with Methylocystis sp. were detected only in plants sown under low levels of nitrogen. Moreover, clones affiliated with Paenibacillus durus could be found in libraries from the cultivar IS 5322-C sown either in high or low amounts of fertilizer. This study showed that the amount of nitrogen used for fertilization is the overriding determinative factor that influenced the nitrogen-fixing community structures in sorghum rhizospheres cultivated in Cerrado soil.

Diversity of Paenibacillus spp. in the rhizosphere of four sorghum (Sorghum bicolor) cultivars sown with two contrasting levels of nitrogen fertilizer assessed by rpoB-based PCR-DGGE and sequencing analysis.

The diversity of Paenibacillus species was assessed in the rhizospheres of four cultivars of sorghum sown in Cerrado soil amended with two levels of nitrogen fertilizer (12 and 120 kg/ha). Two cultivars (IS 5322-C and IS 6320) demanded the higher amount of nitrogen to grow, whereas the other two (FBS 8701-9 and IPA 1011) did not. Using the DNA extracted from the rhizospheres, a Paenibacillus-specific PCR system based on the RNA polymerase gene (rpoB) was chosen for the molecular analyses. The resulting PCR products were separated into community fingerprints by DGGE and the results showed a clear distinction between cultivars. In addition, clone libraries were generated from the rpoB fragments of two cultivars (IPA 1011 and IS 5322-C) using both fertilization conditions, and 318 selected clones were sequenced. Analyzed sequences were grouped into 14 Paenibacillus species. A greater diversity of Paenibacillus species was observed in cultivar IPA 1011 compared with cultivar IS 5322-C. Moreover, statistical analyses of the sequences showed that the bacterial diversity was more influenced by cultivar type than nitrogen fertilization, corroborating the DGGE results. Thus, the sorghum cultivar type was the overriding determinative factor that influenced the community structures of the Paenibacillus communities in the habitats investigated.

Assessment of the diversity of Paenibacillus species in environmental samples by a novel rpoB-based PCR-DGGE method.

A specific PCR system based on the gene encoding the RNA polymerase beta subunit, rpoB, was developed for amplification and denaturing gradient gel electrophoresis (DGGE) fingerprinting of Paenibacillus communities in environmental samples. This gene has been previously proven to be a powerful identification tool for the discrimination of species within the genus Paenibacillus and could avoid the limitations of 16S rRNA-based phylogenetic analysis. Initially, the PCR system based on universal rpoB primers were used to amplify DNAs of different Paenibacillus species. A new reverse primer (rpoBPAEN) was further designed based on an insertion of six nucleotides in the Paenibacillus sequences analyzed. This semi-nested PCR system was evaluated for specificity using DNAs isolated from 27 Paenibacillus species belonging to different 16S rRNA-based phylogenetic groups and seven non-Paenibacillus species. The non-Paenibacillus species were not amplified using this PCR approach and one group of Paenibacillus species consisting of strains without the six-base insert also were not amplified; these latter strains were found to be distinct based on 16S rRNA gene phylogeny. In addition, a clone library was generated from the rpoB fragments amplified from two Brazilian soil types (Cerrado and Forest) and all 62 clones sequenced were closely related to one of the 22 sequences from Paenibacillus previously obtained in this study. To assess the diversity of Paenibacillus species in Cerrado and Forest soils and in the rhizosphere of different cultivars of maize, a PCR-DGGE system was used. The Paenibacillus DGGE fingerprints showed a clear distinction between communities of Paenibacillus in Forest and Cerrado soils and rhizosphere samples clustered along Cerrado soil. Profiles of cultivars CMS22 and CMS36 clustered together, with only 53% of similarity to CMS11 and CMS04. The results presented here demonstrate the potential use of the rpoB-based Paenibacillus-specific PCR-DGGE method for studying the diversity of Paenibacillus populations in natural environments.

Effect of Baculovirus spodoptera isolates in Spodoptera frugiperda (J.E. Smith) (Lepidoptera: Noctuidae) larvae and their characterization by RAPD

The total of 22 Baculovirus isolates surveyed in different corn producing regions in Brazil were used against fall armyworm, Spodoptera frugiperda (J.E. Smith). The viruses were purified and their suspensions were used to feed fall armyworm larvae from 4th and 5th instar. The mortality rate was checked daily and the infected larvae were frost after death, what generally occurred between the 5th and 7th day after virus ingestion. The 22 Baculovirus isolates were used in six concentrations (from 10³ to 10(8) polyhedra/ml) and one check treatment with water. Mortality rate, larval period, pupal period, pupa weight and lethal concentration (LC50) were determined for all isolates. Significant differences were found among all isolates and different concentrations, also interaction between isolate x virus concentration for all characteristics evaluated, except for pupal period. Amplification patterns of 54 RAPD markers, being 41 polymorphic among the isolates, were used to evaluate the genetic distance and its correlation with the fall armyworm larvae mortality rate. The genetic diversity calculated by the Jaccard's coefficient using the molecular data allowed a division of the isolates into two groups, with a high level of confidence. These groups did not present any association with the mortality rate caused by the isolates or with their geographical distribution. However, a RAPD fragment OPW04.2280 was highly associated with the larvae mortality rate and with LC50, explaining 23 and 65 percent of the phenotypic variation for these traits among the isolates, respectively.

Foram utilizados 22 isolados de vírus amostrados em diferentes regiões produtoras de milho do Brasil. Os vírus foram purificados e suas suspensões fornecidas a lagartas sadias do 3° e 4° ínstar de Spodoptera frugiperda (J.E. Smith). A mortalidade foi avaliada diariamente, e as lagartas infectadas foram congeladas logo após sua morte, o que em geral ocorreu do 5° ao 7° dia após ingestão do vírus. Os isolados foram usados em seis concentrações (10³ a 10(8) poliedros/ml) e uma testemunha (água). Os percentuais de mortalidade, duração do período larval e período pupal, peso de pupa e a concentração letal (CL50) foram determinados para todos os isolados. Foram observadas diferenças significativas entre todos os isolados e concentrações testadas para todos os parâmetros avaliados, e também foi constatada a presença da interação isolado x concentração, exceto para período pupal. Os padrões de amplificação de 54 marcadores RAPD, sendo 41 polimórficos, foram utilizados para avaliar a distância genética e a sua correlação com os índices de mortalidade das lagartas. A divergência genética calculada pelo coeficiente Jaccard utilizando os dados moleculares permitiu dividir os isolados em dois grupos, com um elevada confiabilidade. O agrupamento não apresentou associação com a taxa de mortalidade causada pelos isolados ou com sua distribuição geográfica. No entanto, um fragmento de RAPD OPW04.2280 apresentou-se altamente associado com a mortalidade das lagartas e com a CL50, explicando 23 por cento e 65 por cento da variação fenotípica para essas características entre os isolados virais, respectivamente.

Characterization of rhizobia that nodulate Arachis pintoi by RAPD analysis

As relações genéticas de 85 estirpes de Rhizobium capazes de nodular Arachis pintoi foram determinadas usando o método de "RAPD" (Random Amplified Polymorphic DNA). As análises incluíram 75 estirpes isoladas de solos de Cerrado e 10 de diferentes origens. Os resultados indicaram que existe um alto grau de similaridade entre estas estirpes e que a distribuição geográfica pode afetar suas relações filogenéticas. Além disso, os resultados permitiram a seleção de "primers" mais adequados para a caracterização dessas estirpes de Rhizobium, os quais serão úteis para a implementação de estudos de competitividade nos solos de Cerrado.

Variability of isolated colonies in bean nodulating Rhizobium strains before and after exposure to high temperature

Irregular response to bean plants to Rhizobium inoculation has been attributed to among other factors, low competitive ability, low N2 fixation efficiency and genetic instability of the symbiont. This genetic instability caused by high rates of genomic rearrangements and/or plasmid deletions can be accentuated by high temperatures. This fact may limit the utilization of these strains as inoculants, especially in tropical soils. In this study, the variability of isolated colonies derived from effective R. leguminosarum bv. phaseoli (SLP1.3 and BR 10.026) and R tropici (SLA2.2 and BR322) strains was evaluated before and after exposure to high temperatures (four consecutive thermal shocks at 45ºC). This evaluation involved plant dry matter analysis of inoculated plants and genotypic (plasmid profile and genomic patterns via RAPD) analysis of the Rhizobium strains. The results evidenced that high temperature improve the natural performance variability especially between isolated colonies from R. leguminosarum bv. phaseoli strains. The plasmid profile of isolated colonies from R. tropici strains were identical regardless of temperature treatment whereas isolated colonies from R. leguminosarum bv. phaseoli alterations were detected especially after the thermal treatment. The genomic patterns generated by AP-PCR showed more alterations and genetic variation in isolated colonies from R. leguminosarum bv. phaseoli strains indicating that R. tropici strains are more stable and lower affected by high temperature.

Analyses of genetic variability in Lentinula Edodes through Mycelia responses to different abiotic conditions and RAPD molecular markers

The growth of thirty-four Lentinula edodes strains submitted to different mycelial cultivation conditions (pH and temperature) was evaluated and strain variability was assessed by RAPD molecular markers. The growth at three pH values (5, 6 and 7) and four different temperatures (16, 25, 28 and 37§C) was measured using the in vitro mycelial development rate and water retention as parameters. Mycelial cultivation was successful at all pH tested, while the ideal temperature for mycelial cultivation ranged between 25 and 28§C. The water content was lower in strains grown at 37§C. Among 20 OPA primers (Operon Technologies, Inc.) used for the RAPD analyses, seventeen presented good polymorphism (OPA01 to OPA05, OPA07 to OPA14, OPA17 to OPA20). The clustering based on similarity coefficients allowed the separation of strain in two groups with different geographic origins.

Prospecting sugarcane genes involved in aluminum tolerance

Alumínio (Al) é um dos principais fatores que afetam o desenvolvimento de plantas em solos ácidos, reduzindo substancialmente a produtividade agrícola. Na América do Sul, cerca de 66 por cento da superfície do solo apresentam acidez, onde a alta saturaçäo de alumínio é uma das maiores limitações à prática agrícola. Apesar do crescente número de estudos, uma compreensäo completa das bases bioquímicas e moleculares da tolerância ao alumínio em plantas está longe de ser alcançada. No caso da cana-de-açúcar, näo há nada publicado sobre a regulaçäo gênica induzida durante o stress por alumínio. O objetivo deste trabalho foi identificar genes de cana-de-açúcar relacionados com as várias vias metabólicas reconhecidamente envolvidas na resposta à toxidez do alumínio em outras espécies de plantas e leveduras. Para a maioria dos genes relacionados com alumínio em outras espécies foram identificados similares em cana-de-açúcar, tais como aqueles que codificam enzimas que combatem o stress oxidativo ou a infestaçäo por patógenos, proteínas responsáveis pela exudaçäo de ácidos orgânicos e pela transduçäo de sinais. O papel desses genes na tolerância ao alumínio é revisado. Devido ao alto grau de conservaçäo do genoma entre espécies próximas de gramíneas como milho, cevada, sorgo e cana-de-açúcar, esses genes seräo uma ferramenta valiosa para a melhor compreensäo e manipulaçäo da tolerância ao alumínio nestas espécies.

Random amplified polymorphic DNA analysis of effective "Rhizobium" sp. associated with beans cultivated in brazilian cerrado soils

Efficient bean nodulating Rhizobium strains, isolated from different Brazilian cerrado soils, were characterized by RAPD. This study showed great genetic heterogeneity among R. tropici and R. leguminosarum bv. phaseoli strains and allowed the constitution of genetic clusters, besides indicating the most suitable primers for this characterization. The groups of genetically distinct strains can be used in competitiveness studies to select appropriate Rhizobium strains for bean inoculation in cerrado soils.

Effectes of high temperature on survival, symbiotic performance and genomic modifications of bean nodulating Rhizobium strains

High temperatures can affect the survival, establishment and symbiotic properties of "Rhizobium" strains. Bean nodulating "Rhizobium" strains are considered particularly sensitive because on this strains genetic recombinations and/or deletions occur frequently, thus compromising the use of these bacteria as inoculants. In this study "R. tropici" and "R. leguminosarum" bv. "phaseoli" strains isolated from Cerrado soils were exposed to thermal stress and the strains' growth, survival and symbiotic relationships as well as alterations in their genotypic and phenotypic were analysed. After successive thermal shocks at 45ºC for four hours, survival capacity appeared to be strain-specifc, independent of thermo-tolerance and was more apparent in "R. tropici" strains (with the exception of FJ2.21) were more stable than "R. leguminosarum" bv. "phaseoli" strains because no significant phenotypic alterations were observed following thermal treatments and they maintained their original genotypic pattern after innoculation in plants.

Use of the random amplified polymorphic DNA technique to characterize soybean (Glycine max (L.) Merrill)genotypes

We have started a breeding program to genetically eliminate the lipoxygenase isozymes (LOX) from soybean seeds. These enzymes are believed to be the main cause of off-flavors in soybean products. LOX are present in the seed as three isozymes encoded by three different genes, which are inherited in a simple mendelian fashion. Mutants lacking each one of these isozymes have been identified in the world germplasm. To introduce these null alleles into the Brazilian variety Cristalina, three mutant progenitors were chosen: PI 408.251 (LOX1 minus), PI 86.023 (LOX2 minus), and Ichigowase (LOX3 minus). The random amplified polymorphic DNA (RAPD) technique was used to charactetize these progenitors, as well as lines lacking LOX1 (CR1), LOX3 (CR3), LOX1 and 3 (CR1,3), and LOX2 and 3 (UFV 91-263, UFV 91-401 and UFV 91-717). The results enabled us to establish the fingerprint of each genotype and the genetic distances among them.

Seleçäo e caracterizaçäo de estirpes de rhizobium estáveis e capazes de fixar nitrogênio em feijäo(phaseolus vulgaris L.) / Selection and characterization of rhizobium spp.strains stable and capable in fixing nitrogen in bean(phaseolus vulgaris L.)

resumo:Determinou-se a variabilidade na capacidade de fixaçäo de N2, através de testes de reduçäo de acetileno em nódulos formados por estirpes de Rhizobium, antes e após exposiçäo das bactérias "in vitro" à temperaturas elevadas (38-39ºC).Nódulos formados tanto por estirpes de R.leguminosarum bv.phaseoli como R.tropici mais tolerantes a altas temperaturas quando inoculadas em feijäo, näo sofreram alteraçöes nas características simbióticas tais como, atividade de nitrogenase, peso seco de planta e nitrogênio total fixado.O padräo de proteínas(eletroforese SDS-PAGE) diferenciou estirpes entre e dentro das espécies.A hibridizaçäo do DNA total usando "nifprob" marcada via "nick translation"(biotina 14 dATP), quando a digestäo foi efetuada com EcoRI, diferenciou a espécie de R.leguminosarumbv.phaseoli de R.tropici.Foi observado polimorfismo entre as estirpes de R.leguminosarum bv.phaseoli após digestäo com Bam HI e entre R.leguminosarum bv.phaseoli e R.tropici após a digestäo com Hind III.Näo foram detectadas alteraçöes nos padröes protéicos ou genômicos e na atividade da nitrogenase da mesma estirpe antes e após crescimento a temperaturas elevadas, indicando que as estirpes de ambas as espécies(R.leguminosarum bv.phaseoli e R.tropici), tolerantes a altas temperaturas säo também mais estáveis geneticamente