Identificação de genes candidatos relacionados a traços de desempenho em transcriptomas do camarão marinho Litopenaeus vannamei (Penaeidae, Decapoda)

• Ano de defesa: 2016
• Autor(a) principal: Santos, Camilla Alves
• Orientador(a): Freitas, Patrícia Domingues de
• Tipo de documento: Tese
• Tipo de acesso: Acesso aberto
• Idioma: por
• Instituição de defesa: Universidade Federal de São Carlos; Câmpus São Carlos
• Programa de Pós-Graduação: Programa de Pós-Graduação em Genética Evolutiva e Biologia Molecular - PPGGEv
• Palavras-chave em Português: Genética; Expressão diferencial; Polimorfismos; Transcriptomas
• Palavras-chave em Inglês: Polymorphisms; Transcriptomes; Differentially expressed (DE) genes
• Área do conhecimento CNPq: CIENCIAS BIOLOGICAS::GENETICA
• Link de acesso: https://repositorio.ufscar.br/handle/ufscar/8590

The present work had as general objective to perform the genomic annotation of Expressed Sequences (ESTs) of Litopenaeus vannamei shrimp, available in the database of Project ShEST and to evaluate the polymorphism of mined SSR and SNP tags. These markers were located in the main chain of protein genes with function related to performance traits and were validated in SPF (Specific Pathogen Free) shrimp families submitted to selection for rapid growth and survival. In addition to the EST-SSR and EST-SNP loci, obtained by Sanger sequencing, Next Generation Sequencing (NGS) analyzes were included in the initial proposal of work with the objective of expanding the set of SNPs available and verifying the differential gene expression. The new assembly of ESTs was performed and produced a set of 2.984 unigenes with protein products for 41% of them, with 1.983 SSRs and 3.472 SNPs being identified. Among the loci with gene product identified, 231 were enzymes with 127 unique EC numbers inserted in 94 KEGG metabolic pathways. Loci validation showed that the loci of the 60S ribosomal (SSR-EST) and crustacyanin (SNP-EST) proteins were polymorphic in the animals sampled from Genearch. Statistical analyzes were conducted to verify the existence of a possible association between the genotypes and the analyzed weight phenotypes, although no association was observed. In addition, cross-species amplification tests were performed on seven species of marine and two freshwater prawns, demonstrating successful transferability for these species. The RNAseq approach was included in the present work with the purpose of increasing the number of SNPs detected in candidate genes with performance-related function and identifying differentially expressed (DE) genes in animals under experimental conditions. A second transcriptome was assembled from the muscle and hepatopancreas tissues of L. vannamei individuals (i) evaluated for rapid growth and survival and (ii) exposed to the White Spot Syndrome Virus (WSSV). A total of 63.105 transcripts were generated, with an average size of 2.511 bp and N50 of 3.464 bp. More than 15.500 SNPs were identified (frequency > 50%). Functional annotation was also performed on the bases of SwissProt, Gene Ontology (GO) and KEGG. Differential gene expression analyzes were performed on the animal samples evaluated for growth and response to WSSV infection. The data generated showed differences in the expression profile between the genes of (i) high and low growth animals, (ii) the hepatopancreas and muscle and (iii) the uninfected (healthy) and infected (ill) animals by WSSV, considering the effect of the tissue. Two-hundred and seven DE genes were identified for growth, 5.816 for hepatopancreas and muscle and 1.017 for ill and healthy animals.