The Bioinformatics Tools for Discovery of Genetic Diversity by Means of Elastic Net and Hurst Exponent

The genome era allowed us to evaluate different aspects on genetic variation, with a precise manner followed by a valuable tip to guide the improvement of knowledge and direct to upgrade to human life. In order to scrutinize these treasured resources, some bioinformatics tools permit us a deep exploration of these data. Among them, we show the importance of the discrete non-decimated wavelet transform (NDWT). The wavelets have a better ability to capture hidden components of biological data and an efficient link between biological systems and the mathematical objects used to describe them. The decomposition of signals/sequences at different levels of resolution allows obtaining distinct characteristics in each level. The analysis using technique of wavelets has been growing increasingly in the study of genomes. One of the great advantages associated to this method corresponds to the computational gain, that is, the analyses are processed almost in real time. The applicability is in several areas of science, such as physics, mathematics, engineering, and genetics, among others. In this context, we believe that using R software and applied NDWT coupled with elastic net domains and Hurst exponent will be of valuable guideline to researchers of genetics in the investigation of the genetic variability

Applications of biotechnology in olive

Many scientific and technological fields make use of biotechnology. Among the most important applications of biotechnology in agriculture are large-scale commercial micropropagation, genetic transformation and the development of transgenic varieties, embryo rescue in plant breeding programs, genotyping based on DNA markers, studies of genetic evolution and diversity, and genome sequencing. These myriad applications of modern biotechnology and molecular biology are being applied to the olive tree, a crop cultivated for thousands of years in many places of the world and whose products are consumed globally. The selection and development of olive cultivars by conventional breeding methods is costly and time consuming, therefore, the application of biotechnology procedures and techniques, such as in vitro cultivation, molecular markers, and genomic and genetic transformation in this species may facilitate the improvement of important traits of this crop, such as biotic and abiotic resistance and tolerance, yield performance and oil quality. In this review, we present current applications of modern biotechnology and molecular biology in olive species.Keywords: Olea europaea, tissue culture, molecular markers, genetic transformation, genomic diversityAfrican Journal of Biotechnology Vol. 12(8), pp. 767-77

Genetic Diversity of <em>Coffea arabica</em>

Coffea arabica L. is a native coffee species probably originated in Abyssinia, now Ethiopia. The genetic diversity of C. arabica has economic implications directly related to profits by breeding for developing new varieties to a global market. The economic value of C. arabica genetic resources are estimated at US$ 420 million, considered a 10% discount rate. Understanding the extent of traits variability and genetic diversity is essential to guide crosses between genotypes, targeting the development of new varieties with high economic value. This chapter will present the C. arabica economic importance, primarily to Brazil, the most significant world producer; we will outline the origin and dispersion of arabica coffee and briefly show the leading germplasm banks. We will also point out contribution of genetic diversity studies based on morphological, agronomic traits, and molecular markers supporting the development of new varieties. Finally, we present an outline for the future

Outcrossing rate in olive assessed by microsatellite and inter simple sequence repeat (ISSR) markers

Olive is known to be an allogamous species. The aim of this study was to estimate the magnitude of cross-pollination rate using microsatellite simple sequence repeats (SSR) and inter simple sequence repeats (ISSR) molecular markers in olive genotypes. The DNA from maternal plants and 23 progenies of two different accessions, Ascolano USA and MGS GRAP541 were extracted and screened with two microsatellite and ten ISSR markers. The outcrossing rate and other related parameters were analyzed using the MLTR application. The set of estimates, individually and collectively, support the hypothesis of frequent allogamy in both olive genotypes evaluated, with high rates of outcrossing in both markers.Keywords: Olea europaea L., outcrossing rate, zygotic embryos, mating system, molecular marker

Gene flow analysis in common bean

O objetivo deste trabalho foi investigar o fluxo gênico, estimado pela taxa de fecundação cruzada entre cultivares de feijão, pertencente ao pool gênico mesoamericano, por meio de um esquema especialmente delineado para esse fim. O experimento foi realizado em duas etapas. A primeira etapa foi a instalação simultânea no campo do cultivar fonte de pólen (Diamante Negro) de flor violeta e do receptor (Talismã) de flor branca. O cultivar fonte foi semeado no centro, e ao seu redor foi semeado, em quadrados concêntricos, o cultivar receptor de pólen. Na maturação foram amostradas fileiras de tamanho fixo em distâncias variadas da fonte; e, em cada direção, essas constituíram as fontes de sementes a serem plantadas na etapa seguinte do experimento. Na segunda etapa do experimento, foram semeadas as sementes amostradas na etapa anterior. No florescimento dessas plantas avaliou-se a porcentagem de fecundação cruzada no feijoeiro, por meio de verificação da cor da flor. As flores violetas indicam ocorrência de cruzamentos naturais. A maior freqüência de híbridos naturais ocorreu à distância da fonte de 0,5 m (0,136%) e 1,0 m (0,11%). Essa freqüência foi reduzida a praticamente 0% a 3,25 m da fonte.The objective of this work was to investigate gene flow, esteem for the rate of out crossed between varieties cultivated of beans, pertaining to gene pool Mesoamerican, by means of a project especially delineated for this purpose. The experiment was accomplished in two stages. The first stage was the simultaneous installation in the field of variety cultivated source of pollen (Diamante Negro) of violet flower and the receiver (Talismã) of white flower. The source was sown in the center and around they had been sown, in concentrical squares, the variety cultivated pollen receiver. In the maturation rows of fixed size had been sampled at varied distance of the source and in each direction, these had constituted the sources of seeds to be planted in the next stage to the experiment. In the second stage of the experiment, had been sown the sampled seeds of the previous stage, and in the flowering of these plants it was evaluated percentage of out crossed in the common bean by means of verification of the color of the flower. The violet flowers indicate occurrence of natural crossings. The biggest frequency of natural hybrids occurred at a distance of the source of 0.5 m (0.136%) and 1.0 m (0.11%). This frequency was reduced practically to 0% at 3.25 m of the source.Conselho Nacional de Desenvolvimento Científico e Tecnológic

Wavelet-domain elastic net for clustering on genomes strains

Abstract We propose to evaluate genome similarity by combining discrete non-decimated wavelet transform (NDWT) and elastic net. The wavelets represent a signal with levels of detail, that is, hidden components are detected by means of the decomposition of this signal, where each level provides a different characteristic. The main feature of the elastic net is the grouping of correlated variables where the number of predictors is greater than the number of observations. The combination of these two methodologies applied in the clustering analysis of the Mycobacterium tuberculosis genome strains proved very effective, being able to identify clusters at each level of decomposition

Avaliação de três características fisiológicas em 4 ciclos de seleção no cultivar de milho BRS-4154 sob o solo encharcado

Conduziu-se este trabalho, com o objetivo de avaliar plantas de milho (Zea mays L.) dos diferentes ciclos de seleção recorrentes da variedade de milho BRS 4154 - 'Saracura' quanto aos ganhos genéticos obtidos ao longo dos ciclos de seleção sob encharcamento do solo. Quatro ciclos de seleção da variedade de milho BRS 4154 foram plantados sob delineamento em blocos casualizados nos quais foram avaliados os ciclos 1, 5, 9 e 15, incluindo a variedade BR 107 e o híbrido simples BRS 1010 como testemunhas, por serem sensíveis ao encharcamento. Foram avaliados: fluorescência e teor de clorofila, área foliar e porosidade de raiz. O estresse causado pelo excesso de água no solo não influenciou a característica fluorescência da clorofila, demonstrando que essa não é uma boa característica para avaliação de tolerância ao encharcamento do solo. Houve uma significativa redução de área foliar do milho nas áreas de solo encharcado. Adicionalmente, a porosidade da raiz foi uma característica que apresentou significativa discrepância entre os dois ambientes de cultivo, tendo um aumento significativo em função do encharcamento.This work aimed to evaluate plants of different cycles of recurrent selection of the maize (Zea mays L.) variety BRS 4154 - 'Saracura' for the genetic faced to the gains obtained along the selection cycles under waterlogging of the soil. Four cycles of selection of the maize variety BRS 4154 were planted in randomized block outline for evaluation of cycles 1, 5, 9 and 15, including the variety BR 107 and the simple hybrid BRS 1010 used as control, once they are sensitive to the waterlogging. One evaluated: chlorophylls fluorescence and content, leaf surface area and root porosity. The stress caused by the excess of water in the soil didn't influence the characteristic of chlorophyll fluorescence, demonstrating this is not a good characteristic to evaluate flooding tolerance. There was significant leaf surface area decrease of the corn in the areas of soaked soil. Additionally, the porosity of the root was a characteristic that presented significant discrepancy between the two cultivation environments, having a significant increase in function of waterlogging