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

Diversidade genética e introgressão do genoma em café

Para estudar a diversidade genética e o padrão de melhoramento entre cultivares de C. arabica lançados entre 1939 e 2009, foi utilizado um total de 110 cultivares. A fim de avaliar a introgressão do genoma do Híbrido de Timor e sua relação com outras espécies de café, foram utilizados cinco acessos de C. arabica, dez de C. canephora var conilon, quinze de C. canephora var robusta e quarenta e seis de Híbrido de Timor, com os marcadores moleculares AFLP, RAPD e SSR. O coeficiente de parentesco estimado entre cultivares de C. arabica foi usado para o estudo da diversidade genética e do padrão de melhoramento do café arábica no Brasil, mostrando uma baixa diversidade genética. O padrão de melhoramento de C. arabica no Brasil foi definido pelas treze linhagens ancestrais. Entre elas, Bourbon Vermelho, Sumatra e Híbrido de Timor contribuíram com mais de 80.00% dos genes para os cultivares de C. arabica. As duas primeiras progênies, Mundo Novo e Icatu Vermelho, contribuíram com 87.56% dos genes para os cultivares de C. arabica no Brasil. A diversidade genética entre cultivares de C. arabica lançados recentemente foi aumentada com a introdução de novas linhagens parentais no programa de melhoramento. O estudo de relação genética entre Híbrido de Timor e outras espécies mostrou alta similaridade genética entre Híbrido de Timor e C. arabica. A análise de introgressão do genoma entre Híbrido de Timor CIFC 4106 com C. arabica e C. canephora var robusta mostrou 18.9% de introgressão do genoma de C. canephora. A mesma análise, considerando todos os acessos de Híbrido de Timor, foi de 10.00%, o que confirma a baixa introgressão de C. canephora. Este resultado confirma que Híbrido de Timor não é planta F1, mas que é proveniente de, no mínimo, dois retrocruzamentos com C. arabica. Além disso, este estudo mostrou a existência de alta diversidade genética entre acessos de Híbrido de Timor, o que é importante no melhoramento de C. arabica no Brasil e no mundo, uma vez que Híbrido de Timor é usado como fonte de resistência para doenças e pragas no café.Conselho Nacional de Desenvolvimento Científico e TecnológicoTo study the genetic diversity among cultivars of C. arabica released from 1939 to 2009 and to study the breeding pattern, a total of 110 cultivars were included. Five C. arabica, ten C. canephora var conilon, fifteen C. canephora var robusta and forty six accessions of Híbrido de Timor were included to study the genome introgression of C. canephora into Híbrido de Timor and its relationship with other coffee species. To study the genome introgression and the genetic diversity within Híbrido de Timor, AFLP, RAPD and SSR molecular markers were used. The estimated coefficient of parentage among cultivars of C. arabica was used to study the genetic diversity and the breeding pattern of C. arabica in Brazil. The study showed low genetic diversity among Brazilian C. arabica cultivars. The breeding pattern of cultivars of C. arabica was defined by 13 ancestral lines. Among them, Bourbon Vermelho, Sumatra and Híbrido de Timor contributed more than 80% of the gene to C. arabica cultivars in Brazil. Mundo Novo and Icatu Vermelho, the first progenies, contributed 87.65% of the gene to Brazilian C. arabica cultivars. The genetic diversity among cultivars released in recent years increased due to the introduction of new parental lines in the breeding program of C. arabica. The genetic relationship study between Híbrido de Timor and other species showed high genetic similarity between Híbrido de Timor and C. arabica. The genome introgression analysis between Híbrido de Timor CIFC 4106 with C. arabica and C. canephora showed 18.9% of the genome of Híbrido de Timor introgressed from C. canephora. The mean genome introgression of C. canephora into Híbrido de Timor considering all accessions of Híbrido de Timor was 10.00%, which confirmed Híbrido de Timor is not an F1 plant instead at least two times backcrossed with C. arabica. In addition, the study demonstrated the existence of high genetic diversity among accessions of Híbrido de Timor, which is important for the future breeding program of arabica coffee, since it is used as source for resistance gene for diseases and pests

Genetic divergence among barley accessions from Ethiopia

The study was done with the objective of assessing the genetic diversity existing among Ethiopian and ICARDAbarley germplasm using multivariate data analyses. The experiment was conducted at Asasa and Ambo in Ethiopia, in 10 x 10simple lattices with two replications. To quantify the differentiation among genotypes canonical discriminant analysis, clusteringanalysis and Mahanalobis (D2) distance were used. The study indicated that the first two canonical variates explained 95%and 91% of the total variation at Asasa and Ambo, respectively. At both the locations, genotypes showed maximum differentiationon days to maturity, grain filling period, tiller per plant and spike per plant. Analysis of clustering grouped the 100 genotypesinto four cluster groups at Asasa and six clusters at Ambo. Ethiopian landraces and genotypes from ICARDA grouped in thesame cluster groups indicated the germplasm exchange between the Ethiopian and ICARDA barley breeding programs

Breeding potential and genetic diversity of "Híbrido do Timor" coffee evaluated by molecular markers

AFLP, RAPD and SSR molecular markers were used to study the genetic diversity and genetic structure of the Híbrido de Timor germplasm. The principal coordinate analysis, UPGMA cluster analysis based on genetic dissimilarity of Jaccard, Bayesian model-based cluster analysis, percentage of polymorphic loci, Shannon's information index and Nei gene diversity were employed to assess the genetic diversity. The analyses demonstrated a high genetic diversity among Híbrido de Timor accessions. UPGMA and Bayesian cluster analyses grouped the accessions into three clusters. The genetic structure of Híbrido de Timor is reported. The management of Híbrido de Timor germplasm variability and its potential use in breeding programs are discussed

Genetic diversity in Brazilian soybean germplasm

<div><p>Abstract Genetic diversity is an essential factor for the success of any plant breeding program and should be considered to ensure genetic gain through breeding. In Brazil, research on the genetic diversity and population structure of soybean is required since the species is an important commodity of the country. The study addressed the genetic diversity and population structure of 77 soybean genotypes using 35 SSR markers. The estimate of the diversity index showed that the level of genetic diversity in the soybean collection is low. Similarly, the Jaccard coefficient and Bayesian model based on clustering analysis confirmed the low diversity among soybean genotypes, providing evidence for the assumption of a genetic bottleneck effect on Brazilian soybean genotypes. The results also reinforced the importance of finding and incorporating new genetic resources of soybean in the genetic pool of Brazilian soybean to warrant genetic gain in soybean breeding in the future.</p></div

Effect of coconut water on growth of olive embryos cultured in vitro Efeito da água de coco no crescimento de embriões de oliveira cultivados in vitro

The experiment was carried out to determine the appropriate dose of coconut water as supplement for in vitro cultivation of zygotic embryos from 19 olive genotypes. The isolated embryos of the olive seeds were immersed on culture medium containing 0 (control), 25, 50, and 100mL L-1 of fresh and sterile coconut water and kept for 45 days under controlled environment. The percentage of germination, shoot length, number of roots, number of leaves and number of internodes were measured for all 19 olive genotypes. The ANOVA of the parameters evaluated showed significant genotypes x doses of coconut water interaction for shoot length, number of leaves and number of internodes and the dose of 100mL L-1 produced the best results overall as indicated by the means of measured parameters. However, the study showed the importance of determining the appropriate dose of coconut water for each genotype under consideration as shown by significant genotype x dose of coconut water interaction effect.O experimento foi realizado para determinar a dose adequada de água de coco como suplemento para cultivo in vitro de embriões zigóticos de 19 genótipos de oliveira. Os embriões isolados das sementes de oliveira foram imersos em meio de cultura contendo 0 (controle), 25, 50, e 100mL L-1 de água de coco fresca e estéril, em condição de ambiente controlado durante 45 dias. A porcentagem de germinação, comprimento da parte aérea, número de raízes, número de folhas e número de internódios foram medidos para todos os 19 genótipos de oliveira. A ANOVA dos parâmetros avaliados apresentou interação significativa entre genótipos e dose de água de coco para o comprimento da parte aérea, número de folhas e número de internódios, e a dose de 100mL L-1, de forma geral, produziu os melhores resultados, como indicado pelas médias dos parâmetros analisados. No entanto, como mostra a interação significativa observada entre genótipos e tratamentos, é importante determinar a dose adequada de água de coco para cada genótipo

Genetic diversity in Brazilian soybean germplasm

<div><p>Abstract Genetic diversity is an essential factor for the success of any plant breeding program and should be considered to ensure genetic gain through breeding. In Brazil, research on the genetic diversity and population structure of soybean is required since the species is an important commodity of the country. The study addressed the genetic diversity and population structure of 77 soybean genotypes using 35 SSR markers. The estimate of the diversity index showed that the level of genetic diversity in the soybean collection is low. Similarly, the Jaccard coefficient and Bayesian model based on clustering analysis confirmed the low diversity among soybean genotypes, providing evidence for the assumption of a genetic bottleneck effect on Brazilian soybean genotypes. The results also reinforced the importance of finding and incorporating new genetic resources of soybean in the genetic pool of Brazilian soybean to warrant genetic gain in soybean breeding in the future.</p></div