Evaluation of PRNP polymorphisms in Brazilian local adapted breeds

The present study was conducted to genotype and estimate haplotypes and haplotypic and genotypic frequencies on three previously reported PRNP polymorphisms in Brazilian local adapted/naturalized breeds, and to evaluate the flock‘s genetic potential in relation to scrapie usceptibility/resistance

Detecção e avaliação de assinaturas de seleção em ovinos

O recente desenvolvimento de painéis de “single nucleotide polymorphisms” (SNPs) distribuídos ao longo do genoma possibilitou a realização de diversos trabalhos com diferentes espécies. O processo seletivo promove o aumento ou a diminuição da frequência alélica (ou gênica) em loci específicos do genoma, além de promover o arrasto dos alelos próximos no cromossomo. Desta forma, são formadas regiões do genoma com o aumento na frequência de determinados alelos na população, o que caracteriza a assinatura de seleção. A detecção destas assinaturas é importante para a caracterização dos recursos genéticos, bem como a identificação de genes ou regiões envolvidos no controle e na expressão de características de importância produtiva e econômica. Os ovinos são uma importante espécie para estes estudos, uma vez que encontram-se amplamente dispersos em diferentes ambientes e apresentam grande diversidade fenotípica. Devido à grande quantidade de dados gerados nas análises genômicas, são necessários métodos estatísticos e programas específicos para a detecção de assinaturas de seleção. Assim, os objetivos deste artigo de revisão são apresentar os principais métodos estatísticos e os programas atualmente utilizados para análise de dados genômicos e a detecção de assinaturas de seleção; descrever os resultados dos recentes trabalhos publicados sobre assinaturas de seleção em ovinos; e discutir alguns desafios e oportunidades nesta área de pesquisa.The recent development of genome-wide single nucleotide polymorphism (SNP) arrays made it possible to carry out several studies with different species. The selection process can increase or reduce allelic (or genic) frequencies at specific loci in the genome, besides dragging neighboring alleles in the chromosome. This way, genomic regions with increased frequencies of specific alleles are formed, caracterizing selection signatures or selective sweeps. The detection of these signatures is important to characterize genetic resources, as well as to identify genes or regions involved in the control and expression of important production and economic traits. Sheep are an important species for theses studies as they are dispersed worldwide and have great phenotypic diversity. Due to the large amounts of genomic data generated, specific statistical methods and softwares are necessary for the detection of selection signatures. Therefore, the objectives of this review are to address the main statistical methods and softwares currently used for the analysis of genomic data and the identification of selection signatures; to describe the results of recent works published on selection signatures in sheep; and to discuss some challenges and opportunities in this research field

D-loop haplotype diversity in brazilian horse breeds

The first horses were brought to Brazil by the colonizers after 1534. Over the centuries, these animals evolved and adapted to local environmental conditions usually unsuitable for exotic breeds, thereby originating locally adapted Brazilian breeds. The present work represents the first description of maternal genetic diversity in these horse breeds based on D-loop sequences. A D-Loop HSV-I fragment of 252 bp, from 141 horses belonging to ten Brazilian breeds / genetic groups (locally adapted and specialized breeds) were analysed. Thirty-five different haplotypes belonging to 18 haplogroups were identified with 33 polymorphic sites. Haplotype diversity (varying from 0.20 to 0.96) and nucleotide diversity (varying from 0.0039 to 0.0239) was lower for locally adapted than for specialized breeds, with the same pattern observed for FST values. Haplogroups identified in Brazilian breeds are in agreement with previous findings in South American samples. The low variability observed mainly in locally adapted breeds, indicates that, to ensure conservation of these breeds, careful reproductive management is needed. Additional genetic characterization studies are required to support accurate decision-making

Mapeamento RH comparativo do cromossomo X de búfalo de rio (Bubalus bubalis) / Patrícia Ianella

O cromossomo X apresenta conteúdo conservado entre as diferentes espécies de mamíferos. No de búfalo de rio (Bubalus bubalis), espécie que vem ganhando interesse econômico no Brasil e no mundo, sua morfologia é acrocêntrica. No presente trabalho, apresentamos o primeiro mapa RH do cromossomo X bubalino gerado a partir do recentemente construído painel de células híbridas irradiadas búfalo-roedor (BBURH5000). Este mapa contém um total de 33 marcadores derivados de bovino, incluindo dez genes, quatro ESTs e 19 microssatélites. Estes marcadores estão distribuídos em dois grupos de ligação: LG1 com oito marcadores e abrangendo 125.6 cR, e o LG2 com 25 marcadores abrangendo 366.3 cR. As freqüências de retenção (FR) dos marcadores variaram de 7,8% para o gene UREB1 a 28,9% para os microssatélites MAF45 e INRA30. O BBUXRH5000 foi comparado ao mapa de seqüência e mapa RH3000 do cromossomo X bovino evidenciando alguns poucos rearranjos entre as duas espécies, e alguns prováveis erros de mapeamento em uma das duas espécies quando comparado com BTAX build 3.1 bovino. A utilização de primers derivados de boi para mapeamento em búfalo foi realizada com êxito, e a distribuição dos marcadores ao longo do X considerada satisfatória, culminando em uma cobertura adequada para os primeiros esforços de mapeamento deste cromossomo. Análises comparativas do BBUX com o cromossomo X de outras espécies de mamíferos (humano, camundongo, ovelha, cavalo e cachorro) foram realizadas, revelando grande conservação de sintenia deste cromossomo na classe mamífera e, extensa conservação da ordem gênica entre búfalo e ovelha e búfalo e boi. O BBUXRH5000 aqui apresentado é um ponto de partida para a construção de mapas de alta resolução, necessários para caracterização de rearranjos que ocorreram durante a evolução e futuros estudos com o objetivo de dissecar características genéticas de interesse econômico.The X chromosome shows conserved content among different mammalian species. In river buffalo (Bubalus bubalis), a brazilian and worldwide economic important specie, the X chromosome morphology is acrocentric. Here we report the first radiation hybrid map of the river buffalo X chromosome generated from a recently constructed river buffalo (Bubalus bubalis) whole-genome radiation hybrid panel (BBURH5000). This map contains a total of 33 cattle-derived markers, including ten genes, four ESTs and 19 microsatellites. The markers are distributed in two linkage groups: LG1 contains eight markers spanning 125.6 cR, and LG2 contains 25 markers spanning 366.3 cR. The retention frequency (RF) of individual markers across the panel ranged from 7.8% to the gene UREB1 and 28,9 to the microsatellites MAF45 and INRA30. The BBUXRH5000 was compared with the bovine sequence assembly (build 3.1) and RH3000 bovine X chromosome maps and showed few rearrangements between these species, and possible mapping errors in one of the two species when compared with BTAX build 3.1. The use of cattle-derived primers using carried out successfully and the markers distribution along the chromosome was satisfactory, resulting in adequate coverage for a first mapping effort of this chromosome. Comparative analysis between BBUX and X chromosome from other mammalian species (human, hamster, sheep, horse and dog) were carried out showed extensive sinteny conservation of the X chromosome in the Mammalian Class, and gene order conservation between river buffalo and sheep and river buffalo and cattle. The BBUXRH5000 here presented is the start-pointing for the construction of high-resolution map, which is necessary for characterization of rearrangements occurring during evolution and futures studies in order to dissect economically important traits.Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES

Population structure and genetic diversity of rainbow trout (Oncorhynchus mykiss) broodstocks from Brazil using SNP markers

Rainbow trout (Oncorhynchus mykiss) are native to the Pacific Ocean coast of North America and the Kamchatka Peninsula of Russia. Brazilian populations of rainbow trout derive from various imports from European countries, the United States of America (U.S.A.) and Canada, from the 1950 s onwards. A total of 347 samples from nine commercial broodstock groups sampled from five farms in Brazil were genotyped with a panel of 96 SNPs to analyze the genetic diversity and structure of commercial rainbow trout farmed in Brazil. Pairwise coefficients of relatedness of individual animals and coefficients of genetic differentiation and inbreeding of broodstock groups were obtained, in addition to tests of genetic allocation of animals to their respective group. The mean observed and expected heterozygosities were 0.405 and 0.398, respectively. The total Fst was 0.172 and the pairwise Fst estimates considering all strains ranged from 0.036 to 0.338. The UPGMA genetic distance tree shows that broodstocks declared to be originally from Canada (Kamloops region) and from Northern California (Mount Shasta) are the most genetically distant from each other and from the remaining studied groups. Genetic structure analyses suggest a best value of K= 2, separating broodstock groups originally from the U.S.A. and Canada. Structure and Principal Component Analyses (PCA) indicate that the management practices of one of the farms was efficient in properly maintaining different broodstocks separated, while in another farm unwanted admixture has been occurring. Reclassification of these animals using Structure analysis results were corroborated with PCA and GeneClass2 analyses, providing evidence that advanced analyzes with low-density SNP data can be used to improve farm management practices and even correct past errors. The present study represents the first analysis of diversity and genetic structure of commercial rainbow trout farmed in Brazil using SNP markers