# Identification of Genes Associated with the Pan-Vibrios Resistance (PVR) Trait of Pacific White Shrimp (Litopenaeus vannamei) Using a Genome-Wide Association Study

## TL;DR

This study identifies genes linked to broad resistance against Vibrio bacteria in Pacific white shrimp, offering a strategy for sustainable aquaculture.

## Contribution

The study introduces the concept of pan-vibrios resistance (PVR) and identifies specific SNPs and a gene (LvHEATR1) associated with this trait in shrimp.

## Key findings

- 26 SNPs within genes were found to be associated with pan-vibrios resistance (PVR) in Litopenaeus vannamei.
- Two genotypes (GG at SNP20 and AA at SNP21) and their combination were significantly linked to PVR.
- The LvHEATR1 gene, located in the intron of the identified SNPs, showed higher expression in resistant shrimp.

## Abstract

The Pacific white shrimp, Litopenaeus vannamei, is the most extensively cultivated shrimp species worldwide, accounting for over 75% of global production. However, intensive farming practices have frequently led to outbreaks of bacterial diseases, predominantly caused by various pathogenic Vibrio species, resulting in substantial economic losses. Current breeding efforts have largely focused on developing shrimp resistance to individual Vibrio species. Given the high diversity of Vibrio species, resistance to a single Vibrio species is insufficient to address the complex environments of aquaculture. Therefore, breeding shrimp with pan-vibrios resistance (PVR) has emerged as a crucial strategy for achieving sustainable shrimp aquaculture. This study aims to identify single nucleotide polymorphisms (SNPs) associated with PVR traits and pinpoint candidate functional genes using a genome-wide association study (GWAS), with subsequent validation. The results of the study are of great significance for promoting healthy aquaculture development and the sustainable development of marine fishery resources.

Vibriosis, caused by diverse Vibrio species, is among the most devastating bacterial diseases in shrimp aquaculture. Consequently, breeding shrimp for pan-vibrios resistance (PVR) presents a crucial strategy for sustainable shrimp farming. In this work, we performed a GWAS in Litopenaeus vannamei to identify genetic loci underlying resistance to pan-vibrios and validate the identified SNPs. A total of 300 shrimp from nine different regions were subjected to a comprehensive challenge. Selective genotyping of 300 resistant and susceptible individuals was conducted using a specific length amplified fragment sequencing (SLAF-seq) approach. A total of 18,184,608 high-quality SNPs were detected across the whole genome of L. vannamei. Screening identified 283 SNPs located within genes, 26 of which were associated with the PVR trait. These SNPs were subsequently validated in verification group of 80 shrimps, leading to the identification of two genotypes (GG at SNP20 and AA at SNP21) and one genotype combination (GG/AA at SNP20 and SNP21) that were significantly associated with the PVR trait. Notably, these linked SNPs were identified in the intron of LvHEATR1 gene. The highest LvHEATR1 expression was observed in immune-related tissues including hemocytes, the gills, and the hepatopancreas. Furthermore, qPCR results showed that LvHEATR1 expression was significantly higher in the vibrios-resistant (RES) group than in the vibrios-susceptible (SUS) group. This study proposed the PVR concept and provided valuable molecular markers for the genetic improvement of vibrios-resistance in L. vannamei.