SSR-EST and SNP-EST genomic annotation and population validation for candidate gen...
Patterns and processes of marine invertebrate diversity in West Atlantic mangroves
| Grant number: | 12/17322-8 |
| Support Opportunities: | Regular Research Grants |
| Start date: | May 01, 2013 |
| End date: | October 31, 2015 |
| Field of knowledge: | Biological Sciences - Genetics - Animal Genetics |
| Principal Investigator: | Patrícia Domingues de Freitas |
| Grantee: | Patrícia Domingues de Freitas |
| Host Institution: | Centro de Ciências Biológicas e da Saúde (CCBS). Universidade Federal de São Carlos (UFSCAR). São Carlos , SP, Brazil |
| Associated researchers: | João Luíz Rocha ; Jorge Manuel de Oliveira Fernandes ; Pedro Manoel Galetti Junior |
Abstract
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)
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