Identification of Genes Associated with Pan-Vibrios Resistance (Pvr) Trait of Shrimp Litopenaeus Vannamei Through Genome-Wide Association Study

Abstract

Vibriosis caused by various Vibrio species is the most serious bacterial disease of shrimps. Due to the prevalence of pathogenic vibrios, genetic breeding of shrimps with the pan-vibrios resistance (PVR) trait has more practical significance for successful shrimp farming. To explore the genetic loci associated with the PVR trait of Litopenaeus vannamei, a genome-wide association study (GWAS) aiming at the PVR trait of the shrimp was conducted by using 300 shrimp individuals from various sources. After stringent screening, 243 single nucleotide polymorphisms (SNPs) corresponding to a selection threshold of -log10(p) value ≥ 2.5 were evaluated for their association with the PVR trait. Twenty candidate SNPs in genes and upstream region of genes (≤ 5000 bp) were screened out for further validation of the association. The genotypes of three SNPs (SNP15, SNP16, and SNP17) were different between G1 (uninfected) and G4/G5 groups (seriously infected), among which GG genotype of SNP15 was significantly associated with low vibrios load. The genotype combination of GG-TT-AA at the three SNPs was linked, and it was significantly associated with the strongest performance of the trait. Notably, three SNPs were found located in the intron region of a gene, LvCthrc1. The genotype combination can lead to the disappearance of a donor splicing site of LvCthrc1, which predictably generates a novel transcript affecting the gene function. The highest expression level of LvCthrc1 was observed in immune-related tissues such as hemocytes, gills, and hepatopancreas. This study first put forward the concept of the PVR trait and provides valuable molecular markers for the genetic selection on the trait of shrimp, L. vannamei.

Keywords: GWAS；Litopenaeus vannamei；pan-vibrio resistance；SNPs；LvCthrc1 gene