Finding a minimal set of SNPs for paternity identification in Nelore cattle.

Cattle breeding programs often demand pedigree information to associate the herdability of genetic markers to animal performance, like milk and beef quality or disease predisposition. Paternity mistakes are a common problem in cattle herds and genetic markers have been used in parentage exclusion tests for resolving pedigree disagreements. The most common markers used in these tests are microsatellites and SNPs (Single Nucleotide Polymorphisms). SNPs have also been used in GWAS (Genome Wide Association Studies) based on the novel commercial high density bovine SNP chips. Such platforms possess around 770k SNPs which can be used also as a rich resource for paternity exclusion tests. However genotyping such a large amount of SNPs for individuals of a whole flock to perform paternity exclusion tests is not economically feasible. Furthermore, many of these SNPs are non-informative because of high levels of linkage disequilibrium among them and because of low levels of minimum allele frequency (MAF), call rate and genotyping accuracy (GC score). In this work we devised a method to select a minimal set of SNPs from Nelore cattle samples, which are highly informative and are independent, so they could be used in a small genotyping panel for paternity exclusion tests. Samples from 32 Nelore sires chosen to represent the main genealogies marketed in Brazil and 762 nelore bulls produced by artificial insemination were genotyped. The platform used was Illumina BovineHD Genotyping Beadchip that has ~770k SNPs. The algorithm developed first run a quality control filter that selected, from the starting 770k SNPs, only markers that: i) were in Hardy Weinberg equilibrium, ii) had MAF>0.4, iii) had Illumina's accuracy GC Score > 0.8, iv) had call rate >=0.95 and v) had a D?<0.5 with other marker. 126 pairs of father-sons (151 samples), with the paternity already resolved, were selected to compose the test set. The other 643 animals that were left composed the training set. From the training set, 325 SNPs passed the quality control filter. The selected 325 SNPs were used in the test set to perform paternity tests, following the methodology adapted from Fung et al., 2002. The results show that values of the combined power of exclusion (Q) for all markers, between 0.2 and 0.7, gives the correct paternity answer for all pairs of individuals. We believe that this set of 325 SNPs could be used in a small genotyping chip to perform paternity exclusion tests for Nelore cattle; a low-cost solution to be used by cattle producers to correct paternity disagreements. All procedures were performed using the R language in a local linux server machine.X-MEETING, 2011

Avaliação da utilização de composto orgânico produzido a partir dos resíduos de fábrica de celulose quanto aos níveis de organoclorados e metais

Lodos gerados em Estações de Tratamento de Efluentes de fábricas de celulose kraft branqueada podem conter metais pesados e compostos organoclorados mesmo para fábricas que possuam sequências de branqueamento ECF (livres de cloro elementar), devido à presença de dióxido de cloro. Neste trabalho, buscou-se avaliar o potencial de absorção de metais pesados e compostos organoclorados (PCDD e PCDF) por Brassica juncea, utilizando como substrato o composto orgânico constituído por lodo biológico de uma Estação de Tratamento de Efluentes por lodos ativados misturado com cascas de eucalipto de uma fábrica de celulose brasileira. As plantas de Brassica juncea foram cultivadas em vasos de 0,63 dm³ em casa de vegetação, durante 73 dias. Os seguintes parâmetros foram monitorados no substrato e nas plantas: Fe, Mn, Pb, Ni, Cu, Zn, Cr, Cl-, carbono orgânico total e AOX (compostos organo-halogenados adsorvíveis). Os níveis de metais pesados presentes no solo após a aplicação do composto ficaram dentro de faixas permissíveis da legislação brasileira para aplicação de composto orgânico para uso agrícola. Traços de PCDD e PCDF foram encontrados no substrato em concentrações menores do que 0,5 ng I-TEQ/kg (ppt). Tais valores ficaram abaixo de 17 ng I-TEQ/kg, considerado o limite mais exigente de qualidade de compostos adotados na Alemanha e no Canadá

MamMiBase: a mitochondrial genome database for mammalian phylogenetic studies

Summary: MamMibase, the Mammalian Mitochondrial Genome Database, is a relational database of complete mitochondrial genome sequences of mammalian species. The database is useful for phyloge-netic analysis, since it allows a ready retrieval of nucleotide and aminoacid individual alignments, in three different formats (NEXUS for PAUP program, for MEGA program and for PHYLIP program) of the 13 protein coding mitochondrial genes. The user may download the sequences that is useful for him/her based on their parameters values, such as sequence length, p-distances, base content, transition transversion ratio, gamma, that are also given by Mammibase. A simple phylogenetic tree (neighborjoining tree with Jukes Cantor distance) is also available for download, useful for parameter calculations and other simple tasks. Availability: MamMiBase is available at www.mammibase.lncc.br Contact