A Bayesian approach for constructing genetic maps when markers are miscoded

The advent of molecular markers has created opportunities for a better understanding of quantitative inheritance and for developing novel strategies for genetic improvement of agricultural species, using information on quantitative trait loci (QTL). A QTL analysis relies on accurate genetic marker maps. At present, most statistical methods used for map construction ignore the fact that molecular data may be read with error. Often, however, there is ambiguity about some marker genotypes. A Bayesian MCMC approach for inferences about a genetic marker map when random miscoding of genotypes occurs is presented, and simulated and real data sets are analyzed. The results suggest that unless there is strong reason to believe that genotypes are ascertained without error, the proposed approach provides more reliable inference on the genetic map.

Isolation and characterization of microsatellite loci from the forage species Arachis pintoi (Genus Arachis)

Arachis pintoi is an alternative to forage production in the tropics. Its germplasm comprises more than 150 accessions, that could be used to improve it. Our objective was the isolation and characterization of microsatellite loci in A. pintoi to be used to molecular evaluation of this germplasm and of A. repens (section Caulorrhizae). Seven loci were analyzed using five accessions of A. repens and 20 accessions of A. pintoi. The high variation found makes clear the high potential of this marker in genetic studies in these species. The developed markers showed total transferability to A. repens.

Strong selection against hybrids at a hybrid zone in the Ensatina ring species complex and its evolutionary implications

The analysis of interactions between lineages at varying levels of genetic divergence can provide insights into the process of speciation through the accumulation of incompatible mutations. Ring species, and especially the Ensatina eschscholtzii system exemplify this approach. The plethodontid salamanders E. eschscholtzii xanthoptica and E. eschscholtzii platensis hybridize in the central Sierran foothills of California. We compared the genetic structure across two transects (southern and northern Calaveras Co.), one of which was resampled over 20 years, and examined diagnostic molecular markers (eight allozyme loci and mitochondrial DNA) and a diagnostic quantitative trait (color pattern). Key results across all studies were: (1) cline centers for all markers were coincident and the zones were narrow, with width estimates of 730 m to 2000 m; (2) cline centers at the northern Calaveras transect were coincident between 1981 and 2001, demonstrating repeatability over five generations; (3) there were very few if any putative F1s, but a relatively high number of backcrossed individuals in the central portion of transects: and (4) we found substantial linkage disequilibrium in all three studies and strong heterozygote deficit both in northern Calaveras, in 2001, and southern Calaveras. Both linkage disequilibrium and heterozygote deficit showed maximum values near the center of the zones. Using estimates of cline width and dispersal, we infer strong selection against hybrids. This is sufficient to promote accumulation of differences at loci that are neutral or under divergent selection, but would still allow for introgression of adaptive alleles. The evidence for strong but incomplete isolation across this centrally located contact is consistent with theory suggesting a gradual increase in postzygotic incompatibility between allopatric populations subject to divergent selection and reinforces the value of Ensatina as a system for the study of divergence and speciation at multiple stages. © 2005 The Society for the Study of Evolution. All rights reserved.

Comparative cytogenetics of nine species of Hypoptopomatinae (Teleostei: Siluriformes: Loricariidae): The importance of structural rearrangements in chromosome evolution

Fishes of the subfamily Hypoptopomatinae are very common and found in the lowlands of cis-Andean South America from Venezuela to the north of Argentina. With the main objective of contributing for a better understanding of the importance of chromosome rearrangements in the loricariid evolution, cytogenetic analyses were conducted in nine species of Hypoptopomatinae. The results showed a marked gross karyotypic conservation with the presence of 2n=54 chromosomes in all species analyzed. The main differences were found in the karyotypic formulae level. Most species had a single interstitial Ag-NORs, however terminal Ag-NORs were observed in three species. One species exhibited two Ag-NOR-bearing chromosome pairs. The distribution of C-band positive segments was species specific but chromosome markers were observed among the species analyzed. The gross cytogenetic characteristics observed among the Hypoptopomatinae species are similar to those observed in other primitive Loricariidae species suggesting that small changes, mainly paracentric and pericentric inversion were the main events in the karyotypic evolution of this fish group.

Taenia solium and Taenia saginata: Identification of sequence characterized amplified region (SCAR) markers

Cysticercosis is one of the most important zoonosis, not only because of the effects on animal health and its economic consequences, but also due to the serious danger it poses to humans. The two main parasites involved in the taeniasis-cysticercosis complex in Brazil are Taenia saginata and Taenia solium. Differentiating between these two parasites is important both for disease control and for epidemiological studies. The purpose of this work was to identify genetic markers that could be used to differentiate these parasites. Out of 120 oligonucleotide decamers tested in random amplified polymorphic DNA (RAPD) assays, 107 were shown to discriminate between the two species of Taenia. Twenty-one DNA fragments that were specific for each species of Taenia were chosen for DNA cloning and sequencing. Seven RAPD markers were converted into sequence characterized amplified region (SCAR) markers with two specific for T. saginata and five specific for T. solium as shown by agarose gel electrophoresis. These markers were developed as potential tools to differentiate T. solium from T. saginata in epidemiological studies. © 2007 Elsevier Inc. All rights reserved.

Assessing genetic variability in bat species of Emballonuridae, Phyllostomidae, Vespertilionidae and Molossidae families (Chiroptera) by RFLP-PCR

A PCR-RFLP analysis of the restriction pattern in nuclear (RAG2) and mitochondrial (12S/16S) gene sequences of bat species from the Molossidae, Phyllostomidae, Vespertilionidae, and Emballonuridae families produced a large number of fragments: 107 for RAG2 and 155 for 12S/16S combined in 139 and 402 haplotypes, respectively. The values detected for gene variation were low for both sequences (0.13 for RAG2 and 0.15 for 12S/16S) and reflected their conservative feature, reinforced by high values of inter- and intraspecies genetic identity (70-100%). The species with a high gene divergence were variable in the analyses of RAG2 (Eumops perotis, Artibeus lituratus, and Carollia perspicillata) and of 12S/16S (Nyctinomops laticaudatus, C. perspicillata, and Cynomops abrasus), and furthermore, one of them, C. perspicillata, also showed the highest intraspecific variation. The species that exhibited the lowest variation for both genes was Molossus rufus. In the families, the highest variation was observed in the Molossidae and this can be attributed to variation exhibited by Eumops and Nyctinomops species. The variations observed were interpreted as a natural variability within the species and genus that exhibited a conserved pattern in the two gene sequences in different species and family analyzed. Our data reinforce the idea that the analyses of mitochondrial and nuclear genes contribute to our knowledge of the diversity of New World bats. The genetic variability found in different taxa suggests that an additional diversity, unnoticed by other methods, can be revealed with the use of different molecular strategies. ©FUNPEC-RP.

Genetic polymorphism, molecular characterization and relatedness of Macrobrachium species (Palaemonidae) based on RAPD-PCR.

The prawn genus Macrobrachium belongs to the family Palaemonidae. Its species are widely distributed in lakes, reservoirs, floodplains, and rivers in tropical and subtropical regions of South America. Globally, the genus Macrobrachium includes nearly 210 known species, many of which have economic and ecological importance. We analyzed three species of this genus (M. jelskii, M. amazonicum and M. brasiliense) using RAPD-PCR to assess their genetic variability, genetic structure and the phylogenetic relationship between them and to look for molecular markers that enable separation of M. jelskii and M. amazonicum, which are closely related syntopic species. Ten different random decamer primers were used for DNA amplification, yielding 182 fragments. Three of these fragments were monomorphic and exclusive to M. amazonicum or M. jelskii and can be used as specific molecular markers to identify and separate these two species. Similarity indices and a phylogenetic tree showed that M. amazonicum and M. jelskii are closest to each other, while M. brasiliense was the most differentiated species among them; this may be attributed to the different habitat conditions to which these species have been submitted. This information will be useful for further studies on these important crustacean species.

Development of microsatellite markers for the Neotropical endemic Brazilian Guanabara frog, Euparkerella brasiliensis, through 454 shotgun pyrosequencing

The new-generation 454 GS-FLX Titanium pyrosequencing was used to isolate microsatellite markers for the Brazilian Guanabara frog, Euparkerella brasiliensis, an Atlantic forest endemic species. Three multiplex polymerase chain reaction sets were optimized for genotyping of 11 polymorphic (di- and tetranucleotide) microsatellite markers. Genetic diversity was assessed in 21 individuals from a population (Reserva Ecológica de Guapiaçu, REGUA) locatedin the central region of the Rio de Janeiro State, in Brazil. The mean number of alleles per locus ranged from 3 to 12. Observed and expected heterozygosities ranged from 0.095 to 0.905 and from 0.094 to 0.904, respectively. After using the Bonferroni correction for multiple tests, there was no evidence of linkage disequilibrium between pairs of loci but deviations for Hardy-Weinberg equilibrium were found in 4 loci. We found no evidence for allele dropouts or stuttering, but we detected the presence of null alleles at loci Eb10 and Eb36. These markers will be useful for analyses of fine-scale population structure and determination of relative effects of habitat loss and fragmentation on population genetic variability within species. © FUNPEC-RP.

Hisonotus bocaiuva, a new species from the rio São Francisco basin, Brazil (Teleostei: Loricariidae)

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Genetic Structure of Lutzomyia longipalpis Populations in Mato Grosso Do Sul, Brazil, Based on Microsatellite Markers

Background:Lutzomyia longipalpis (Diptera: Psychodidae) is the major vector of Leishmania (Leishmania) infantum and thus plays a crucial role in the epidemiology of American visceral leishmaniasis (AVL). This vector is the best studied species of sand fly in the Neotropical region. Many studies claim that this vector is in fact a species complex; however there is still no consensus regarding the number of species that belong into this complex or the geographical distribution of sibling species. The aim of the present study was to analyze the genetic relationships within Lu. longipalpis populations in the state of Mato Grosso do Sul (MS), Brazil.Methodology/Principal Findings:We collected 30 Lu. longipalpis (15 females and 15 males) from five localities (Campo Grande, Três Lagoas, Aquidauana, Miranda and Bonito) and 30 Lu. Cruzi from Corumbá, totaling 180 sandflies from MS, and 30 Lu. longipalpis from Estrela de Alagoas, state of Alagoas (AL), Northeast Brazil. We show that eight previously described microsatellite loci were sufficient in distinguishing Lu. longipalpis from Lu. Cruzi, which is a closely related species, and in differentiating between Lu. longipalpis collected in MS versus Estrela de Alagoas. Analyses of the genotypes revealed introgression between sympatric Lu. longipalpis and Lu. Cruzi.Conclusions/Significance:Our findings support the hypothesis of cryptic species within the Lu. longipalpis complex. Furthermore, our data revealed introgression between Lu. longipalpis and Lu. cruzi. This phenomenon should be further investigated to determine the level and incidence of hybridization between these two species. We also demonstrated that microsatellite markers are a powerful tool for differentiating sand fly populations and species. The present study has elucidated the population structure of Lu. longipalpis in MS and, by extension, the Neotropical Lu. longipalpis complex itself. © 2013 Santos et al.

Caracterização molecular e bioquímica de uma esterase macho-específica em Zaprionus indianus

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Variações estruturais do lenho de espécies de cerrado do estado de São Paulo

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Determination of phenolic compounds and coumarins in sugar cane spirit aged in different species of wood

The identities and quantities of the phenolic compounds and coumarins in twelve samples of sugar cane spirit aged in Quercus sp., Amburana cearensis, Cariniana legalis, Castanea sativa Mill, Ocotea sp., Cotyledon orbiculata L., and Hymenaea sp. casks were determined. These compounds have a direct influence on the sensory characteristics of aged beverages; some of them are considered to be markers for the aging process. The analysis of phenolic compounds was performed by HPLC. Solid phase extraction (SPE) was also used for the determination of coumarins. The concentrations of the principal compounds extracted varied according to the species of wood. The concentrations of total phenolic compounds ranged from 0.08 for a sample stored in a 4000-L jatobá barrel for a period of six months to 40.9 mg · L−1 for a sample aged in a 50000-L oak barrel for a period of 48 months. The use of the SPE technique removed interfering compounds from the samples, thereby improving the detection of coumarin.

Metodologias para a avaliação do potencial fisiológico de sementes de tabaco

Despite tobacco being a culture propagated by seeds, there is little information concerning tests that allow the distinction of similar germination lots in different levels of vigor. The diversity of cultivars available in the market, and a few peculiarities of the species, such as uneven maturation of the flowers, fruits and seeds, small size and seed dormancy, are considered obstacles for obtaining lots of tobacco of high physiological potential. Thus, this research was developed with the objective of adapting feasibility and vigor tests for evaluating the physiological potential of tobacco seed lots. We used nine lots of tobacco seeds of cultivar CSC 447 and nine lots of seeds of cultivar BAT 2101, belonging to variety groups Virginia and Burley, respectively. Initially, germination test was conducted to characterize the profile of the lots. For determining the feasibility and vigor of the tobacco seeds, germination tests were conducted in distinct temperatures, controlled emergence conditions, electric conductivity, artificial aging and in tetrazolium. For determining the isoenzymatic marker for seed quality, analyses were conducted with enzymes catalase, esterase, malate dehydrogenase and alcohol dehydrogenase. In conclusion, the emergence tests at 25oC and artificial aging at 41oC for 72 hours, are efficient in discriminating the lots of tobacco seeds in different levels of vigor. The electric conductivity and germination tests in different temperatures have distinct responses in relation to the genotype of the tobacco seeds. The tetrazolium test using the methodology with pre-conditioning in 3.5% sodium hypochlorite solution and subsequent emersion in 1.0% tetrazolium solution for 18 hours is efficient for the quick evaluation of the feasibility of tobacco seeds. The analysis of the profiles of enzymes catalase, esterase, malate dehydrogenase and alcohol dehydrogenase is efficient as markers for tobacco seed quality.

Caracterização da diversidade genética de Stryphnodendron adstringens (Mart.) Coville por marcador molecular AFLP e transferência de microssatélites

Pós-graduação em Agronomia (Horticultura) - FCA