In order to understand the genetic responses resulting from physiological changes that occur in plants displaying citrus variegated chlorosis (CVC) symptoms, we adopted a strategy of comparing two EST libraries from sweet orange [Citrus sinensis (L.) Osbeck]. One of them was prepared with plants showing typical CVC symptoms caused by Xylella fastidiosa and the other with non-inoculated plants. We obtained 15,944 ESTs by sequencing the two cDNA libraries. Using an in silico hybridization strategy, 37 genes were found to have significant variation at the transcriptional level. Within this subset, 21 were up-regulated and 16 were down-regulated in plants with CVC. The main functional categories of the down-regulated transcripts in plants with CVC were associated with metabolism, protein modification, energy and transport facilitation. The majority of the up-regulated transcripts were associated with metabolism and defense response. Some transcripts associated with adaptation to stress conditions were up-regulated in plants with CVC and could explain why plants remain alive even under severe water and nutritional stress. Others of the up-regulated transcripts are related to defense response suggesting that sweet orange plants activate their defense machinery. The genes associated with stress response might be expressed as part of a secondary response related to physiological alterations caused by the infection.

CitEST project resulted in the construction of cDNA libraries from different Citrus sp. tissues under various physiological conditions. Among them, plantlets of Rangpur lime were exposed to hydroponic conditions with and without water stress using PEG6000. RNA from roots was obtained and generated a total of 4,130 valid cDNA reads, with 2,020 from the non-stressed condition and 2,110 from the stressed set. Bioinformatic analyses measured the frequency of each read in the libraries and yielded an in silico transcriptional profile for each condition. A total of 40 contigs were differentially expressed and allowed to detect up-regulated homologue sequences to well known genes involved in stress response, such as aquaporins, dehydrin, sucrose synthase, and proline-related synthase. Some sequences could not be classified by using FunCat and remained with an unknown function. A large number of sequences presented high similarities to annotated genes involved with cell energy, protein synthesis and cellular transport, suggesting that Rangpur lime may sustain active cell growth under stressed condition. The presence of membrane transporters and cell signaling components could be an indication of a coordinated morphological adaptation and biochemical response during drought, helping to explain the higher tolerance of this rootstock to water stress.

Citrus is the most important fruit crop in Brazil and Citrus tristeza virus (CTV) is considered one of the most important pathogens of citrus. Most citrus species and varieties are susceptible to CTV infection. However, Poncirus trifoliata, a close relative of citrus, is resistant to the virus. In order to better understand the responses of citrus plants to the infection of CTV, we constructed expressed sequence tag (EST) libraries with tissues collected from Poncirus trifoliata plants, inoculated or not with Citrus tristeza virus at 90 days after inoculation, grafted on Rangpur lime rootstocks. We generated 17,867 sequence tags from Poncirus trifoliata inoculated (8,926 reads) and not (8,941 reads) with a severe CTV isolate. A total of 2,782 TCs (Tentative Consensi sequences) were obtained using both cDNA libraries in a single clusterization procedure. By the in silico hybridization approach, 289 TCs were identified as differentially expressed in the two libraries. A total of 121 TCs were found to be overexpressed in plants infected with CTV and were grouped in 12 primary functional categories. The majority of them were associated with metabolism and defense response. Some others were related to lignin, ethylene biosynthesis and PR proteins. In general, the differentially expressed transcripts seem to be somehow involved in secondary plant response to CTV infection.

Locos de microssatélites são úteis como marcadores genéticos pois são numerosos, ocorrem em todos os cromossomos e possuem um alto nível de polimorfismo. Além disso, podem ser amplificados por meio da PCR e resolvidos em géis de agarose. O maior problema, no entanto, reside no fato de que os primers utilizados em sua amplificação apresentam diferentes comprimentos e composição de nucleotídeos, o que gera a necessidade de otimizar programas de PCR para cada loco. Este trabalho descreve programas de PCR "touchdown" utilizados com sucesso na amplificação de um conjunto de 125 locos de microssatélites de milho escolhidos por serem representativos de todos os cromossomos. Os programas variaram tanto em relação à temperatura de anelamento (Tm), como na concentração dos primers. Assim, os primers puderam ser agrupados em quatro grupos: um grupo maior, constituído por primers que mostraram boa amplificação quando utilizados em um programa básico já publicado porém com concentrações diferentes de primers; um segundo grupo que amplificou em programas alternativos, nos quais as Tm foram modificadas de modo a incluir as Tm de ambos os primers ou a maior Tm do par de primers, estimadas em base da composição nucleotídica dos primers; um terceiro grupo foi composto por primers que amplificaram em programas com Tm mais elevadas que as estimadas, e um quarto grupo, com apenas dois pares de primers, em que a situação oposta ocorreu.

Maize (Zea mays L.) microsatellite loci are useful as genetic markers because they are numerous, occur in every chromosome, and have a high content of polymorphism information. Furthermore, they can be amplified by PCR and the resulting fragments resolved on agarose gels. A major problem, however, is that the primers used in their amplification often have different length and nucleic acid content, requiring optimization of PCR amplification programs for each locus. We developed "touchdown" PCR programs successfully used in the amplification of a set of 125-maize microsatellite loci, chosen as representative of all chromosomes. The programs varied both in relation to the annealing temperature (Tm) and primer concentration. Primers could be divided into four groups. A large group included primers that amplified well in a basic previously published amplification program but with different primer concentrations. A second group amplified in alternative programs in which the annealing temperatures were changed so as to include the Tm of either both primers or the highest Tm of the primer pair estimated based on their nucleotide composition. A third group included primers that amplified in programs with Tm higher than those estimated, and in a fourth group, with just two pairs of primers, the opposite situation prevailed.

Marcadores moleculares foram utilizados para estudar os efeitos do nitrogênio mineral na expressão fenotípica de QTLs associados ao número de nódulos (NN) e à resistência a Xanthomonas axonopodis pv. phaseoli em feijoeiro. Linhagens recombinantes obtidas do cruzamento BAT-93 x Jalo EEP558 foram avaliadas em casa-de-vegetação, sob dois níveis de adubação nitrogenada (0 e 5 mM de NH4NO3). A resistência ao patógeno foi avaliada pela medição da área foliar lesionada (DLA) e o NN por meio de contagem direta. Análises de variância foram empregadas para detectar associações significativas entre características quantitativas e genótipos das linhagens em 85 loci marcadores distribuídos em 12 grupos de ligação (LG). Sob a condição de ausência de N mineral, foram encontradas associações significativas entre 15 marcadores distribuídos em 7 LG para NN e 11 marcadores em 5 LG para DLA, explicando 34 e 42% da variação fenotípica destas características, respectivamente. Na presença de N, foram detectadas somente cinco associações significativas para NN e oito para DLA, explicando 28 e 26% da variação fenotípica de cada respectiva característica. Alguns QTLs foram detectados somente na ausência de N, evidenciando o efeito deste elemento na expressão destes QTLs. Entretanto, em alguns QTLs associados a NN, a contribuição dos alelos parentais foi dependente da concentração de N utilizada. Quatro QTLs foram encontrados associados tanto a número de nódulos como resistência a Xanthomonas, sugerindo um controle genético comum do feijoeiro à infecções bacterianas. Por outro lado, a expressão fenotípica de alguns QTLs não foi significativamente afetada pelo nível de nitrogênio utilizado. A estabilidade destes QTLs é interessante do ponto de vista de um programa de melhoramento voltado para o desenvolvimento de cultivares adaptadas a condições variáveis de fertilidade de solo.

Molecular markers were used to estimate the effect of mineral nitrogen on the phenotypic expression of quantitative trait loci (QTL) controlling the number of Rhizobium nodules (NN) and resistance to Xanthomonas axonopodis pv. phaseoli in the common bean. Recombinant inbred lines derived from a BAT-93 x Jalo EEP558 cross were grown in a greenhouse in the absence or presence (5 mM NH4NO3) of nitrogen. Resistance to Xanthomonas was assessed as diseased leaf area (DLA) and the number of nodules was obtained by direct counting. Analyses of variance were used to detect significant associations between 85 marker loci from 12 linkage groups (LG) and quantitative traits. In the absence of nitrogen, 15 and 11 markers, distributed over 7 and 5 LG, showed a significant association with NN and DLA, respectively. The combined percentage of phenotypic variance explained by the marker-loci and QTL associations was 34% for NN and 42% for DLA. In the presence of nitrogen, there were only five significant associations for NN and eight for DLA, which explained 28 and 26% of the total phenotypic variance, respectively. The effects of some QTL were detected only at a certain level of nitrogen. The contribution of parental alleles at two NN QTL was dependent on the level of nitrogen. Four QTL were associated with both the number of Rhizobium nodules and resistance to Xanthomonas, suggesting a common genetic control of responses to bacterial infections in the common bean. Despite the dramatic environmental interactions noted with some QTL, in other cases the phenotypic effects were not affected by the amount of nitrogen. The stability of the latter QTL may be relevant when breeding cultivars adapted to variable soil fertility.