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(Reference retrieved automatically from Web of Science through information on FAPESP grant and its corresponding number as mentioned in the publication by the authors.)

Identification of SNPs potentially related to immune responses and growth performance in Litopenaeus vannamei by RNA-seq analyses

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Author(s):
Santos, Camilla A. [1] ; Andrade, Sonia C. S. [2] ; Freitas, Patricia D. [1]
Total Authors: 3
Affiliation:
[1] Univ Fed Sao Carlos, Dept Genet & Evolucao, Sao Carlos, SP - Brazil
[2] Univ Sao Paulo, Dept Genet & Biol Evolut, Sao Paulo, SP - Brazil
Total Affiliations: 2
Document type: Journal article
Source: PeerJ; v. 6, JUL 4 2018.
Web of Science Citations: 2
Abstract

Litopenaeus vannamei is one of the most important shrimp species for worldwide aquaculture. Despite this, little genomic information is available for this penaeid and other closely related taxonomic crustaceans. Consequently, genes, proteins and their respective polymorphisms are poorly known for these species. In this work, we used the RNA sequencing technology (RNA-seq) in L. vannamei shrimp evaluated for growth performance, and exposed to the White Spot Syndrome Virus (WSSV), in order to investigate the presence of Single Nucleotide Polymorphisms (SNPs) within genes related to innate immunity and growth, both features of great interest for aquaculture activity. We analyzed individuals with higher and lower growth rates; and infected (unhealthy) and non-infected (healthy), after exposure to WSSV. Approximately 7,000 SNPs were detected in the samples evaluated for growth, being 3,186 and 3,978 exclusive for individuals with higher and lower growth rates, respectively. In the animals exposed to WSSV we found about 16,300 unique SNPs, in which 9,338 were specific to noninfected shrimp, and 7,008 were exclusive to individuals infected with WSSV and symptomatic. In total, we describe 4,312 unigenes containing SNPs. About 60% of these unigenes returned GO blastX hits for Biological Process, Molecular Function and Cellular Component ontologies. We identified 512 KEGG unique KOs distributed among 275 pathways, elucidating the majority of metabolism roles related to high protein metabolism, growth and immunity. These polymorphisms are all located in coding regions, and certainly can be applied in further studies involving phenotype expression of complex traits, such as growth and immunity. Overall, the set of variants raised herein enriches the genomic databases available for shrimp, given that SNPs originated from nextgen are still rare for this relevant crustacean group, despite their huge potential of use in genomic selection approaches. (AU)

FAPESP's process: 12/17322-8 - SSR-EST and SNP-EST genomic annotation and population validation for candidate genes identification in marine shrimp Litopenaeus vannamei (Penaeidae, Decapoda)
Grantee:Patrícia Domingues de Freitas
Support Opportunities: Regular Research Grants
FAPESP's process: 12/13069-6 - SSR-EST and SNP-EST genomic annotation and population validation for candidate genes identification in marine shrimp Litopenaeus vannamei (Penaeidae, Decapoda)
Grantee:Camilla Alves Santos
Support Opportunities: Scholarships in Brazil - Doctorate