Conservation

Diversity and genetic structure among subpopulations of Gossypium mustelinum (Malvaceae)

M. F. Alves, Barroso, P. A. V., Ciampi, A. Y., Hoffmann, L. V., Azevedo, V. C. R., and Cavalcante, U., Diversity and genetic structure among subpopulations of Gossypium mustelinum (Malvaceae), vol. 12, pp. 597-609, 2013.

Gossypium mustelinum is the only cotton species native to Brazil; it is endemic to the semi-arid region of the northeast. The populations are found near perennial and semi-perennial sources of water, such as ponds or pools in intermittent streams. Problems with in situ conservation derive from human interference in its habitat, mainly because of excessive cattle grazing and deforestation. Establishing efficient strategies for in situ conservation requires knowledge of the genetic structure of the populations.

Genetic variability of watermelon accessions based on microsatellite markers

R. N. Cde S. Gama, Santos, C. A. F., and R. Dias, deC. S., Genetic variability of watermelon accessions based on microsatellite markers, vol. 12, pp. 747-754, 2013.

We analyzed the genetic variability of 40 watermelon accessions collected from 8 regions of Northeastern Brazil using microsatellite markers, in order to suggest strategies of conservation and utilization of genetic variability in this species. These accessions are not commercial cultivars. They were sampled in areas of traditional farmers that usually keep their own seeds for future plantings year after year. An UPGMA dendrogram was generated from a distance matrix of the Jaccard coefficient, based on 41 alleles of 13 microsatellite loci.

Genetic diversity of Vriesea cacuminis (Bromeliaceae): an endangered and endemic Brazilian species

P. C. C. Ribeiro, Pinheiro, L. C., Domingues, R., Forzza, R. C., Machado, M. A., and Viccini, L. F., Genetic diversity of Vriesea cacuminis (Bromeliaceae): an endangered and endemic Brazilian species, vol. 12, pp. 1934-1943, 2013.

Data about the genetic structure can help to understand the evolutionary process of natural populations as well as to drive strategies of conservation. Vriesea cacuminis, an endemic Brazilian Bromeliad, has been found in 2 areas of Minas Gerais State. One is a legal preservation unit (Ibitipoca State Park) and the other an unprotected area (Serra Negra). The 2 areas belong to the Mantiqueira Mountain Range Complex; both are characterized by steep relief with high altitudes and by heterogenic vegetation formed by a mosaic of rocky fields and forest fragments.

Genetic variability in Melipona scutellaris from Recôncavo, Bahia, Brazil

J. L. Viana, Francisco, A. K., Carvalho, C. A. L., and Waldschmidt, A. M., Genetic variability in Melipona scutellaris from Recôncavo, Bahia, Brazil, vol. 12, pp. 3444-3454, 2013.

Bees play a key role in pollination and thereby help maintain plant diversity. The stingless bee Melipona scutellaris is an important pollinator in northeastern Brazil because it is endemic to this region. Both deforestation and timber harvesting have reduced the nesting sites for this species, thus reducing its population and range. Genetic studies may help reverse this process by providing important tools for their proper management with a view to conservation of this species. Microsatellite markers have proven to be ideal for mapping genes and population genetic studies.

Genetic diversity of gabiroba based on random amplified polymorphic DNA markers and morphological characteristics

E. S. de Assis, Reis, E. Fdos, Pinto, J. F. N., Contim, L. A. S., and Dias, L. A. S., Genetic diversity of gabiroba based on random amplified polymorphic DNA markers and morphological characteristics, vol. 12, pp. 3500-3509, 2013.

The fragmentation of the original vegetation of the Cerrado biome, caused by the expansion of agricultural areas, mainly in central-west Brazil, calls for an assessment of the native population of this vegetation, especially of the species of interest for domestication and sustainable use. The purpose of this study was to characterize the genetic diversity of 140 gabiroba mother plants (Campomanesia spp) and their progenies from 17 locations in Goiás.

Inbreeding effects in Solanum lycocarpum A. St.-Hil populations, an endangered species of the Brazilian Cerrado

T. M. Moura, Siqueira, M. V. B. M., and Oliveira, G. C. X., Inbreeding effects in Solanum lycocarpum A. St.-Hil populations, an endangered species of the Brazilian Cerrado, vol. 12, pp. 6006-6010, 2013.

The inbreeding effective population size is an estimate of inbreeding and genetic drift in populations. It is an important tool for conservation genetics because it represents the number of individuals that are effectively contributing alleles to the subsequent generations. Several studies have been published in the last decades on the genetic structure of natural plant populations of the Cerrado, the Central-Brazilian savannahs, but most of them do not present effective size estimates.

Identification and characterization of conserved microRNAs and their target genes in wheat (Triticum aestivum)

Z. J. Yin and Shen, F. F., Identification and characterization of conserved microRNAs and their target genes in wheat (Triticum aestivum), vol. 9, pp. 1186-1196, 2010.

MicroRNAs (miRNAs) are non-coding small RNAs that regulate gene expression by translational repression or transcript degradation. A large number of miRNAs have been identified from model plant species; however, the character of conserved miRNAs is poorly understood. We studied 42 miRNA families that are conserved within the plant kingdom, using the miRBase database. Some conserved miRNA families were found to be preferentially expressed in dicots relative to monocots, especially miR403, miR472 and miR479.

Genetic diversity in wild species of passion fruit (Passiflora trintae) based on molecular markers

C. B. M. Cerqueira-Silva, Cardoso-Silva, C. B., Santos, E. S. L., Conceição, L. D. H. C. S., Pereira, A. S., Oliveira, A. C., and Corrêa, R. X., Genetic diversity in wild species of passion fruit (Passiflora trintae) based on molecular markers, vol. 9, pp. 2123-2130, 2010.

In spite of the importance of and the considerable variability observed in Passiflora (Passifloraceae), little is known about the genetic diversity of most of the species of this genus. We evaluated the genetic diversity by RAPD markers in 18 genotypes of Passiflora trintae. The 15 primers generated 112 markers, 84% of which were polymorphic. The genetic distance estimated by the complement of the Dice index (average dissimilarity = 0.30) and genotype grouping based on the UPGMA algorithm showed low variability among genotypes.

Genetic algorithm-based efficient feature selection for classification of pre-miRNAs

P. Xuan, Guo, M. Z., Wang, J., Wang, C. Y., Liu, X. Y., and Liu, Y., Genetic algorithm-based efficient feature selection for classification of pre-miRNAs, vol. 10, pp. 588-603, 2011.

In order to classify the real/pseudo human precursor microRNA (pre-miRNAs) hairpins with ab initio methods, numerous features are extracted from the primary sequence and second structure of pre-miRNAs. However, they include some redundant and useless features. It is essential to select the most representative feature subset; this contributes to improving the classification accuracy. We propose a novel feature selection method based on a genetic algorithm, according to the characteristics of human pre-miRNAs.

Effective sample selection for classification of pre-miRNAs

K. Han, Effective sample selection for classification of pre-miRNAs, vol. 10, pp. 506-518, 2011.

To solve the class imbalance problem in the classification of pre-miRNAs with the ab initio method, we developed a novel sample selection method according to the characteristics of pre-miRNAs. Real/pseudo pre-miRNAs are clustered based on their stem similarity and their distribution in high dimensional sample space, respectively. The training samples are selected according to the sample density of each cluster. Experimental results are validated by the cross-validation and other testing datasets composed of human real/pseudo pre-miRNAs.

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