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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: 12/13069-6
Support type:Scholarships in Brazil - Doctorate
Effective date (Start): November 01, 2012
Effective date (End): May 31, 2016
Field of knowledge:Biological Sciences - Genetics
Principal Investigator:Patrícia Domingues de Freitas
Grantee:Camilla Alves Santos
Home Institution: Centro de Ciências Biológicas e da Saúde (CCBS). Universidade Federal de São Carlos (UFSCAR). São Carlos , SP, Brazil

Abstract

Litopenaeus vannamei is known as Pacific white shrimp, the main penaeid marketed worldwide. Despite its excellent performance in captivity, there is a concern to properly manage the herds, due to the absence of introduction of a new gene pool, resulting in increased inbreeding and decreased levels of genetic diversity. In this context, 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), are useful in accessing stocks genetic variation, identification of loci linked to traits of interest and establishment of breeding programs based on Marker Assisted Selection (MAS). The development of the L.vannamei EST Genome Project(ShEST) allowed the characterization of thousands of SSR and SNP, and most of these markers were not evaluated in populations nor elucidated with its gene product yet. Thus, this work aims to describe the gene products of EST-SSR and EST-SNP loci and their possible pathways, as well as validation in superior stocks for growth and pathogen resistance. Based on the gene products from genome annotation, some of these loci, contained in genes of interest, will be selected for verification of a possible association with economically important traits. The breeding and measurement of performance characteristics will be conducted by Aquatec and Genearch Ltda Companies (RN, Brazil). The analysis of association between genotypes and phenotypes observed may provide a set of informative markers to assist an efficient management and monitoring of stocks of this species in Brazil.

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: 6.
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: 1.

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