DendroSSR: SSRs and sequence alignment as tools for building phylogeny trees / DendroSSR: SSRs e alinhamento de sequência como ferramentas para a construção de árvores filogenéticas

Abstract This study introduces a new method to construct phylogenetic trees by combining both of the Simple Sequence Repeats (SSRs) and sequence alignments. The purpose of this work is to present the DendroSSR program and show it via a case study involving diverse Aspergillus species. To show how the DendroSSR program works to resolve complicated species relationships in phylogenetic trees, we employed the Aspergillus species as an example of a research case. The DendroSSR employs a technique containing multiple phases beginning with, detecting SSRs, computing SSRs similarities, sequences alignment, building a distance matrix based on SSRs similarity and sequences alignments, and then hierarchical clustering, and presenting the findings in a dendrogram. Sometimes sequence alignments alone may not give adequate information to generate a phylogenetic tree to resolve complicated species relationships. Therefore, establishing a distance matrix that is formed of addition of SSRs similarity across sequences to the traditional sequence alignment helps the process substantially and resolves the connections of complex species on phylogenetic trees. Additionally, it may be hard to distinguish complex relationships across species when studying conserved sequences, which could lead to an incomplete representation of their evolutionary relationships. These limitations are addressed by DendroSSR, which offers a technique to produce phylogenetic trees by incorporating SSRs similarity across species into the approach of generating phylogenetic trees. As it is known, SSRs are extensively scattered across the genomes of species and exhibit a great variation. Therefore, SSRs may support the knowledge gathered from sequence alignments by providing more information on genetic variation and even evolutionary relationships. The use of DendroSSR analysis might be considered for creating phylogenetic trees as a complementary or secondary strategy among the species under examination in circumstances where traditional phylogenetic analysis fails to clarify the species complex phylogenetic relationships.

Resumo Este estudo apresenta um novo método para construir árvores filogenéticas, combinando tanto as Sequências Repetitivas Simples (SSRs) quanto os alinhamentos de sequência. O objetivo deste trabalho é apresentar o programa DendroSSR por meio de um estudo de caso envolvendo diversas espécies de Aspergillus. Para mostrar como o programa DendroSSR funciona a fim de resolver relações complicadas de espécies em árvores filogenéticas, empregamos a espécie Aspergillus como exemplo de caso de pesquisa. O DendroSSR utiliza uma técnica contendo várias fases, começando com detecção de SSRs, computação de similaridades de SSRs, alinhamento de sequências, construção de uma matriz de distância baseada na similaridade de SSRs e alinhamentos de sequências e, em seguida, agrupamento hierárquico e apresentação das descobertas em um dendrograma. Às vezes, os alinhamentos de sequência sozinhos podem não fornecer informações adequadas para gerar uma árvore filogenética a fim de resolver relações complicadas de espécies. Portanto, estabelecer uma matriz de distância, que é formada pela adição de similaridade de SSRs entre sequências ao alinhamento de sequência tradicional, ajuda substancialmente o processo e resolve as conexões de espécies complexas em árvores filogenéticas. Além disso, pode ser difícil distinguir relações complexas entre espécies ao estudar sequências conservadas, o que pode levar a uma representação incompleta de suas relações evolutivas. Essas limitações são abordadas pelo DendroSSR, que oferece uma técnica para produzir árvores filogenéticas ao incorporar a similaridade de SSRs entre as espécies na abordagem de geração de árvores filogenéticas. Como se sabe, os SSRs estão amplamente dispersos nos genomas das espécies e exibem grande variação. Portanto, os SSRs podem apoiar o conhecimento obtido a partir de alinhamentos de sequências, fornecendo mais informações sobre variação genética e até mesmo relações evolutivas. O uso da análise DendroSSR pode ser considerado para a criação de árvores filogenéticas como uma estratégia complementar ou secundária entre as espécies sob exame em circunstâncias em que a análise filogenética tradicional falha em esclarecer as complexas relações filogenéticas das espécies.

Simple Sequence Repeat Markers Reveal Genetic Diversity and Population Structure of Bolivian Wild and Cultivated Tomatoes (Solanum lycopersicum L.).

The western part of South America is a centre of diversity for tomatoes, but genetic diversity studies are lacking for parts of that region, including Bolivia. We used 11 simple sequence repeat (SSR) markers (including seven novel markers) to evaluate genetic diversity and population structure of 28 accessions (four modern cultivars, four advanced lines, nine landraces, 11 wild populations), and to compare their genetic variation against phenotypic traits, geographical origin and altitude. In total, 33 alleles were detected across all loci, with 2-5 alleles per locus. The top three informative SSRs were SLM6-11, LE20592 and TomSatX11-1, with polymorphism information content (PIC) of 0.65, 0.55 and 0.49, respectively. The genetic diversity of Bolivian tomatoes was low, as shown by mean expected heterozygosity (He) of 0.07. Analysis of molecular variance (AMOVA) revealed that 77.3% of the total variation was due to variation between accessions. Significant genetic differentiation was found for geographical origin, cultivation status, fruit shape, fruit size and growth type, each explaining 16-23% of the total variation. Unweighted Pair Group Method with Arithmetic Mean (UPGMA) tree and principal coordinate analysis (PCoA) scatter plot both revealed differentiation between accessions with determinate flowers and accessions with indeterminate flowers, regardless of cultivation status. The genetic profiles of the accessions suggest that the Bolivian tomato gene pool comprises both strictly self-pollinating and open-pollinating genotypes.

Genetic diversity of Peltophorum dubium (Spreng.) Taub. progenies from the states of Minas Gerais and Mato Grosso do Sul, Brazil / Diversidade genética de progênies de Peltophorum dubium (Spreng.) Taub. procedentes de Minas Gerais e Mato Grosso do Sul, Brasil

There is little information regarding the genetic diversity of native species aimed at identifying the best viable progenies for in situ and ex situ conservation. Furthermore, there is a lack of future forest improvement programs. We aimed to know the genetic diversity of 64 Peltophorum dubium (Spreng.) Taub. (Fabaceae) progenies. We determined this species' dendrometric characteristics, and when using multivariate techniques and cluster analysis, we verified the differences between the progenies and groups with less heterogeneity. The progeny and provenance test was installed in Dourados (Mato Grosso do Sul - MS), with seeds collected in three MS regions (Vale do Ivinhema, Serra de Maracaju, and Serra da Bodoquena) and in the micro-region of Lavras (Minas Gerais - MG). The experiment was conducted in an alpha lattice 8 x 8 with four repetitions. We found genetic variability among and within P. dubium populations for all height, diameter, circumference at breast height, volume, and basal area characters. We suggest that P. dubium populations have high genetic variability, which indicates possible genetic improvement through best progeny selection. The UPGMA and Tocher methods grouped the progenies into three and nine groups, respectively, in which the most divergent individuals come from MG and the Bonito region in MS. Based on morphological characters, P. dubium progenies identified as 45, 47, 49, 50, 55, and 59 from MG are the most promising, while progenies 6 and 9 were the least promising.

Informações quanto à diversidade genética de espécies nativas visando identificar melhores progênies viáveis para conservação in situ e ex situ, além de futuros programas de melhoramento florestal são incipientes. Objetivamos conhecer a diversidade genética de 64 progênies de Peltophorum dubium (Spreng.) Taub. (Fabaceae). Determinamos os caracteres dendrométricos dessa espécie, e ao utilizarmos técnicas multivariadas e análises de agrupamento verificamos as diferenças entre as progênies e grupos de menor heterogeneidade. O teste de progênies e procedências foi instalado em Dourados (MS), cujas sementes foram coletadas em três regiões de MS (Vale do Ivinhema, Serra de Maracaju e Serra da Bodoquena) e na microrregião de Lavras-MG. O experimento foi conduzido em alfa-látice 8 x 8, com quatro repetições. Constatamos variabilidade genética entre e dentro das populações de P. dubium para todos os caracteres altura, diâmetro, circunferência à altura do peito, volume e área basal. Sugerimos que as populações de P. dubium tem alta variabilidade genética, o que indicou possibilidade de melhoramento genético pela seleção das melhores progênies. Os métodos UPGMA e Tocher agruparam as progênies em três e nove grupos, respectivamente, em que os indivíduos mais divergentes são procedentes de MG e da região de Bonito em MS. As progênies de P. dubium de identificação 45, 47, 49, 50, 55 e 59, todas de MG, são as mais promissoras, enquanto que as progênies 6 e 9, foram as menos promissoras, baseando-se nos caracteres morfológicos.

A Parametric Bootstrap for the Mean Measure of Divergence.

For more than 50 years the Mean Measure of Divergence (MMD) has been one of the most prominent tools used in anthropology for the study of non-metric traits. However, one of the problems, in anthropology including palaeoanthropology (more often there), is the lack of big enough samples or the existence of samples without sufficiently measured traits. Since 1969, with the advent of bootstrapping techniques, this issue has been tackled successfully in many different ways. Here, we present a parametric bootstrap technique based on the fact that the transformed θ, obtained from the Anscombe transformation to stabilize the variance, nearly follows a normal distribution with standard deviation $\sigma = 1 / \sqrt{N + 1/2}$σ=1/N+1/2, where N is the size of the measured trait. When the probabilistic distribution is known, parametric procedures offer more powerful results than non-parametric ones. We profit from knowing the probabilistic distribution of θ to develop a parametric bootstrapping method. We explain it carefully with mathematical support. We give examples, both with artificial data and with real ones. Our results show that this parametric bootstrap procedure is a powerful tool to study samples with scarcity of data.

Estimates of genetic divergence in cowpea by multivariate analysis in different environments / Estimativa de divergência genética em feijão-caupi por meio de análise multivariada em diferentes ambientes

Cowpea is a legume of great importance in the Brazilian nutrition, mainly in the Northeast region. Despite the low yield of Brazilian cowpea, the species presents a genetic potential to be explored. Thus, this work aimed to characterize the genetic diversity of cowpea genotypes by agronomic traits and select genotypes for possible crosses by multivariate analysis. Four value for cultivation and use tests were carried out with cowpea genotypes in 2005 and 2006, in the municipalities of Aquidauana, Chapadão do Sul, and Dourados, in the state of Mato Grosso do Sul. The experimental design was a complete randomized block with 20 genotypes and four replications. The evaluated traits were value for cultivation, plant lodging, pod length, grain weight of five pods, number of grains per pod, pod weight, severity of powdery mildew, and grain yield. To estimate the genetic diversity among the genotypes, the optimization methods of Tocher and UPGMA were used. The generalized distance of Mahalanobis was used as a dissimilarity measure. The clustering methods revealed genetic variability among the cowpea genotypes evaluated. The methods used formed a different number of groups for each environment. Genotypes TE97-309G-24, MNC99-542F-5, BRS Paraguaçu, BRS Paraguaçu, BR 17-Gurguéia, and CNC x 409-11F-P2 can be used to obtain promising combinations and high genetic variability.

O feijão-caupi é de grande importância na nutrição brasileira, principalmente na região Nordeste. Apesar do baixo rendimento do feijão-caupi no Brasil, esta leguminosa apresenta potencial genético a ser explorado. Dessa forma, o objetivo do trabalho foi caracterizar a variabilidade genética de caracteres agronômicos e estimar a divergência genética entre genótipos de feijão-caupi por meio de análise multivariada. Quatro ensaios de valor de cultivo e uso com genótipos de feijão-caupi foram conduzidos nos anos de 2005 e 2006, nos municípios de Aquidauana, Chapadão do Sul e Dourados. Os experimentos foram conduzidos em delineamento blocos casualizados, com 20 genótipos e quatro repetições. Os caracteres avaliados foram acamamento de plantas, comprimento de vagem, peso de grãos de cinco vagens, número de grãos por vagem, peso de vagem e produtividade de grãos. Realizou-se análise de variância individual e conjunta. Para estimar a diversidade genética entre os genótipos, foram utilizados o métodos de otimização de Tocher e UPGMA. A distância generalizada de Mahalanobis foi utilizada como medida de dissimilaridade. Foi possível detectar variabilidade genética entre os genótipos de feijão-caupi avaliados por meio dos métodos de agrupamento utilizados. Os métodos utilizados formaram números de grupos distintos para cada ambiente. Os genótipos TE97-309G-24, MNC99-542F-5, BRS Paraguaçu, BRS Paraguaçu, BR 17-Gurguéia e CNC x 409-11F-P2 podem ser usados para obter combinações promissoras e elevada variabilidade genética.

Physicochemical characterization of 'Cerrado' cashew (Anacardium othonianum Rizzini) fruits and pseudofruits.

BACKGROUND: The Cerrado occupies 23% of Brazil. A. othonianum is a native Cerrado species that presents differently colored pseudofruits. This report describes the morphometric properties, physicochemical characterization, and phenolic and flavonoid compound compositions of 30 accessions of A. othonianum. RESULTS: The morphometric properties show that an average fruit had 21.97 mm length, 18.61 mm width, and 11.13 mm thickness, with 2.52 g mass. The pseudofruits had 28.84 mm apex width with 12.83 g of mass. The hue parameters of the pseudofruits were 18.67 ± 2.00 and 83.32 ± 1.97° (P < 0.05), reflecting their red to yellow color. The titratable acidity of the accessions was 0.91 ± 0.09 to 3.02 ± 0.02% (P < 0.05), soluble solid content was 9.60 ± 0.17 to 13.47 ± 0.38 °Brix (P < 0.05), and pH ranged from 2.83 ± 0.06 to 3.83 ± 0.06 (P < 0.05). Fourteen flavonoid compounds were identified. The most common compounds in the accessions were vitexin (93% of the accessions), hesperidin (57% of the accessions), epicatechin (34% of the accessions), and kaempferol-3-O-glucoside (30% of the accessions). Cluster analysis generated four groups with the traits ΔE, °h, C, soluble solid content, titratable acidity, pH, total flavonoids, and their identified compounds. CONCLUSIONS: Although all accessions are A. othonianum, there the chemical composition and the physical characteristics of these fruits vary. This is the first report in the literature using wild accessions. Greater disclosure of the species characteristic is interesting because it can increase income for the local population. © 2019 Society of Chemical Industry.

Genetic and Morphological Differentiation of the Semiterrestrial Crab Armases angustipes (Brachyura: Sesarmidae) along the Brazilian Coast.

The genetic and morphometric population structures of the semiterrestrial crab Armases angustipes from along the Brazilian coast were examined. The influence of the Central South Equatorial Current on larval dispersal of A. angustipes also was evaluated. Six populations were sampled from estuarine areas in São Luis do Maranhão, Maranhão; Natal, Rio Grande do Norte; Maceió, Alagoas; Ilhéus, Bahia; Aracruz, Espírito Santo; and Guaratuba, Paraná. Patterns of genetic differentiation were assessed using DNA sequence data corresponding to parts of the mitochondrial cytochrome c oxidase subunit 1. Geometric morphometric techniques were used to evaluate morphological variation in shape and size of the carapace and right cheliped propodus. Our results revealed low genetic variability and lack of phylogeographic structure; geometric morphometrics showed statistically significant morphological differentiation and geographic structuring. Our data indicate the absence of possible barriers to gene flow for this mobile species, and no clear correlation of morphological or genetic variation with ocean currents and/or geographic distance. Our results also suggest that historical geological and climatological events and/or possible bottleneck effects influenced the current low genetic variability among the populations of A. angustipes.

Variabilidade genética de germoplasma tradicional de feijoeiro comum na região de Cáceres-MT / Genetic variability of traditional germplasm of common bean in Cáceres region, Brazil

RESUMO:O presente trabalho foi conduzido na unidade experimental da Empresa Mato-Grossense de Pesquisa, Assistência Técnica e Extensão Rural (Cáceres-MT) e teve como objetivo determinar a variabilidade genética existente entre 40 acessos tradicionais de Phaseolus vulgaris L. do banco ativo de germoplasma da região de Cáceres-MT. Foi utilizado um delineamento de blocos ao acaso com três repetições e analisadas onze características morfoagronômicas. Os dados obtidos foram submetidos à análise de variância, foi estimada a variabilidade genética entre os acessos empregando-se análise multivariada com base na distância generalizada de Mahalanobis, realizando as análises de agrupamento. Houve diferenças significativas a 1% de probabilidade para todas as características avaliadas. A maior distância genética foi encontrada entre os acessos 13 e 20 (D2ii'=364,99), e a menor distância entre os acessos 13 e 26 (D2ii'=2,23). Os métodos de Tocher e UPGMA ordenaram os acessos mais divergentes em grupos distintos, evidenciando a existência de variabilidade, podendo ser inclusos em programas de melhoramento com enfoque regional.

ABSTRACT:The present research was conducted at the experimental unit of the Empresa Mato-Grossense de Pesquisa, Assistência e Extensão Rural-EMPAER (Caceres-MT) and aimed to determine the genetic variability that exaist among 40 accesses from active germplasm bank of Phaseolus vulgaris L. of the region Caceres-MT. It was used a random blocks design with three replications and analyzed eleven agronomic characteristics. Data were submitted to analysis of variance, it was estimated the genetic variability among the accessions through multivariate analysis based on Mahalanobis distance, performing cluster analysis. There were significant differences at 1% probability for all the characteristics evaluated. The largest genetic distance was found between accessions 13 and 20 (D2ii'=364.99), and the smallest distance between accessions 13 and 26 (D2ii'=2.23). Methods of Tocher and UPGMA ordered the most divergent accessions into distinct groups, showing the existence of variability and can be included in breeding programs with a regional focus.

Genetic variability of traditional germplasm of common bean in Cáceres region, Brazil / Variabilidade genética de germoplasma tradicional de feijoeiro comum na região de Cáceres-MT

The present research was conducted at the experimental unit of the Empresa Mato-Grossense de Pesquisa, Assistência e Extensão Rural-EMPAER (Caceres-MT) and aimed to determine the genetic variability that exaist among 40 accesses from active germplasm bank of Phaseolus vulgaris L. of the region Caceres-MT. It was used a random blocks design with three replications and analyzed eleven agronomic characteristics. Data were submitted to analysis of variance, it was estimated the genetic variability among the accessions through multivariate analysis based on Mahalanobis distance, performing cluster analysis. There were significant differences at 1% probability for all the characteristics evaluated. The largest genetic distance was found between accessions 13 and 20 (D2ii'=364.99), and the smallest distance between accessions 13 and 26 (D2ii'=2.23). Methods of Tocher and UPGMA ordered the most divergent accessions into distinct groups, showing the existence of variability and can be included in breeding programs with a regional focus.(AU)

O presente trabalho foi conduzido na unidade experimental da Empresa Mato-Grossense de Pesquisa, Assistência Técnica e Extensão Rural (Cáceres-MT) e teve como objetivo determinar a variabilidade genética existente entre 40 acessos tradicionais de Phaseolus vulgaris L. do banco ativo de germoplasma da região de Cáceres-MT. Foi utilizado um delineamento de blocos ao acaso com três repetições e analisadas onze características morfoagronômicas. Os dados obtidos foram submetidos à análise de variância, foi estimada a variabilidade genética entre os acessos empregando-se análise multivariada com base na distância generalizada de Mahalanobis, realizando as análises de agrupamento. Houve diferenças significativas a 1% de probabilidade para todas as características avaliadas. A maior distância genética foi encontrada entre os acessos 13 e 20 (D2ii'=364,99), e a menor distância entre os acessos 13 e 26 (D2ii'=2,23). Os métodos de Tocher e UPGMA ordenaram os acessos mais divergentes em grupos distintos, evidenciando a existência de variabilidade, podendo ser inclusos em programas de melhoramento com enfoque regional.(AU)

Variabilidade genética de germoplasma tradicional de feijoeiro comum na região de Cáceres-MT

ABSTRACT: The present research was conducted at the experimental unit of the Empresa Mato-Grossense de Pesquisa, Assistência e Extensão Rural-EMPAER (Caceres-MT) and aimed to determine the genetic variability that exaist among 40 accesses from active germplasm bank of Phaseolus vulgaris L. of the region Caceres-MT. It was used a random blocks design with three replications and analyzed eleven agronomic characteristics. Data were submitted to analysis of variance, it was estimated the genetic variability among the accessions through multivariate analysis based on Mahalanobis distance, performing cluster analysis. There were significant differences at 1% probability for all the characteristics evaluated. The largest genetic distance was found between accessions 13 and 20 (D2ii'=364.99), and the smallest distance between accessions 13 and 26 (D2ii'=2.23). Methods of Tocher and UPGMA ordered the most divergent accessions into distinct groups, showing the existence of variability and can be included in breeding programs with a regional focus.

RESUMO: O presente trabalho foi conduzido na unidade experimental da Empresa Mato-Grossense de Pesquisa, Assistência Técnica e Extensão Rural (Cáceres-MT) e teve como objetivo determinar a variabilidade genética existente entre 40 acessos tradicionais de Phaseolus vulgaris L. do banco ativo de germoplasma da região de Cáceres-MT. Foi utilizado um delineamento de blocos ao acaso com três repetições e analisadas onze características morfoagronômicas. Os dados obtidos foram submetidos à análise de variância, foi estimada a variabilidade genética entre os acessos empregando-se análise multivariada com base na distância generalizada de Mahalanobis, realizando as análises de agrupamento. Houve diferenças significativas a 1% de probabilidade para todas as características avaliadas. A maior distância genética foi encontrada entre os acessos 13 e 20 (D2ii'=364,99), e a menor distância entre os acessos 13 e 26 (D2ii'=2,23). Os métodos de Tocher e UPGMA ordenaram os acessos mais divergentes em grupos distintos, evidenciando a existência de variabilidade, podendo ser inclusos em programas de melhoramento com enfoque regional.

Application of RAPD-PCR for Determining the Clonality of Methicillin Resistant Staphylococcus aureus Isolated from Different Hospitals

Randomly amplified polymorphic DNA (RAPD)-PCR was applied with ten random 10-mer primers to examine the molecular diversity among methicillin resistant Staphylococcus aureus (MRSA) strains in the hospitals and to investigate the epidemiological spread of these strains between different hospitals. The main objective of the study was to identify appropriate primers, which successfully established the clonality of MRSA. Three of the primers yielded particularly discriminatory patterns and they were used to perform the RAPD analysis which revealed different bands ranging from 200 to 1500 bp. Dendogram was created by the un-weighted pair group method using arithmetic (UPGMA) average clustering and it was constructed based on the combination results of the new primers (S224, S232 and S395) which represented a novel approach for rapid screening of the strains and also provided the opportunity for monitoring the emergence and determining clonal dissemination of MRSA strains between the hospitals. Dendogram generated two main groups (Group I and II) with three clusters (A, B and C) and indicated that the strains isolated from the same hospital were closely related and they placed together in the same group. This technique could be of attractive use in controlling the sources and routes of transmission, tracking the spread of strains within hospital and between the hospitals, and especially preventing the nosocomial infections caused by the MRSA.

Morphological phenotypic dispersion of garlic cultivars by cluster analysis and multidimensional scaling

Multivariate techniques have become a useful tool for studying the phenotypic diversity of Germplasm Bank accessions, since they make it possible to combine a variety of different information from these accessions. This study aimed to characterize the phenotypic dispersion of garlic (Allium sativum L.) using two multivariate techniques with different objective functions. Twenty accessions were morphologically characterized for bulb diameter, length, and weight; number of cloves per bulb; number of leaves per plant; and leaf area. Techniques based on generalized quadratic distance of Mahalanobis, UPGMA (Unweighted Pair Group Method with Arithmetic Mean) clustering, and nMDS (nonmetrric MultiDimensional Scaling) were applied and the relative importance of variables quantified. The two multivariate techniques were capable of identifying cultivars with different characteristics, mainly regarding their classification in subgroups of common garlic or noble garlic, according to the number of cloves per bulb. The representation of the phenotypic distance of cultivars by multidimensional scaling was slightly more effective than that with UPGMA clustering.(AU)

Morphological phenotypic dispersion of garlic cultivars by cluster analysis and multidimensional scaling

Multivariate techniques have become a useful tool for studying the phenotypic diversity of Germplasm Bank accessions, since they make it possible to combine a variety of different information from these accessions. This study aimed to characterize the phenotypic dispersion of garlic (Allium sativum L.) using two multivariate techniques with different objective functions. Twenty accessions were morphologically characterized for bulb diameter, length, and weight; number of cloves per bulb; number of leaves per plant; and leaf area. Techniques based on generalized quadratic distance of Mahalanobis, UPGMA (Unweighted Pair Group Method with Arithmetic Mean) clustering, and nMDS (nonmetrric MultiDimensional Scaling) were applied and the relative importance of variables quantified. The two multivariate techniques were capable of identifying cultivars with different characteristics, mainly regarding their classification in subgroups of common garlic or noble garlic, according to the number of cloves per bulb. The representation of the phenotypic distance of cultivars by multidimensional scaling was slightly more effective than that with UPGMA clustering.

Geographic distribution and taxonomic circumscription of populations within Coryphantha section Robustispina (Cactaceae).

PREMISE OF STUDY: Taxonomic circumscription of subspecific taxa within Coryphantha robustispina was evaluated with morphological data and microsatellites. This study was the first to compare adequately sampled morphological and DNA analyses at the population level in the Cactaceae. This comparison was important to test reliability of both methods and to gain a better understanding of phytogeography, evolution, and systematics of the species, knowledge that could prove useful for other taxa as well. Populations of C. robustispina subsp. robustispina are listed as endangered by the U. S. Fish and Wildlife Service. Our primary goal was to explore correlations among geographical distribution, morphology, and genetics of selected populations throughout the range of the species and the outgroup, C. poselgeriana. • METHODS: Stem characters were measured for 638 individuals among 16 populations. Flower characters were measured for 180 individuals among 12 populations. Ten microsatellite DNA loci were isolated and characterized for 204 individuals among 13 populations. Data were analyzed using various multivariate analyses. • RESULTS: Our results indicated that, within Coryphantha robustispina, there were three morphologically, genetically, and geographically coherent groups represented by the names C. robustispina subsp. robustispina, C. robustispina subsp. uncinata, and C. robustispina subsp. scheeri. For most analyses, distinctions among the three groups were primarily not as great as those between any one of them and the outgroup. • CONCLUSIONS: Results suggested that the three subspecific taxa within Coryphantha robustispina are good subspecies but should not be elevated to species rank. The closely aligned results between morphology and microsatellite data support the design and utility of both methods.

Genetic diversity analysis of Bemisia tabaci populations in Pakistan using RAPD markers

Background: The Bemisia tabaci is one of the most devastating pests of agricultural crops and ornamental plants worldwide. The genetic diversity and biotype status of the Bemisia tabaci in Pakistan was assessed by using random amplified polymorphic DNA-polymerase chain reaction (RAPD-PCR). A total 80 samples of B. tabaci collected from 14 districts of the Punjab province and 7 districts of the Sindh province were included. Results: All 10 primers screened in this study generated 151 scorable amplification products, of which 117 or 77 percent were polymorphic. Pairwise Nei and Li’s similarity had ranged from 0.25 to 0.88 among all individuals analyzed. Based on Nei and Li’s similarity coefficients Bemisia populations were grouped into 3 main clusters and clearly distinguished the non B biotype from the B biotype. Conclusion: The level of similarity among populations of same biotypes was high whereas between populations of non B and B biotypes appeared to be less closely related. This analysis showed that non B biotype is prevalent in both provinces however B biotype is restricted to few locations in Sindh. This monitoring of the spread of B. tabaci in Pakistan will assist in the establishment of appropriate management strategies.

Evaluation of cassava plants generated by somatic embryogenesis at different stages of development using molecular markers

Background: Cassava (Manihot esculenta Crantz) is a crop that is high in carbohydrates in the roots and in protein in the leaves, important for both human consumption and animal feed, and also has a significant industrial use for its starches. In this study we evaluated the genetic variability with molecular markers in different stages in micropropagated plants from somatic embryos of Venezuelan native clone 56. Results: Three markers were used: ISTR, AFLP and SSR, finding that ISTR showed the highest polymorphism among individuals tested. With AFLP a high similarity between the evaluated individuals was observed and with SSR total monomorphism was seen. Using cluster analysis it was found that individuals from an embryo labeled as fasciated at the beginning of the somatic embryogenesis process were grouped as independent of the other plants when analyzed at the acclimatization stage. The differences found with the different markers used are discussed. In field trials, micropropagated plants had a yield between 4 and 5 times the average yield of cassava in Venezuela. Conclusion: Despite variability in terms of DNA markers, somatic embryogenesis is suitable for mass propagation of highly performing cassava clones.

Genetic divergence in maize growing at first and second season / Divergência genética em milho de primeira e segunda safra

The objective of this study was to estimate the genetic divergence among 19 corn hybrids growing at the summer and safrinha season. Two experiments were carried out in Rio Verde, Goias, in the 2007/2008 and 2008/2008 season. Both experiments were conducted at reduced spacing of 0.5 m, with population density of about 65,000 plants per hectare at summer and safrinha season respectively, using a randomized block design with three replications. Were evaluated the following characters: plant height, ear height, length of tassel, leaf area index, number of kernels rows per ear, number of kernels per row, thousand grain weight and grain yield. The genetic divergence was estimated from Mahalanobis dissimilarity and the hybrids were grouped by the methods of Tocher and non-weighted arithmetic averages (UPGMA). The results show greater genetic divergence between hybrids 2A525 and DKB177 and between P30K64 and DKB177 at the summer and safrinha season respectively. The indexes of dissimilarity observed in both seasons suggest the achieving of greater heterosis by crossing lines from the hybrids AG8060, P30F35, 2B587, AG7088 and DKB390 with lines from the hybrids AG7000 and DKB177. 

O objetivo deste trabalho foi estimar a divergência genética entre 19 híbridos simples de milho cultivados na safra de verão e safrinha. Foram instalados dois experimentos no município de Rio Verde, Goiás, sendo um na safra 2007/2008 e outro na safrinha 2008/2008. Ambos os experimentos foram conduzidos em espaçamento entre linhas reduzido de 0,5 m, com população aproximada de 65.000 e 55.000 plantas por hectare na safra e safrinha respectivamente, utilizando-se o delineamento blocos casualizados com 3 repetições. Foram avaliados os seguintes caracteres: altura de plantas, altura de inserção da espiga, comprimento de pendão, índice de área foliar, número de fileiras de grãos por espiga, número de grãos por fileira, massa de mil grãos e produtividade de grãos. A divergência genética foi estimada a partir das distâncias de Mahalanobis e os híbridos foram agrupados pelos métodos de otimização de Tocher e das médias aritméticas não-ponderadas (UPGMA). Constatou-se maior divergência genética entre os híbridos 2A525 e DKB177 e entre P30K64 e DKB177, na safra verão e safrinha respectivamente. Os índices de dissimilaridade observados nas duas safras sugerem a obtenção de maior heterose pelo cruzamento de linhagens extraídas dos híbridos AG8060, P30F35, 2B587, AG7088 e DKB390 com linhagens extraídas dos híbridos AG7000 e DKB177. 

Genetic divergence in maize growing at first and second season / Divergência genética em milho de primeira e segunda safra

The objective of this study was to estimate the genetic divergence among 19 corn hybrids growing at the summer and safrinha season. Two experiments were carried out in Rio Verde, Goias, in the 2007/2008 and 2008/2008 season. Both experiments were conducted at reduced spacing of 0.5 m, with population density of about 65,000 plants per hectare at summer and safrinha season respectively, using a randomized block design with three replications. Were evaluated the following characters: plant height, ear height, length of tassel, leaf area index, number of kernels rows per ear, number of kernels per row, thousand grain weight and grain yield. The genetic divergence was estimated from Mahalanobis dissimilarity and the hybrids were grouped by the methods of Tocher and non-weighted arithmetic averages (UPGMA). The results show greater genetic divergence between hybrids 2A525 and DKB177 and between P30K64 and DKB177 at the summer and safrinha season respectively. The indexes of dissimilarity observed in both seasons suggest the achieving of greater heterosis by crossing lines from the hybrids AG8060, P30F35, 2B587, AG7088 and DKB390 with lines from the hybrids AG7000 and DKB177.

O objetivo deste trabalho foi estimar a divergência genética entre 19 híbridos simples de milho cultivados na safra de verão e safrinha. Foram instalados dois experimentos no município de Rio Verde, Goiás, sendo um na safra 2007/2008 e outro na safrinha 2008/2008. Ambos os experimentos foram conduzidos em espaçamento entre linhas reduzido de 0,5 m, com população aproximada de 65.000 e 55.000 plantas por hectare na safra e safrinha respectivamente, utilizando-se o delineamento blocos casualizados com 3 repetições. Foram avaliados os seguintes caracteres: altura de plantas, altura de inserção da espiga, comprimento de pendão, índice de área foliar, número de fileiras de grãos por espiga, número de grãos por fileira, massa de mil grãos e produtividade de grãos. A divergência genética foi estimada a partir das distâncias de Mahalanobis e os híbridos foram agrupados pelos métodos de otimização de Tocher e das médias aritméticas não-ponderadas (UPGMA). Constatou-se maior divergência genética entre os híbridos 2A525 e DKB177 e entre P30K64 e DKB177, na safra verão e safrinha respectivamente. Os índices de dissimilaridade observados nas duas safras sugerem a obtenção de maior heterose pelo cruzamento de linhagens extraídas dos híbridos AG8060, P30F35, 2B587, AG7088 e DKB390 com linhagens extraídas dos híbridos AG7000 e DKB177.

Characterization of free nitrogen fixing bacteria of the genus Azotobacter in organic vegetable-grown Colombian soils

With the purpose of isolating and characterizing free nitrogen fixing bacteria (FNFB) of the genus Azotobacter, soil samples were collected randomly from different vegetable organic cultures with neutral pH in different zones of Boyacá-Colombia. Isolations were done in selective free nitrogen Ashby-Sucrose agar obtaining a recovery of 40 percent. Twenty four isolates were evaluated for colony and cellular morphology, pigment production and metabolic activities. Molecular characterization was carried out using amplified ribosomal DNA restriction analysis (ARDRA). After digestion of 16S rDNA Y1-Y3 PCR products (1487pb) with AluI, HpaII and RsaI endonucleases, a polymorphism of 16 percent was obtained. Cluster analysis showed three main groups based on DNA fingerprints. Comparison between ribotypes generated by isolates and in silico restriction of 16S rDNA partial sequences with same restriction enzymes was done with Gen Workbench v.2.2.4 software. Nevertheless, Y1-Y2 PCR products were analysed using BLASTn. Isolate C5T from tomato (Lycopersicon esculentum) grown soils presented the same in silico restriction patterns with A. chroococcum (AY353708) and 99 percent of similarity with the same sequence. Isolate C5CO from cauliflower (Brassica oleracea var. botrytis) grown soils showed black pigmentation in Ashby-Benzoate agar and high similarity (91 percent) with A. nigricans (AB175651) sequence. In this work we demonstrated the utility of molecular techniques and bioinformatics tools as a support to conventional techniques in characterization of the genus Azotobacter from vegetable-grown soils.

Characterization of free nitrogen fixing bacteria of the genus Azotobacter in organic vegetable-grown Colombian soils.

With the purpose of isolating and characterizing free nitrogen fixing bacteria (FNFB) of the genus Azotobacter, soil samples were collected randomly from different vegetable organic cultures with neutral pH in different zones of Boyacá-Colombia. Isolations were done in selective free nitrogen Ashby-Sucrose agar obtaining a recovery of 40%. Twenty four isolates were evaluated for colony and cellular morphology, pigment production and metabolic activities. Molecular characterization was carried out using amplified ribosomal DNA restriction analysis (ARDRA). After digestion of 16S rDNA Y1-Y3 PCR products (1487pb) with AluI, HpaII and RsaI endonucleases, a polymorphism of 16% was obtained. Cluster analysis showed three main groups based on DNA fingerprints. Comparison between ribotypes generated by isolates and in silico restriction of 16S rDNA partial sequences with same restriction enzymes was done with Gen Workbench v.2.2.4 software. Nevertheless, Y1-Y2 PCR products were analysed using BLASTn. Isolate C5T from tomato (Lycopersicon esculentum) grown soils presented the same in silico restriction patterns with A. chroococcum (AY353708) and 99% of similarity with the same sequence. Isolate C5CO from cauliflower (Brassica oleracea var. botrytis) grown soils showed black pigmentation in Ashby-Benzoate agar and high similarity (91%) with A. nigricans (AB175651) sequence. In this work we demonstrated the utility of molecular techniques and bioinformatics tools as a support to conventional techniques in characterization of the genus Azotobacter from vegetable-grown soils.