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SSR-EST and SNP-EST genomic annotation and population validation for candidate genes identification in marine shrimp Litopenaeus vannamei (Penaeidae, Decapoda)

Grant number: 12/17322-8
Support type:Regular Research Grants
Duration: May 01, 2013 - October 31, 2015
Field of knowledge:Biological Sciences - Genetics
Principal Investigator:Patrícia Domingues de Freitas
Grantee:Patrícia Domingues de Freitas
Home Institution: Centro de Ciências Biológicas e da Saúde (CCBS). Universidade Federal de São Carlos (UFSCAR). São Carlos , SP, Brazil
Assoc. researchers: João Luíz Rocha ; Jorge Manuel de Oliveira Fernandes ; Pedro Manoel Galetti Junior


Litopenaeus vannamei is known as the Pacific white shrimp, the main worldwide commercial penaeid. Despite its excellent performance in captivity, there is a constant concern to adequate strain management. The inbreeding and reduced levels of genetic diversity can compromise the fitness on adverse captive conditions. Molecular markers contained in expressed regions of the genome (EST, Expressed Sequence Tags), such as microsatellite or SSR (Simple Sequence Repeats) and SNP (Single Nucleotide Polymorphisms), may be useful to access the genetic diversity, identify loci related to economical traits and assist the establishment of breeding programs. The previous development of the Genome Project EST of the L. vannamei shrimp (ShEST) allowed the characterization of thousands of SSR and SNP loci, and a large amount of these markers need to be evaluated in the populations and has its gene product elucidated. Thus, this paper aims to validate SSR-EST and SNP-EST in strains selected for body growth and disease resistance and to describe the protein products and their possible metabolic pathways. Based on the products described by genomic annotation, some loci contained in genes of interest (candidate genes) will be tested for verification phenotype x genotype association. The measurement of the performance characteristics will be conducted by the companies responsible for the selective breeding programs. With this work we hope to provide a set of information to assist management and monitoring of stocks of this important species cultivated in Brazil, and also to be useful for other shrimp species, which consist in an important socio-economic and ecological resource. (AU)

Scientific publications (4)
(References retrieved automatically from Web of Science and SciELO through information on FAPESP grants and their corresponding numbers as mentioned in the publications by the authors)
SANTOS, CAMILLA A.; ANDRADE, SONIA C. S.; FREITAS, PATRICIA D. Identification of SNPs potentially related to immune responses and growth performance in Litopenaeus vannamei by RNA-seq analyses. PeerJ, v. 6, JUL 4 2018. Web of Science Citations: 2.
SANTOS, CAMILLA A.; ANDRADE, SONIA C. S.; TEIXEIRA, ANA K.; FARIAS, FLAVIO; KURKJIAN, KARIN; GUERRELHAS, ANA C.; ROCHA, JOAO L.; GALETTI, JR., PEDRO M.; FREITAS, PATRICIA D. Litopenaeus vannamei Transcriptome Profile of Populations Evaluated for Growth Performance and Exposed to White Spot Syndrome Virus (WSSV). FRONTIERS IN GENETICS, v. 9, APR 10 2018. Web of Science Citations: 5.
CAMILLA ALVES SANTOS; FLAVIO FARIAS; ANA KARINA TEIXEIRA; JOÃO LUÍS ROCHA; ANA CAROLINA GUERRELHAS; PATRÍCIA DOMINGUES DE FREITAS. Polymorphism in Litopenaeus vannamei genes and cross-species amplification in other shrimp species. Pesquisa Agropecuária Brasileira, v. 53, n. 1, p. -, Jan. 2018.
SANTOS, CAMILLA ALVES; FARIAS, FLAVIO; TEIXEIRA, ANA KARINA; ROCHA, JOAO LUIS; GUERRELHAS, ANA CAROLINA; DE FREITAS, PATRICIA DOMINGUES. Polymorphism in Litopenaeus vannamei genes and cross-species amplification in other shrimp species. Pesquisa Agropecuária Brasileira, v. 53, n. 1, p. 121-124, JAN 2018. Web of Science Citations: 0.

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