Plants experience various environmental stresses, but tolerance to these adverse conditions is a very complex phenomenon. The present research aimed to evaluate a set of genes involved in osmotic response, comparing soybean and medicago with the well-described Arabidopsis thaliana model plant. Based on 103 Arabidopsis proteins from 27 categories of osmotic stress response, comparative analyses against Genosoja and Medicago truncatula databases allowed the identification of 1,088 soybean and 1,210 Medicago sequences. The analysis showed a high number of sequences and high diversity, comprising genes from all categories in both organisms. Genes with unknown function were among the most representative, followed by transcription factors, ion transport proteins, water channel, plant defense, protein degradation, cellular structure, organization & biogenesis and senescence. An analysis of sequences with unknown function allowed the annotation of 174 soybean and 217 Medicago sequences, most of them concerning transcription factors. However, for about 30% of the sequences no function could be attributed using in silico procedures. The establishment of a gene set involved in osmotic stress responses in soybean and barrel medic will help to better understand the survival mechanisms for this type of stress condition in legumes.

Plants have the ability to recognize and respond to a multitude of pathogens, resulting in a massive reprogramming of the plant to activate defense responses including Resistance (R) and Pathogenesis-Related (PR) genes. Abiotic stresses can also activate PR genes and enhance pathogen resistance, representing valuable genes for breeding purposes. The present work offers an overview of soybean R and PR genes present in the GENOSOJA (Brazilian Soybean Genome Consortium) platform, regarding their structure, abundance, evolution and role in the plantpathogen metabolic pathway, as compared with Medicago and Arabidopsis. Searches revealed 3,065 R candidates (756 in Soybean, 1,142 in Medicago and 1,167 in Arabidopsis), and PR candidates matching to 1,261 sequences (310, 585 and 366 for the three species, respectively). The identified transcripts were also evaluated regarding their expression pattern in 65 libraries, showing prevalence in seeds and developing tissues. Upon consulting the SuperSAGE libraries, 1,072 R and 481 PR tags were identified in association with the different libraries. Multiple alignments were generated for Xa21 and PR-2 genes, allowing inferences about their evolution. The results revealed interesting insights regarding the variability and complexity of defense genes in soybean, as compared with Medicago and Arabidopsis.

Physical maps are important tools to uncover general chromosome structure as well as to compare different plant lineages and species, helping to elucidate genome structure, evolution and possibilities regarding synteny and colinearity. The increasing production of sequence data has opened an opportunity to link information from mapping studies to the underlying sequences. Genome browsers are invaluable platforms that provide access to these sequences, including tools for genome analysis, allowing the integration of multivariate information, and thus aiding to explain the emergence of complex genomes. The present work presents a tutorial regarding the use of genome browsers to develop targeted physical mapping, providing also a general overview and examples about the possibilities regarding the use of Fluorescent In Situ Hybridization (FISH) using bacterial artificial chromosomes (BAC), simple sequence repeats (SSR) and rDNA probes, highlighting the potential of such studies for map integration and comparative genetics. As a case study, the available genome of soybean was accessed to show how the physical and in silico distribution of such sequences may be compared at different levels. Such evaluations may also be complemented by the identification of sequences beyond the detection level of cytological methods, here using members of the aquaporin gene family as an example. The proposed approach highlights the complementation power of the combination of molecular cytogenetics and computational approaches for the anchoring of coding or repetitive sequences in plant genomes using available genome browsers, helping in the determination of sequence location, arrangement and number of repeats, and also filling gaps found in computational pseudochromosome assemblies.

Nos últimos anos a ferrugem asiática, causada pelo fungo Phakopsora pachyrhizi tornou-se uma das mais sérias ameaças a produção de soja Brasileira. Linhagens melhoradas e variedades têm sido selecionadas para a resistência à ferrugem da soja na Ásia, entretanto para a seleção e utilização dessas fontes de resistência, diferenças de virulência entre populações Asiáticas e Brasileiras desse fungo devem ser consideradas. Neste trabalho sugerimos um critério para se distinguir resistência de susceptibilidade pela análise de quatro caracteres de resistência: freqüência de lesões contendo urédias, número de urédias por lesão, freqüência de urédias abertas e nível de esporulação determinados pela utilização de 63 genótipos. Sob condições controladas em câmaras de crescimento, treze variedades de soja foram expostas a três populações de fungos - uma população proveniente do Japão e duas populações provenientes do Brasil-e avaliadas quanto aos caracteres de resistência mencionados acima. As populações Brasileiras diferiram entre si claramente quanto a virulência e em relação à população de isolados do Japão. Apenas dois genes de resistência, Rpp4 presente na variedade PI459025 e Rpp5 presente na variedade Shiranui conferiram resistência as três populações da ferrugem. O número de variedades ou genes resistentes úteis em ambos os países parece ser limitado. Assim, um cultivar universalmente efetivo contra a ferrugem da soja deveria ser desenvolvido pela piramidação de genes maiores de resistência e pela introdução de resistência horizontal.

In recent years soybean rust, caused by Phakopsora pachyrhizi has become one of the most serious threats to soybean production in Brazil. Breeding lines and varieties have been selected for resistance to soybean rust in Asia. However, differences in virulence between Asian and Brazilian rust populations should be considered in order to select and use resistant resources from Asia. Here, we suggest criteria for distinguishing resistant from susceptible types by the analysis of four resistance characters: frequency of lesions having uredinia, number of uredinia per lesion, frequency of open uredinia, and sporulation level, determined by the utilization of 63 genotypes. Under growth chamber conditions, a set of 13 soybean varieties were exposed to three rust populations-one from Japan and two from Brazil-and evaluated for the resistance characters mentioned above. The Japanese and Brazilian populations clearly differed in virulence, as did the two Brazilian populations. Only two resistance genes, Rpp4 from PI459025 and Rpp5 from Shiranui, commonly conferred resistance on all three rust populations. The number of resistant varieties or resistance genes useful in both countries appears limited. Therefore, a resistant cultivar that is universally effective against soybean rust should be developed by pyramiding some major resistance genes and by introducing horizontal resistance.

Podridão de carvão, causada por Macrophomina phaseolina é uma das mais importantes doenças da soja. Variabilidade genética tem sido observada entre isolados. Entretanto, o efeito de especialização deste fungo, de acordo com a planta hospedeira, não foi ainda relatado. Isolados de soja, milho e girassol foram avaliados, em inoculações cruzadas, quanto à capacidade de formação de microesclerócios em raiz. A maior e menor produção significativa de microesclerócios (P<0.005) foram observadas em raízes de soja (863 microesclerócios/g de raiz) e girassol (578 microesclerócios/g de raiz), respectivamente, independente da origem do isolado. Além disso, estudou-se a variabilidade de isolados do fungo, obtidos de sistemas de rotação de culturas estabelecido há 20 anos utilizando-se RAPD. Oitenta e nove isolados, oriundos de cinco populações foram coletados em amostras de solo de quatro sistemas de rotação e uma amostra de solo virgem. Sete agrupamentos foram observados com 85% de similaridade. As análises indicaram que M. phaseolina é uma espécie com alta variabilidade genética com forte efeito do sistema de rotação. AMOVA foi realizada com os dados de RAPD. Da variabilidade genética total, 21% (P<0.0001) foi explicada pelas diferenças entre populações e, 79% foi explicada por diferenças dentro das populações ( Φst = 0.2110; P<0.0001). A média do coeficiente de diferenciação gênica (G ST) estimada entre as cinco populações foi de 27%, similar aos resultados da AMOVA ( Φst= 0.2110). A diversidade genética total mostrou que as cinco populações têm alto grau de variabilidade (H T =0.3484). Os resultados sugerem que a diferenciação genética de M. phaseolina pode ser alterada pela rotação de culturas.

Charcoal rot, caused by Macrophomina phaseolina, is one of the most important diseases of soybean. Genetic variability among soybean isolates has been observed but the effect of host specialization on genetic variability has not been reported. In this work, isolates from soybean, corn and sunflower were evaluated based on cross inoculations and number of microsclerotia/g of roots. The highest and lowest significant (P<0.005) production of microsclerotia was obtained in soybean (863 microsclerotia/g of roots) and sunflower (578 microsclerotia/g of roots), respectively, regardless of the origin of the isolate. Additionally, the effect of a 20-year crop rotation on genetic variability based on RAPD was studied. Eighty-nine isolates from five populations were obtained from soil samples under four crop rotation systems and an uncropped soil. Seven clusters were obtained considering a similarity level of 85%. Analysis indicated that M. phaseolina is a highly diverse species and also revealed a strong effect of the rotation system on genetic diversity. AMOVA was conducted for the RAPD data. From the total genetic variability, 21% (P<0.0001) could be explained by the differences between populations while 79% could be explained by differences within populations ( Φst = 0.2110; P<0.0001). The mean coefficient of gene differentiation (G ST) estimated among the five populations indicated 27% of differentiation between populations similar to the AMOVA results where Φst= 0.2110. Total gene diversity estimated indicated high levels of variability (H T =0.3484). Results suggest that genetic differentiation of M. phaseolina can be altered by crop rotation.

Macrophomina phaseolina é considerado como um dos fungos mais prevalecentes em infecções radiculares de soja, no Brasil. Nenhuma fonte de resistência genética foi ainda encontrada. Além disso, nenhuma informação foi obtida quanto à variabilidade genética deste patógeno, em regiões tropicais. Cinqüenta e cinco isolados de raízes de soja (Glycine Max), obtidos de diferentes regiões geográficas, foram analisados por RAPD para avaliação da diversidade genética. Análise de agrupamento (UPGMA), utilizando 74 loci, permitiu identificar três grupos, com uma média de 99%, 92% e 88% de similaridade genética, respectivamente. Os três grupos correspondem a 5,45%, 59,95% e 34,6% de todos os isolados utilizados. Apenas uma planta estava infetada por três diferentes haplotipos, enquanto 10,9% de todas as plantas estavam infetadas por haplotipos pertencentes a dois diferentes grupos. Em outro estudo a similaridade genética foi determinada entre isolados originários de diferentes hospedeiros [soja, sorgo (Sorghum bicolor), girassol (Helianthus annuus), caupi (Vigna unguiculata), milho (Zea mays) e trigo (Triticum aestivum)] e de duas amostras de solo de áreas virgens. Os resultados mostraram que isolados mais divergentes são oriundos de áreas com monocultura. Amplificação da região ITS produziram apenas um fragmento com 620 pb. Nenhum dos isolados foi diferenciado quando o produto amplificado por PCR foi digerido com enzimas de restrição. Os resultados demonstram a existência de variabilidade genética entre os isolados brasileiros de M. phaseolina e mostram que uma única raiz pode ter mais de um haplotipo. Além disso, a rotação de cultura induz menos diversidade genética entre os isolados. O conhecimento dessa variabilidade pode ser útil na seleção de genótipos resistentes à podridão de carvão.

Macrophomina phaseolina has been considered one of the most prevalent soybean (Glycine max) pathogens in Brazil. No genetic resistance has been determined in soybean and very little is known about the genetic diversity of this pathogen in tropical and sub-tropical regions. Fifty-five isolates from soybean roots were collected in different regions and analyzed through RAPD for genetic diversity. The UPGMA cluster analysis for 74 loci scored permitted identification of three divergent groups with an average similarity of 99%, 92% and 88%, respectively. The three groups corresponded to 5.45%, 59.95% and 34.6%, respectively of all isolates used. A single plant had three different haplotypes, while 10.9% of the analyzed plants had two different haplotypes. In another study the genetic similarity was evaluated among isolates from different hosts [soybean, sorghum (Sorghum bicolor), sunflower (Helianthus annuus), cowpea (Vigna unguiculata), corn (Zea mays) and wheat (Triticum aestivum)] as well as two soil samples from native areas. Results showed that more divergent isolates originated from areas with a single crop. Isolates from areas with crop rotation were less divergent, showing high similarity values and consequently formed the largest group. Amplification of the ITS region using primers ITS1 and ITS4 produced only one DNA fragment of 620 bp. None of the isolates were differentiated through PCR-RFLP. Our results demonstrated genetic variability among Brazilian isolates of M. phaseolina and showed that one single root can harbor more than one haplotype. Moreover, cultivation with crop rotation tends to induce less specialization of the pathogen isolates. Knowledge of this variation may be useful in screening soybean genotypes for resistance to charcoal rot.

Euphorbia heterophylla, também conhecida como amendoim-bravo ou leiteira, é considerada planta invasora importante em mais de 56 países, inclusive no Brasil, tendo acarretado perdas de até 33 % na cultura da soja. Fenotipicamente, é uma espécie de características variáveis, especialmente em relação ao formato do limbo foliar. Esta variabilidade fenotípica tem sido utilizada para diferenciar e classificar as plantas, sugerindo a vários autores que a leiteira seria, de fato, constituída por diferentes espécies. Para estudar a variabilidade genética a nível de DNA entre plantas de Euphorbia heterophylla, que apresentam folhas morfologicamente diferentes, foram analisadas dez plantas diferentes coletadas em campos de soja, em Londrina/PR. As plantas foram transplantadas para casa-devegetação e o DNA das folhas foi extraído para análise pela técnica de RAPD. Vinte seis diferentes "primers", de dez nucleotídeos de sequência aleatória, geraram total de 102 bandas de DNA, sendo 38 delas polimórficas. A distância genética entre os indivíduos foi calculada em função da presença e da ausência das bandas, variando de 1 a 39% entre plantas. A análise de agrupamento dividiu as plantas em dois grupos, considerando limite de distância relativa de 22%. Os grupos gerados separaram nitidamente as plantas quanto ao formato do limbo foliar (estreito ou arredondado) e quanto á ramificação (densa ou normal).

Euphorbia heterophylla is an important weed affecting the performance of annual and perennial crops. It is native from tropical and subtropical regions in the American continent, and has been detected at high densities in 20 different countries worldwide, and at low densities in other 40 countries. In Brazil, it has been inclued among the ten most important weeds affecting different crops, causing yield losses up to 33% in soybean fields. Phenotypically, this species is extremely variable, especially in relation to leaf shape and size, which can vary among and within populations. This variability suggested to several authors that E. heterophylla was, in fact, formed by different species. To systematize the study of E. heterophylla and to determine if the phenotypic variability correspond to modifications at the DNA level, we analyzed 10 different plants collected in the soybean field in Londrina (Parana, Brazil). The plants were transplanted to the greenhouse and leaf DNA was extracted for RAPD technique analysis. Twenty-six RAPD "primers" different amplified 102 DNA bands, 38 of them being polymorphic. Genetic distances among the individuals were calculated based on the presence (1) or absence (0) of those bands. Cluster analyses divided the plants into two distinct groups considering an upper limit of 22% relative genetic distance. The genetic distances among the plants were between 1 and 39%, in agreement with the variability obseved at the morphological level.