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.

Variation in the CXCR1 gene (IL8RA) is not associated with susceptibility to chronic periodontitis

Background: The chemokine receptor 1 CXCR-1 (or IL8R-alpha) is a specific receptor for the interleukin 8 (IL-8), which is chemoattractant for neutrophils and has an important role in the inflammatory response. The polymorphism rs2234671 at position Ex2+860G > C of the CXCR1 gene causes a conservative amino acid substitution (S276T). This single nucleotide polymorphism (SNP) seemed to be functional as it was associated with decreased lung cancer risk. Previous studies of our group found association of haplotypes in the IL8 and in the CXCR2 genes with the multifactorial disease chronic periodontitis. In this study we investigated the polymorphism rs2234671 in 395 Brazilian subjects with and without chronic periodontitis. Findings. Similar distribution of the allelic and genotypic frequencies were observed between the groups (p > 0.05). Conclusions: The polymorphism rs2234671 in the CXCR1 gene was not associated with the susceptibility to chronic periodontitis in the studied Brazilian population. © 2011 Scarel-Caminaga et al; licensee BioMed Central Ltd.

Comparison of three molecular typing methods to assess genetic diversity for Mycobacterium tuberculosis

This study describes the comparison of three methods for genotyping of Mycobacterium tuberculosis, namely MIRU-VNTR (mycobacterial interspersed repetitive units-variable number of tandem repeats), spoligotyping and, for the first time, MLST (Multilocus Sequence Typing). In order to evaluate the discriminatory power of these methods, a total of 44 M. tuberculosis isolates obtained from sputum specimens of patients from Brazil were genotyped. Among the three methods, MLST showed the lowest discriminatory power compared to the other two techniques. MIRU-VNTR showed better discriminatory power when compared to spoligotyping, however, the combination of both methods provides the greatest level of discrimination and therefore this combination is the most useful genotyping tool to be applied to M. tuberculosis isolates. © 2013 Elsevier B.V.

Global sampling reveals low genetic diversity within Compsopogon (Compsopogonales, Rhodophyta)

Twenty-five specimens of the freshwater red alga Compsopogon were collected from locations in North America, South America, Europe, Asia, Australasia and Oceania, and from an aquarium, with the goal of determining genetic diversity among specimens and ascertaining the number of phylogenetic species. Specimens were morphologically identified as having either the 'caeruleus' morphology, with regular polyhedral cortical cells, or the 'leptoclados' morphology, with irregular cortical cells with rhizoidal outgrowths. The 'leptoclados' morphology has been used by some researchers to distinguish the genus Compsopogonopsis from Compsopogon, or at least to distinguish C. leptoclados from other Compsopogon species. Sequence data for the rbcL gene and cox1 barcoding region were obtained for most specimens. In addition, SSU and partial LSU (barcode) rDNA were explored for a few specimens, but all sequences were identical. For the 25 newly generated and eight previously published rbcL gene data, there were seven unique haplotypes, but the sequence divergence was very low (≤7 bp, ≤ 0.7%). One haplotype was widespread, represented by 21 specimens from diverse locations in all regions sampled. Likewise, the 22 new and one previously published cox1 barcode region sequences yielded seven unique haplotypes with little sequence divergence (≤13 bp, ≤ 2.0%). One haplotype was widespread, being shared among 16 specimens from all regions. The combined molecular and morphological data showed no genetic differentiation between the 'caeruleus' and 'leptoclados' morphologies. The ubiquitous distribution of Compsopogon in tropical/subtropical regions and its low genetic variation are probably facilitated by the alga's ability to tolerate a wide range of stream conditions and its propagation via asexual spores. Given the findings of previous culture-based studies, morphometric research and field observations, coupled with the results of our study, we conclude there is only a single monospecific genus worldwide and that the species is correctly called C. caeruleus, since this is the oldest validly published name; all other previously described species of Compsopogon and Compsopogonopsis are synonyms. © 2013 British Phycological Society.

Initial description of the phylogeography, population structure and genetic diversity of Atlantic spotted dolphins from Brazil and the Caribbean, inferred from analyses of mitochondrial and nuclear DNA

We provide initial information regarding the population structure and genetic diversity of Stenella frontalis from the Caribbean and southeastern Brazil from analyses of mitochondrial control region sequences and sequences from the first intron of the α-lactalbumin gene. Comparisons with previously described S. frontalis sequences showed a high number of haplotypes shared between populations throughout their distribution range. High diversity was found for southeastern Brazil and Caribbean samples, and population structure analyses indicate significant differentiation among population units at the FST level, but not at the ΦST level. Significant differentiation at the FST level was found between the Caribbean population unit and all other populations units. These results suggest historical or present connectivity between the Azores and Madeira and the southeastern Brazil groups and population differentiation between the Caribbean and southeastern Brazil, supporting the notion of two separate stocks in the waters around the Atlantic coast of South America. © 2013 Elsevier Ltd.

The population genetic structure of Rhizoctonia solani AG-3PT from potato in the Colombian Andes

The soilborne fungus Rhizoctonia solani anastomosis group 3 (AG-3PT) is a globally important potato pathogen. However, little is known about the population genetic processes affecting field populations of R. solani AG-3PT, especially in the South American Colombian Andes, which is near the center of diversity of the two most common groups of cultivated potato, Solanum tuberosum and S. phureja. We analyzed the genetic structure of 15 populations of R. solani AG-3PT infecting potato in Colombia using 11 simple-sequence repeat (SSR) markers. In total, 288 different multilocus genotypes were identified among 349 fungal isolates. Clonal fractions within field populations were 7 to 33%. R ST statistics indicated a very low level of population differentiation overall, consistent with high contemporary gene flow, though moderate differentiation was found for the most distant southern populations. Genotype flow was also detected, with the most common genotype found widely distributed among field populations. All populations showed evidence of a mixed reproductive mode, including both asexual and sexual reproduction, but two populations displayed evidence of inbreeding. © 2013 The American Phytopathological Society.

The genetic characterization of myrmelachista roger assemblages (hymenoptera: formicidae: formicinae) in the atlantic forest of southeastern Brazil

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Genetic Parameters for Productive and Reproductive Traits for Milk Buffalo in Brazil

Knowing the genetic parameters of productive and reproductive traits in milking buffaloes is essential for planning and implementing of a program genetic selection. In Brazil, this information is still scarce. The objective of this study was to verify the existence of genetic variability in milk yield of buffaloes and their constituents, and reproductive traits for the possibility of application of the selection. A total of 9,318 lactations records from 3,061 cows were used to estimate heritabilities for milk yield (MY), fat percentage (%F), protein percentage (%P), length of lactation (LL), age of first calving (AFC) and calving interval (CI) and the genetic correlations among traits MY, %F and %P. The (co) variance components were estimated using multiple-trait analysis by Bayesian inference method, applying an animal model, through Gibbs sampling. The model included the fixed effects of contemporary groups (herd-year and calving season), number of milking (2 levels), and age of cow at calving as (co) variable (quadratic and linear effect). The additive genetic, permanent environmental, and residual effects were included as random effects in the model. Estimated heritability values for MY, % F, % P, LL, AFC and CI were 0.24, 0.34, 0.40, 0.09, 0.16 and 0.05, respectively. The genetic correlation estimates among MY and % F, MY and % P and % F and % P were -0.29, -0.18 and 0.25, respectively. The production of milk and its constituents showed enough genetic variation to respond to a selection program. Negative estimates of genetic correlations between milk production and its components suggest that selection entails a reduction in the other.

Estimates of genetic parameters for total milk yield over multiple ages in Brazilian Murrah buffaloes using different models

The objective of this study was to estimate variance components and genetic parameters for accumulated 305-day milk yield (MY305) over multiple ages, from 24 to 120 months of age, applying random regression (RRM), repeatability (REP) and multi-trait (MT) models. A total of 4472 lactation records from 1882 buffaloes of the Murrah breed were utilized. The contemporary group (herd-year-calving season) and number of milkings (two levels) were considered as fixed effects in all models. For REP and RRM, additive genetic, permanent environmental and residual effects were included as random effects. MT considered the same random effects as did REP and RRM with the exception of permanent environmental effect. Residual variances were modeled by a step function with 1, 4, and 6 classes. The heritabilities estimated with RRM increased with age, ranging from 0.19 to 0.34, and were slightly higher than that obtained with the REP model. For the MT model, heritability estimates ranged from 0.20 (37 months of age) to 0.32 (94 months of age). The genetic correlation estimates for MY305 obtained by RRM (L23.res4) and MT models were very similar, and varied from 0.77 to 0.99 and from 0.77 to 0.99, respectively. The rank correlation between breeding values for MY305 at different ages predicted by REP, MT, and RRM were high. It seems that a linear and quadratic Legendre polynomial to model the additive genetic and animal permanent environmental effects, respectively, may be sufficient to explain more parsimoniously the changes in MY305 genetic variation with age.

Phenotypic and genetic variability for body weight of ostriches (Struthio camelus)

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

The Genetic Architecture of Climatic Adaptation of Tropical Cattle

Adaptation of global food systems to climate change is essential to feed the world. Tropical cattle production, a mainstay of profitability for farmers in the developing world, is dominated by heat, lack of water, poor quality feedstuffs, parasites, and tropical diseases. In these systems European cattle suffer significant stock loss, and the cross breeding of taurine x indicine cattle is unpredictable due to the dilution of adaptation to heat and tropical diseases. We explored the genetic architecture of ten traits of tropical cattle production using genome wide association studies of 4,662 animals varying from 0% to 100% indicine. We show that nine of the ten have genetic architectures that include genes of major effect, and in one case, a single location that accounted for more than 71% of the genetic variation. One genetic region in particular had effects on parasite resistance, yearling weight, body condition score, coat colour and penile sheath score. This region, extending 20 Mb on BTA5, appeared to be under genetic selection possibly through maintenance of haplotypes by breeders. We found that the amount of genetic variation and the genetic correlations between traits did not depend upon the degree of indicine content in the animals. Climate change is expected to expand some conditions of the tropics to more temperate environments, which may impact negatively on global livestock health and production. Our results point to several important genes that have large effects on adaptation that could be introduced into more temperate cattle without detrimental effects on productivity.

Genetic parameters and investigation of genotype x environment interactions in Nellore x Hereford crossbred for resistance to cattle ticks in different regions of Brazil

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Genetic variability in open pollinated progenies of Jatropha curcas

The objective of the present work was to estimate the genetic parameters of morphological traits, such as plant growth, fruit and seed production; and oil content and also to provide a source of superior genetic material for the breeding program of Jatropha curcas. For that, a J. curcas open pollination progeny test was set up in Sao Manuel Experimental Station, of College of Agricultural Sciences (FCA) of Sao Paulo State University (UNESP). The experimental design was of completely randomized blocks with 30 progenies, three replications, and eight plants per linear plot. We evaluated plants height (ALT), number of branches per plant (NRP), number of inflorescences per plant (NINE), number of fruits per plant (NF), weight of fruits (PE), weight of seeds (PS) and oil content % (TO). The software SELEGEN was the used to estimate the genetic parameters. The individual genetic variation coefficients (CVg) and progeny genetic variation coefficients (CVgp) at 24 months were 26.7% and 13.4% for height and 21.2% and 10.6% for number of branches. At 48 months the heritability coefficients among the progeny averages (h(mp)(2)) were 0.41 (ALT); 0.31 (NRP); 0.77 (NINF), and 0.44 (NF). The coefficient of heritability for individual plant level of oil content (TO %) was very low (h(a)(2) = 0.03), therefore, for the heritability of progeny means was higher than the individual level (h(mp)(2) = 0.37). Among progenies, some of them were superior for both, and seed production and oil content. We conclude that the present J. curcas population has enough genetic variability allowing obtaining gains through advanced generations.

Contemporary and historic factors influence differently genetic differentiation and diversity in a tropical palm

Population genetics theory predicts loss in genetic variability because of drift and inbreeding in isolated plant populations; however, it has been argued that long-distance pollination and seed dispersal may be able to maintain gene flow, even in highly fragmented landscapes. We tested how historical effective population size, historical migration and contemporary landscape structure, such as forest cover, patch isolation and matrix resistance, affect genetic variability and differentiation of seedlings in a tropical palm (Euterpe edulis) in a human-modified rainforest. We sampled 16 sites within five landscapes in the Brazilian Atlantic forest and assessed genetic variability and differentiation using eight microsatellite loci. Using a model selection approach, none of the covariates explained the variation observed in inbreeding coefficients among populations. The variation in genetic diversity among sites was best explained by historical effective population size. Allelic richness was best explained by historical effective population size and matrix resistance, whereas genetic differentiation was explained by matrix resistance. Coalescence analysis revealed high historical migration between sites within landscapes and constant historical population sizes, showing that the genetic differentiation is most likely due to recent changes caused by habitat loss and fragmentation. Overall, recent landscape changes have a greater influence on among-population genetic variation than historical gene flow process. As immediate restoration actions in landscapes with low forest amount, the development of more permeable matrices to allow the movement of pollinators and seed dispersers may be an effective strategy to maintain microevolutionary processes.

Breeding potential of maize composite Isanao VF1 in small spacing in the second growing season

The purpose of this study was to verify the breeding potential of the maize composite Isanao VF1 in the second growing season. One hundred and fifty half-sib progenies were evaluated of spacing of 0.45 m, densities of 57,778 and 80,000 plants ha(-1), in a randomized block design with three replications. Gains of 16.0 and 19.2% were estimated for grain Yield, H. I and 10.5% for prolificacy and 12.3 and 12.9% for ear height, respectively, at 57,778 and 80,000 plants ha(-1). The heritabilities for plant height, ear height and grain yield were 65.2 and 61.3%, 64.3 and 66.9% and 53.5 and 63.3%, respectively, confirming the potential for breeding at both densities. The absence of progeny by density interaction indicates that no further selection programs are necessary. The occurrence of segregation for modifier genes for height suggests stabilizing selection based on ear height.