PATERNITYHD versão 1.0 - um software para cálculo da probabilidade de exclusão de paternidade com dados de genotipagem em painel de alta densidade de SNPs em bovinos.

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What's in your next-generation sequence data? An exploration of unmapped DNA and RNA sequence reads from the bovine reference individual.

BackgroundNext-generation sequencing projects commonly commence by aligning reads to a reference genome assembly. While improvements in alignment algorithms and computational hardware have greatly enhanced the efficiency and accuracy of alignments, a significant percentage of reads often remain unmapped.ResultsWe generated de novo assemblies of unmapped reads from the DNA and RNA sequencing of the Bos taurus reference individual and identified the closest matching sequence to each contig by alignment to the NCBI non-redundant nucleotide database using BLAST. As expected, many of these contigs represent vertebrate sequence that is absent, incomplete, or misassembled in the UMD3.1 reference assembly. However, numerous additional contigs represent invertebrate species. Most prominent were several species of Spirurid nematodes and a blood-borne parasite, Babesia bigemina. These species are either not present in the US or are not known to infect taurine cattle and the reference animal appears to have been host to unsequenced sister species.ConclusionsWe demonstrate the importance of exploring unmapped reads to ascertain sequences that are either absent or misassembled in the reference assembly and for detecting sequences indicative of parasitic or commensal organisms

Tissue Tropism in Host Transcriptional Response to Members of the Bovine Respiratory Disease Complex.

Bovine respiratory disease (BRD) is the most common infectious disease of beef and dairy cattle and is characterized by a complex infectious etiology that includes a variety of viral and bacterial pathogens. We examined the global changes in mRNA abundance in healthy lung and lung lesions and in the lymphoid tissues bronchial lymph node, retropharyngeal lymph node, nasopharyngeal lymph node and pharyngeal tonsil collected at the peak of clinical disease from beef cattle experimentally challenged with either bovine respiratory syncytial virus, infectious bovine rhinotracheitis, bovine viral diarrhea virus, Mannheimia haemolytica or Mycoplasma bovis. We identified signatures of tissue-specific transcriptional responses indicative of tropism in the coordination of host's immune tissue responses to infection by viral or bacterial infections. Furthermore, our study shows that this tissue tropism in host transcriptional response to BRD pathogens results in the activation of different networks of response genes. The differential crosstalk among genes expressed in lymphoid tissues was predicted to be orchestrated by specific immune genes that act as 'key players' within expression networks. The results of this study serve as a basis for the development of innovative therapeutic strategies and for the selection of cattle with enhanced resistance to BRD

Prospecção de SNPs no gene TNFa e sua possível associação à verminose gastrintestinal em caprinos.

O objetivo desse estudo foi investigar a associação entre marcadores moleculares do tipo SNP (Polimorfismo de base única) prospectados no gene TNFa (fator de necrose tumoral alfa) e resistência à verminose gastrintestinal em caprinos. Para isso, foram produzidos 229 caprinos a partir de animais das raças Saanen, raça considerada susceptível a endoparasitas gastrintestinais e Anglo-nubiana, raça considerada resistente. Para a prospecção de SNPs, foram sequenciados 44 animais extremos para OPG (contagem de ovos por grama de fezes) escolhidos a partir dos resíduos obtidos através do modelo estatístico usado para corrigir os dados fenotípicos para as variações ambientais. O sequenciamento inclui quatro regiões do gene TNFa. Nestas regiões, foram encontrados dez SNPs: dois estão localizados na região promotora do gene, dois no intron 2 e seis no exon 4. Através da aplicação do teste de Fisher foi encontrada uma associação de cinco dos SNPs prospectados ( P ≤ 0,05), o que indica que esses SNPs são potenciais marcadores moleculares para resistência à verminose gastrintestinal

A network landscape from CNVs to Nellore cattle beef tenderness.

This work aims to perform a couple of in silico network analysis from CNVs standpoint, shedding light to possible metabolic connections to tenderness. It was used 671 Nellore males to infer CNVs, through SNP-chip (Illumina Bovine HD Beadchip®, containing approximately 770 thousand SNPs) and PennCNV software methodology. CNV regions (CNVRs) were inferred by CNVRuler (recurrence 0.1).ISAFG 2013. AB.01

A network landscape from CNVs to Nellore cattle beef tenderness.

This work aims to perform a couple of in silico network analysis from CNVs standpoint, shedding light to possible metabolic connections to tenderness. It was used 671 Nellore males to infer CNVs, through SNP-chip (Illumina Bovine HD Beadchip®, containing approximately 770 thousand SNPs) and PennCNV software methodology. CNV regions (CNVRs) were inferred by CNVRuler (recurrence 0.1).ISAFG 2013. AB.01

Análise haplotípica do gene ASAP1 associado com maciez de carne em bovinos da raça Nelore.

A maciez da carne tem impacto importante na satisfação dos consumidores, portanto, o conhecimento da variação desta característica, assim como a prospecção de genes ou segmentos genômicos que influenciem a mesma, pode ajudar no desenvolvimento de critérios quantitativos e moleculares para seleção de bovinos de corte. A análise haplotípica com os SNPs do gene ASAP1 representados no Illumina BovineHD BeadChip mostram que estes marcadores estão associados com força de cisalhamento medida após 7 dias de maturação da carne nessa população da raça Nelore. A validação desses resultados em outras populações poderá contribuir para inclusão desses marcadores em programas de melhoramento da raça Nelore

Seleção de genes candidatos a referência para estudos de expressão gênica por meio de análises de RNA-Seq e qPCR.

Editores técnicos: João de Mendonça Naime, Caue Ribeiro, Maria Alice Martins, Elaine Cristina Paris, Paulino Ribeiro Villas Boas, Ladislau Marcelino Rabello