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

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 non-infected 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.

Keywords: Aquaculture; Growth; Immunity; Litopenaeus vannamei; Polymorphisms; Shrimp; Transcriptome.

Figure 1. Main Gene Ontology blastX hits for unigenes with SNPs.

Distribution of the GO terms found at level 2 for the categories Biological Process, Molecular Function and Cellular Component(*) for (A) higher and (B) lower growth performance group and (C) healthy and (D) unhealthy WSSV-exposed group unigenes. The x-axis represents the number of loci that compose each GO term and the y-axis the three categories of GO database. Cytoplasm is the most frequent location where cell events take place in all groups (data not shown in chart, but available at Supplemental Information).

Figure 2. Some of the KEGG pathways with the most KO number.

Pathways mapped in KEGG for RNA-seq data of Litopenaeus vannamei. The x-axis represents the pathways found and the y-axis shows the KO number found in each corresponding pathway.