Comparison of different models to estimate genetic parameters for carcass traits in a commercial broiler line

The effect of genetic and non-genetic factors for carcass, breast meat and leg weights, and yields of a commercial broiler line were investigated using the restricted maximum likelihood method, considering four different animal models, including or excluding maternal genetic effect with covariance between direct and maternal genetic effects, and maternal permanent environmental effect. The likelihood ratio test was used to determine the most adequate model for each trait. For carcass, breast, and leg weight, and for carcass and breast yield, maternal genetic and permanent environmental effects as well as the covariance between direct and maternal genetic effects were significant. The estimates of direct and maternal heritability were 0.17 and 0.04 for carcass weight, 0.26 and 0.06 for breast weight, 0.22 and 0.02 for leg weight, 0.32 and 0.02 for carcass yield, and 0.52 and 0.04 for breast yield, respectively. For leg yield, maternal permanent environmental effect was important, in addition to direct genetic effects. For that trait, direct heritability and maternal permanent environmental variance as a proportion of the phenotypic variance were 0.43 and 0.02, respectively. The results indicate that ignoring maternal effects in the models, even though they were of small magnitude (0.02 to 0.06), tended to overestimate direct genetic variance and heritability for all traits.

Phylogeography of the common vampire bat (Desmodus rotundus): Marked population structure, Neotropical Pleistocene vicariance and incongruence between nuclear and mtDNA markers

Background: The common vampire bat Desmodus rotundus is an excellent model organism for studying ecological vicariance in the Neotropics due to its broad geographic range and its preference for forested areas as roosting sites. With the objective of testing for Pleistocene ecological vicariance, we sequenced a mitocondrial DNA (mtDNA) marker and two nuclear markers (RAG2 and DRB) to try to understand how Pleistocene glaciations affected the distribution of intraspecific lineages in this bat. Results: Five reciprocally monophyletic clades were evident in the mitochondrial gene tree, and in most cases with high bootstrap support: Central America (CA), Amazon and Cerrado (AMC), Pantanal (PAN), Northern Atlantic Forest (NAF) and Southern Atlantic Forest (SAF). The Atlantic forest clades formed a monophyletic clade with high bootstrap support, creating an east/west division for this species in South America. On the one hand, all coalescent and non-coalescent estimates point to a Pleistocene time of divergence between the clades. On the other hand, the nuclear markers showed extensive sharing of haplotypes between distant localities, a result compatible with male-biased gene flow. In order to test if the disparity between the mitochondrial and nuclear markers was due to the difference in mutation rate and effective size, we performed a coalescent simulation to examine the feasibility that, given the time of separation between the observed lineages, even with a gene flow rate close to zero, there would not be reciprocal monophyly for a neutral nuclear marker. We used the observed values of theta and an estimated mutation rate for the nuclear marker gene to perform 1000 iterations of the simulation. The results of this simulation were inconclusive: the number of iterations with and without reciprocal monophyly of one or more clades are similar. Conclusions: We therefore conclude that the pattern exhibited by the common vampire bat, with marked geographical structure for a mitochondrial marker and no phylogeographic structure for nuclear markers is compatible with a historical scenario of complete isolation of refuge-like populations during the Pleistocene. The results on demographic history on this species is compatible with the Carnaval-Moritz model of Pleistocene vicariance, with demographic expansions in the southern Atlantic forest.

The Liver Plays a Major Role in Clearance and Destruction of Blood Trypomastigotes in Trypanosoma cruzi Chronically Infected Mice

Intravenous challenge with Trypanosoma cruzi can be used to investigate the process and consequences of blood parasite clearance in experimental Chagas disease. One hour after intravenous challenge of chronically infected mice with 5610 6 trypomastigotes, the liver constituted a major site of parasite accumulation, as revealed by PCR. Intact parasites and/or parasite remnants were visualized at this time point scattered in the liver parenchyma. Moreover, at this time, many of liver-cleared parasites were viable, as estimated by the frequency of positive cultures, which considerably diminished after 48 h. Following clearance, the number of infiltrating cells in the hepatic tissue notably increased: initially (at 24 h) as diffuse infiltrates affecting the whole parenchyma, and at 48 h, in the form of large focal infiltrates in both the parenchyma and perivascular spaces. Phenotypic characterization of liver-infiltrating cells 24 h after challenge revealed an increase in Mac1(+), CD8(+) and CD4(+) cells, followed by natural killer (NK) cells. As evidence that liver-infiltrating CD4(+) and CD8(+) cells were activated, increased frequencies of CD69(+) CD8(+), CD69(+) CD4(+) and CD25(+) CD122(+) CD4(+) cells were observed at 24 and 48 h after challenge, and of CD25(-)CD122(+)CD4(+) cells at 48 h. The major role of CD4(+) cells in liver protection was suggested by data showing a very high frequency of interferon (IFN)-gamma-producing CD4(+) cells 24 h after challenge. In contrast, liver CD8(+) cells produced little IFN-gamma, even though they showed an enhanced potential for secreting this cytokine, as revealed by in vitro T cell receptor (TCR) stimulation. Confirming the effectiveness of the liver immune response in blood parasite control during the chronic phase of infection, no live parasites were detected in this organ 7 days after challenge.

Genome-wide SNP genotyping highlights the role of natural selection in Plasmodium falciparum population divergence

Background: The malaria parasite Plasmodium falciparum exhibits abundant genetic diversity, and this diversity is key to its success as a pathogen. Previous efforts to study genetic diversity in P. falciparum have begun to elucidate the demographic history of the species, as well as patterns of population structure and patterns of linkage disequilibrium within its genome. Such studies will be greatly enhanced by new genomic tools and recent large-scale efforts to map genomic variation. To that end, we have developed a high throughput single nucleotide polymorphism (SNP) genotyping platform for P. falciparum. Results: Using an Affymetrix 3,000 SNP assay array, we found roughly half the assays (1,638) yielded high quality, 100% accurate genotyping calls for both major and minor SNP alleles. Genotype data from 76 global isolates confirm significant genetic differentiation among continental populations and varying levels of SNP diversity and linkage disequilibrium according to geographic location and local epidemiological factors. We further discovered that nonsynonymous and silent (synonymous or noncoding) SNPs differ with respect to within-population diversity, interpopulation differentiation, and the degree to which allele frequencies are correlated between populations. Conclusions: The distinct population profile of nonsynonymous variants indicates that natural selection has a significant influence on genomic diversity in P. falciparum, and that many of these changes may reflect functional variants deserving of follow-up study. Our analysis demonstrates the potential for new high-throughput genotyping technologies to enhance studies of population structure, natural selection, and ultimately enable genome-wide association studies in P. falciparum to find genes underlying key phenotypic traits.

Diversity of free-living marine nematodes (Enoplida) from Baja California assessed by integrative taxonomy

We used morphological and molecular approaches to evaluate the diversity of free-living marine nematodes (order Enoplida) at four coastal sites in the Gulf of California and three on the Pacific coast of Baja California, Mexico. We identified 22 morphological species belonging to six families, of which Thoracostomopsidae and Oncholaimidae were the most diverse. The genus Mesacanthion (Thoracostomopsidae) was the most widespread and diverse. Five allopatric species, genetically and morphologically differentiated, were found in two localities in the Gulf of California (M. sp1 and M. sp2) and three in the Pacific coast (M. sp3, M. sp4 and M. sp5). Overall, we produced 19 and 20 sequences for the 18S and 28S genes, respectively. Neither gene displayed intraspecific polymorphisms, which allowed us to establish that some morphological variation was likely either ontogenetic or due to phenotypic plasticity. Although 18S and 28S phylogenies were topologically congruent (incongruence length difference test, P > 0.05), divergences between species were much higher in the 28S gene. Moreover, this gene possessed a stronger phylogenetic signal to resolve relationships involving Rhabdodemania and Bathylaimus. On the other hand, the close relationship of Pareurystomina (Enchilidiidae) with oncholaimids warrants further study. The 28S sequences (D2D3 domain) may be better suited for DNA barcoding of marine nematodes than those from the 18S rDNA, particularly for differentiating closely related or cryptic species. Finally, our results underline the relevance of adopting an integrative approach encompassing morphological and molecular analyses to improve the assessment of marine nematode diversity and advance their taxonomy.

Facies, delta(13)C, delta(15)N and C/N analyses in a late Quaternary compound estuarine fill, northern Brazil and relation to sea level

The present work integrates sedimentary facies, (14)C dating, delta(13)C, delta(15)N, and C/N with geologic and geomorphologic data available from literature. The aim was to characterize the depositional settings of a late Quaternary estuary in northeastern Marajo Island and analyze its evolution within the context of relative sea level fluctuations. The data derive from four continuous cores along a proximal-to-distal transect of a paleoestuary, previously recognized using remote sensing information. Fifteen sediment samples recorded ages ranging from 42,580 +/- 1430 to 3184 +/- 37 (14)C yr B.P. Fades analysis indicated fine- to coarse-grained sands with parallel lamination or cross stratification, massive or laminated muds and heterolithic deposits. delta(13)C (-28.1 parts per thousand to -19.7 parts per thousand, mean = -23.0 parts per thousand), delta(15)N (+ 14.8 parts per thousand to + 4.7 parts per thousand, mean = + 9.2 parts per thousand) and C/N (14.5 to 1.5, mean = 7.9) indicate mostly marine and freshwater phytoplankton sources for the organic matter. The results confirm a large late Quaternary paleoestuary in northeastern Marajo Island. The distribution of delta(13)C, delta(15)N, and C/N, together with fades associations, led to identify depositional settings related to fluvial channel, floodplain, tidal channel/tidal flat, central basin, tidal delta, and tidal inlet/sand barrier. These deposits are consistent with a wave-dominated estuary. Variations in stratigraphy and geochemistry are controlled by changes in relative sea level, revealing a main transgression from an undetermined time around 42,000 (14)C yr B.P. and 29,340 (+/- 200) (14)C yr B.P., which is synchronous to the overall drop in sea level after the last interglacial. Following this period, and probably until 9110 +/- 37 (14)C yr B.P., i.e., during a time interval encompassing two glacial episodes including the Last Glacial and the Younger Dryas, there was a pronounced drop in sea level, recorded by the development of a major erosional discontinuity due to valley re-incision. Sea level rose again until 5464 +/- 40 (14)C yr B.P, just before the main worldwide mid-Holocene transgressive peak. Mid to late Holocene coastal progradation ended the Marajo paleoestuarine history, and promoted the establishment of continental conditions throughout the island. The divergence comparing the Marajo sea level behavior with the eustatic curve allows hypothesizing that post-rifting tectonics along the Brazilian Equatorial margin influenced the sedimentary evolution of the studied paleoestuary. Considering that sedimentary facies in estuarine settings are highly variable both laterally and vertically, the present integration of facies with isotope and elemental analyses was crucial to provide a more precise interpretation of the Late Pleistocene and Holocene Marajo paleoestuary, and analyze its sea level history within the eustatic and tectonic context. (C) 2010 Elsevier B.V. All rights reserved.

Quaternary paleoenvironments and relative sea-level changes in Marajo Island (Northern Brazil): Facies, delta(13)C, delta(15)N and C/N

The reconstruction of physical environments of Amazonian areas is of great interest to determine the dynamic evolution of the Amazon drainage basin. However. few studies have emphasized the Quaternary deposits in this region. which is mostly due to the lack of natural exposures imposed by the low topography. This work integrates facies analysis. radiocarbon dating, delta(13)C, delta(15)N, and C/N of an 124 m-thick core from an area located at the mouth of the Amazon River. northeastern Amazonia. The study records deposits up to 50.795 (14)C yr B P. in age. which formed in a variety of depositional environments including fluvial channel, tidal flat, outer estuarine basin to shallow marine. inner estuarine basin, estuarine channel and lagoon. Facies interpretation was significantly improved with the inclusion of delta(13)C, delta(15)N, and C/N analyses of organic matter extracted from the sediments The obtained values conform to a transitional. mostly estuarine paleosetting evolved during successive relative sea-level fluctuations. The results suggest fluvial deposition between 40,950 (+/- 590) and 50.795 (14)C yr B P, with a rise in relative sea level that commenced between 35,567 (+/- 649) and 39,079 (+/- 1114) (14)C yr B P. An overall transgression took place until 29,340 (+/- 340) (14)C yr B P., after which the relative sea level dropped, favoring valley rejuvenation and incision. Following this time up to 10,479 (+/- 34) (14)C yr B.P. a rise in relative sea level filled up the valley with estuarine deposits After 10.479(+/- 34) (14)C yr B.P., the estuary was replaced by a lagoon At the end of the Holocene, the coastline prograided approximately 45 km northward, replaci ng the lagoon by a lake system Despite the influence of eustatic fluctuations. regional tectonics played a significant role to create new space where these Late Pleistocene and Holocene sediments accumulated. (C) 2009 Elsevier B V All rights reserved.

Variation in the Distribution of Trace Elements in Renal Cell Carcinoma

The development of cancer is a complex, multistage process during which a normal cell undergoes genetic changes that result in phenotypic alterations and in the acquisition of the ability to invade other sites. Inductively coupled plasma optical emission spectroscopy was used to estimate the contents of Al, Ca, Cd, Cr, Cu, Fe, K, Mg, Mn, Na, P, Pb, and Zn in healthy kidney and renal cell carcinoma (RCC), and significant differences were found for all elements. Along with the progression of the malignant disease, a progressive decrease of Cd and K was observed. In fact, for Cd, the concentration in stage T4 was 263.9 times lower than in stage T1, and for K, the concentration in stage T4 was 1.73 times lower than in stage T1. Progressive accumulation was detected for P, Pb, and Zn in stage T4. For P, the concentration in stage T4 was 11.1 times higher than in stage T1; for Pb, the concentration in stage T4 was 232.7 times higher than in T1; and for Zn, the concentration in T4 was 8.452 times higher than in T1. This study highlights the marked differences in the concentrations of selected trace metals in different malignant tumor stages. These findings indicate that some trace metals may play important roles in the pathogenesis of RCC.

TOPOGRAPHIC REGISTERS OF PALEO-VALLEYS ON THE SOUTHEASTERN BRAZILIAN CONTINENTAL SHELF

The evolution of paleo-incised-valleys in the Sao Paulo State region of the southeastern Brazilian continental shelf is presented in this study in relation to the post Last Glacial Maximum (LGM) sea-level rises based on the submarine topography modeled by a detailed Digital Elevation Model and evidences noted in high resolution seismic profiles. The hypothesis that has guided this study is that the set of paleo-valley characteristics (i.e. the fluvial parameters of modern coastal drainage systems, the topographical shape and dimensions of the valleys and of the subsurface channels) may indicate aspects of the relation between the influence of the fluvial and the eustatic variation regime in geomorphological-stratigraphic registers. Models described in the literature sustain the view that faster marine transgressions tend to increase erosion in estuaries, which may explain the lack of registers of paleo-drainage both in topography and the sub-surface in areas with wider shelves. On the other hand, on narrower shelves, with a higher slope angle, the transgression process can preserve, or even enhance, the incised valley registers during shoreface retreat. In the area studied, we observed that the dimensions and form of the continental shelf varies from the northern to the southern part of the area, affecting aspects of the geomorphological registers of the submerged incised valleys.

Multidimensional cluster stability analysis from a Brazilian Bradyrhizobium sp RFLP/PCR data set

The taxonomy of the N(2)-fixing bacteria belonging to the genus Bradyrhizobium is still poorly refined, mainly due to conflicting results obtained by the analysis of the phenotypic and genotypic properties. This paper presents an application of a method aiming at the identification of possible new clusters within a Brazilian collection of 119 Bradryrhizobium strains showing phenotypic characteristics of B. japonicum and B. elkanii. The stability was studied as a function of the number of restriction enzymes used in the RFLP-PCR analysis of three ribosomal regions with three restriction enzymes per region. The method proposed here uses Clustering algorithms with distances calculated by average-linkage clustering. Introducing perturbations using sub-sampling techniques makes the stability analysis. The method showed efficacy in the grouping of the species B. japonicum and B. elkanii. Furthermore, two new clusters were clearly defined, indicating possible new species, and sub-clusters within each detected cluster. (C) 2008 Elsevier B.V. All rights reserved.

Molecular and morphological diversity in Japanese rice germplasm

Germplasm molecular and phenotypic characterization is instrumental to its utilization and to genetic variability incorporation into rice breeding programmes. The diversity within 192 Japanese rice accessions was analysed for 22 agro-morphological traits and 24 single sequence repeat markers. A total of 181 alleles were detected, 38 of which were exclusive. The number of alleles/marker ranged from 2 to 16, with an average of 7.54 alleles/locus and the H(e) value ranged from 0.01 to 0.82, with an average of 0.46. The accessions showed diversity at molecular and phenotypic level and few showed also good agronomic performance. Tocher`s method applied on a total-dissimilarity matrix was used to determine cluster formation of 13 diversity groups. Most of the accessions (81%) were clustered within a group, whereas eight accessions (Kyuushuu, Eika Ine, Ishiwari Mochi, Col/Fukui/1965, Ookuma Nishiki, Suzume Shirazu, Iwate Ryoon and Toga) did not cluster with other accessions.

QTL mapping for reaction to Phaeosphaeria leaf spot in a tropical maize population

Phaeosphaeria leaf spot (PLS) is an important disease in tropical and subtropical maize (Zea mays, L.) growing areas, but there is limited information on its inheritance. Thus, this research was conducted to study the inheritance of the PLS disease in tropical maize by using QTL mapping and to assess the feasibility of using marker-assisted selection aimed to develop genotypes resistance to this disease. Highly susceptible L14-04B and highly resistant L08-05F inbred lines were crossed to develop an F(2) population. Two-hundred and fifty six F(2) plants were genotyped with 143 microsatellite markers and their F(2:3) progenies were evaluated at seven environments. Ten plants per plot were evaluated 30 days after silk emergence following a rating scale, and the plot means were used for analyses. The heritability coefficient on a progeny mean basis was high (91.37%), and six QTL were mapped, with one QTL on chromosomes 1, 3, 4, and 6, and two QTL on chromosome 8. The gene action of the QTL ranged from additive to partial dominance, and the average level of dominance was partial dominance; also a dominance x dominance epistatic effect was detected between the QTL mapped on chromosome 8. The phenotypic variance explained by each QTL ranged from 2.91 to 11.86%, and the joint QTL effects explained 41.62% of the phenotypic variance. The alleles conditioning resistance to PLS disease of all mapped QTL were in the resistant parental inbred L08-05F. Thus, these alleles could be transferred to other elite maize inbreds by marker-assisted backcross selection to develop hybrids resistant to PLS disease.

Genetic variability in S(1) families from different maize populations.

Genetic variability in S(1) families from different maize populations. The objectives of the present work were directed towards the study of genetic: variablilty In seven maize populations with a broad genetic base, as a guide for population improvement. The field evaluation was conducted in completely randomized blocks, at one location (Anhembi, Sao Paulo state) with different groups, of S(1) families Obtained from seven populations (GO-D: dent type, GO-F: flint type, GO-L: long car, GO-G: thick Car; and composites G3, G4 and GO-S). Estimates were obtained for genetic variance (progeny mean basis), phenotypic variance of families means, and coefficient of heritability (broad sense) for progeny means. Estimates of heritability were high for Car weight (0,89 to 0.94), car length (0.77 to 0.88) and car diameter (0.77 to 0.92); and lower for plant height (0.58 to 0.80) and Car height (0.54 to 0.84), thus showing the high Potential of the populations for recurrent selection based oil S, families. Ear yield in the base populations used as controls varied front 11,200 kg ha(-1) (GO-D) to 12,800 kg ha(-1) (G3). The means of S(1) families varied from 6,070 kg ha(-1) (GO-F) to 7,380 kg ha(-1) (G4); the Inbreeding depression in S(1) Families varied front 37.5% (G4) to 48.0% (G3) relative to the non-inbred population.

Inheritance of growth habit detected by genetic linkage analysis using microsatellites in the common bean (Phaseolus vulgaris L.)

The genetic linkage map for the common bean (Phaseolus vulgaris L.) is a valuable tool for breeding programs. Breeders provide new cultivars that meet the requirements of farmers and consumers, such as seed color, seed size, maturity, and growth habit. A genetic study was conducted to examine the genetics behind certain qualitative traits. Growth habit is usually described as a recessive trait inherited by a single gene, and there is no consensus about the position of the locus. The aim of this study was to develop a new genetic linkage map using genic and genomic microsatellite markers and three morphological traits: growth habit, flower color, and pod tip shape. A mapping population consisting of 380 recombinant F10 lines was generated from IAC-UNA x CAL143. A total of 871 microsatellites were screened for polymorphisms among the parents, and a linkage map was obtained with 198 mapped microsatellites. The total map length was 1865.9 cM, and the average distance between markers was 9.4 cM. Flower color and pod tip shape were mapped and segregated at Mendelian ratios, as expected. The segregation ratio and linkage data analyses indicated that the determinacy growth habit was inherited as two independent and dominant genes, and a genetic model is proposed for this trait.

ADAPTABILITY AND STABILITY OF SOYBEAN GENOTYPES UNDER DIFFERENT TIMES OF SOWING

This study aimed to evaluate the average behavior, the genotype x environment (GxE), adaptability and stability of seven soybean cultivars at three sowing dates in Uberlandia-MG. The tests were conducted at Capim Branco Farm, belonging to the Federal University of Uberlandia. Sowing was held on october 29 (1st season), november 24 (2nd season) and december 17 (3rd season) 2007. The experimental design was a randomized, seven genotypes (UFUS Xavante, UFUS Riqueza, UFUS Guarani, UFUS Milionaria, Msoy 8001, Msoy 8411 and Msoy 8914) with three replications in each of three sowing dates. Means were compared by Tukey test at 5% probability. Analysis of adaptability and phenotypic stability of genotypes was performed using the Eberhart and Russell (1966), Lin and Binns (1988) modified by Carneiro (1998) and centroid (NASCIMENTO et al., 2009). For grain yield, the cultivar UFUS Xavante was classified as specific adaptability to environment and high stability. The other cultivars were classified as being of general adaptability. For oil content, the cultivars Msoy 8914 and UFUS Xavante behaved as high stability and was classified as having high adaptability. For the character content of protein, all cultivars behaved as wide adaptability and low stability.