Estrutura populacional e análise de variabilidade genética em rebanhos ovinos brasileiros

Pós-graduação em Ciência e Tecnologia Animal - FEIS

Restriction fragment length polymorphism (RFLP) in Exon 2 of the BoLA-DRB3 gene in South American cattle

The Bola-DRB3 gene participates in the development of the immune response and is highly polymorphic. For these reasons, it has been a candidate gene in studies of the genetic basis of disease resistance and in population genetic analysis. South American native cattle breeds have been widely replaced by improved exotic breeds leading to a loss of genetic resources. In particular South American native breeds have high levels of fertility and disease resistance. This work describes genetic variability in the BoLA-DRB3 gene in native (Caracu, Pantaneiro, Argentinean Creole) and exotic (Holstein, Jersey, Nelore, Gir) cattle breeds in Brazil and Argentina. PCR-RFLP alleles were identified by combining the restriction patterns for the BoLA-DRB3.2 locus obtained with RsaI, BstY, and HaeIII restriction enzymes. Allelic frequencies and deviations from the Hardy-Weinberg equilibrium were also calculated. Analysis of the 24 BoLA-DRB3 PCR-RFLP alleles identified showed differences in the allele distributions among breeds.

Estimativa de ganho genético a partir de diferenciais de seleção e parâmetros populacionais em um rebanho Caracu

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Diversidade genética em populações-núcleo de Eucalyptus grandis

No melhoramento genético de espécies florestais, uma população base ou indivíduos superiores pré-selecionados tem importância fundamental para a manutenção do programa. Indivíduos de melhores procedências e de ampla base genética propiciam a obtenção de ganhos de forma contínua. O objetivo deste trabalho foi avaliar a diversidade genética em duas populações-núcleo de Eucalyptus grandis. Foram avaliados 39 indivíduos, sendo 19 pertencentes à população 1 e 20, à população 2, utilizando-se 14 primers microssatélite. Os fragmentos foram identificados e analisados a partir dos programas GeneScan e Genotyper, utilizando-se um sequenciador automático ABI Prism 3100. O número de alelos encontrados para cada primer variou de cinco a 15 para a população 1 e, de 8 a 18 para a população 2. A heterozigosidade estimada foi maior na população 2, 0,869, contra 0,843 na população 1. A média da distância genética entre os indivíduos da população 1 foi 0,6220 e na população 2 foi 0,6112. Com a caracterização molecular dos indivíduos destas populações foi construído um banco de dados que permitirá, a partir dos parâmetros de genética de populações, monitorar esses programas de melhoramento em diferentes ciclos de seleção.

Strain variability in the DNA immigration control region (ICR) of Xylella fastidiosa

The genome of the bacterium Xylella fastidiosa contains four ORFs (XF2721, XF2725, XF2739 and XF0295) related to the restriction modification type I system, ordinarily named R-M. This system belongs to the DNA immigration control region (ICR). Each CIRF is related to different operon structures, which are homologues among themselves and with subunit Hsd R from the endonuclease coding genes. In addition, these ORFs are highly homologous to genes in Pseudomonas aeruginosa, Methylococcus capsulatus str. Bath, Legionella pneumophila, Helicobacter pylori, Xanthomonas oryzae pv. Oryzae and Silicibacter pomeroyi, as well as to genes from X. fastidiosa strains that infect grapevine, almond and oleander plants. This study was carried out on R-M ORFs from forty-three X. fastidiosa strains isolated from citrus, coffee, grapevine, periwinkle, almond and plum trees, in order to assess the genetic diversity of these loci through PCR-RFLP. PCR-RFLP analysis of the four ORFs related to the R-M system from these strains enabled the detection of haplotypes for these loci. When the haplotypes were defined, wide genetic diversity and a large range of similar strains originating from different hosts were observed. This analysis also provided information indicating differences in population genetic structures, which led to detection of different levels of gene transfer among the groups of strains. (c) 2005 Elsevier SAS. All rights reserved.

Highly polymorphic in silico-derived microsatellite loci in the potato-infecting fungal pathogen Rhizoctonia solani anastomosis group 3 from the Colombian Andes

Fourteen polymorphic microsatellite DNA markers derived from the draft genome sequence of Rhizoctonia solani anastomosis group 3 (AG-3), strain Rhs 1AP, were designed and characterized from the potato-infecting soil fungus R. solani AG-3. All loci were polymorphic in two field populations collected from Solanum tuberosum and S. phureja in the Colombian Andes. The total number of alleles per locus ranged from two to seven, while gene diversity (expected heterozygosity) varied from 0.11 to 0.81. Considering the variable levels of genetic diversity observed, these markers should be useful for population genetic analyses of this important dikaryotic fungal pathogen on a global scale.

Characterization of gene polymorphisms related to immune system physiology in Mangalarga horses

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

Caracterização da variabilidade de genes relacionados à fertilidade de machos e ao temperamento em eqüinos da raça brasileira Mangalarga

The aims of the present study were to propose a PCR-RFLP genotyping method for the AJ_315378:c.110A>G and AB_264325:c. 771G>C SNPs in the equine CRISP1 and HTR1A genes, respectively, as well as to characterize these and another polymorphism, AB_098561:c.1470G>A of the SLC6A4 gene, in order to provide a basis for future studies investigating the association between DNA markers and traits of interest in this breed. For this, 151 Mangalarga horses of both sexes, representatives of the population of the Sate of São Paulo, Brazil, were used. PCR-RFLP was found to be adequate for the genotyping of the SNPs AJ_315378: c.110A>G of the CRISP1 and AB_264325:c.771G>C of the HTR1A. However, the polymorphism of the CRISP1 probably does not occur in Mangalarga horses, a fact impairing association studies of this marker with traits related to male fertility. The estimative of the population genetic parameters obtained for the polymorphisms AB_264325:c.771G>C of the HTR1A and AB_098561:c.1470G> A of the SLC6A4 in the studied sample discourage the conduct of research addressed the association between markers and traits related to temperament.

Detection of the single nucleotide polymorphism (rs2227307) in the human interleukin 8 gene using a pcr-rflp assay

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

A set of polymorphic microsatellite loci for Vriesea gigantea and Alcantarea imperialis (Bromeliaceae) and cross-amplification in other bromeliad species

Fifteen polymorphic microsatellite markers were isolated and characterized in two species of Bromeliaceae: Vriesea gigantea and Alcantarea imperialis. The number of alleles observed for each locus ranged from three to 16. The loci will be used for studies of the genetic structure of natural populations, reproductive biology, and evolutionary relationships among and within these genera. A cross-amplification test in 22 taxa suggests that the markers will be useful for similar applications in numerous other bromeliad species.

Genetics of neotropical fish: from chromosomes to populations

The Neotropical freshwater fish fauna is very rich-according to the most recent catalogue 71 families and 4,475 species have been described. However, only a small amount of general information is available on the composition of Neotropical marine fishes. In Brazil, 1,298 marine species have been recorded. General analysis of available cytogenetic and population genetic data clearly indicates research has been mainly concentrated on freshwater fishes. Thus, today, cytogenetic information is available for 475 species of Characiformes, 318 species of Siluriformes, 48 species of Gymnotiformes, 199 freshwater species that do not belong to the superorder Ostariophysi, and only 109 species of marine fishes. For the species studied, only about 6% have sex chromosomes and about 5% have supernumerary or B chromosomes. A review of the cytogenetic studies shows that these data have provided valuable information about the relationships between fish groups, the occurrence of cryptic species and species complexes, the mechanism of sex determination and sex chromosome evolution, the distribution of nucleolus organizer regions, the existence supernumerary chromosomes, and the relationship between polyploidy and evolution. In relation to populations in Neotropical marine waters, the studies have shown the presence of cryptic species, which has important implications for fishery management. Different levels of genetic structuring can be found among Neotropical freshwater migratory fish species. This raises important implications for fish population genetic diversity and consequently its sustainable utilization in inland fisheries and aquaculture, specifically for conservation of ichthyo-diversity and survival.

Gene flow networks among American Aedes aegypti populations

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Single Nucleotide Polymorphism Markers in Aedes aegypti Populations in Brazil

Single nucleotide polymorphisms (SNPs) were investigated in eighteen genes of sixteen populations of Aedes aegypti in Brazil. Eight SNP markers were selected in nine genes and surveyed in A. aegypti populations of three localities in different geographical locations. SNPs revealed significant genetic differentiation among populations recently analyzed by mitochondria DNA (mtDNA) and represented by a single genetic group (lineage). Results suggest that a haplotype derived from mtDNA analysis could be represented by different Aedes lineages revealed by SNP characterization. Genetic distances (pairwise F(ST)), AMOVA and cluster analyses indicated a high genetic structure for the A. aegypti populations investigated by SNPs. This set of SNP markers represents a useful tool for genetic studies in A. aegypti populations

The influence of landscape characteristics and home-range size on the quantification of landscape-genetics relationships

A common approach used to estimate landscape resistance involves comparing correlations of ecological and genetic distances calculated among individuals of a species. However, the location of sampled individuals may contain some degree of spatial uncertainty due to the natural variation of animals moving through their home range or measurement error in plant or animal locations. In this study, we evaluate the ways that spatial uncertainty, landscape characteristics, and genetic stochasticity interact to influence the strength and variability of conclusions about landscape-genetics relationships. We used a neutral landscape model to generate 45 landscapes composed of habitat and non-habitat, varying in percent habitat, aggregation, and structural connectivity (patch cohesion). We created true and alternate locations for 500 individuals, calculated ecological distances (least-cost paths), and simulated genetic distances among individuals. We compared correlations between ecological distances for true and alternate locations. We then simulated genotypes at 15 neutral loci and investigated whether the same influences could be detected in simple Mantel tests and while controlling for the effects of isolation-by distance using the partial Mantel test. Spatial uncertainty interacted with the percentage of habitat in the landscape, but led to only small reductions in correlations. Furthermore, the strongest correlations occurred with low percent habitat, high aggregation, and low to intermediate levels of cohesion. Overall genetic stochasticity was relatively low and was influenced by landscape characteristics.

Microsatellite loci isolated from the lowland tapir (Tapirus terrestris), one of the largest Neotropical mammal

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