Identification of Single Nucleotide Polymorphisms Related to the Resistance Against Acute Hepatopancreatic Necrosis Disease in the Pacific White Shrimp Litopenaeus vannamei by Target Sequencing Approach

Abstract

Acute hepatopancreatic necrosis disease (AHPND) is a major bacterial disease in Pacific white shrimp Litopenaeus vannamei farming, which is caused by Vibrio parahaemolyticus . AHPND has led to a significant reduction of shrimp output since its outbreak. Selective breeding of disease-resistant broodstock is regarded as a key strategy in solving the disease problem. Understanding the relationship between genetic variance and AHPND resistance is the basis for marker-assisted selection in shrimp. The purpose of this study was to identify single nucleotide polymorphisms (SNPs) associated with the resistance against AHPND in L. vannamei . In this work, two independent populations were used for V. parahaemolyticus challenge and the resistant or susceptible shrimp were evaluated according to the survival time after Vibrio infection. The above two populations were genotyped separately by a SNP panel designed based on the target sequencing platform using a pooling strategy. The SNP panel contained 508 amplicons from DNA fragments distributed evenly along the genome and some immune-related genes of L. vannamei . By analyzing the allele frequency in the resistant and susceptible groups, 30 SNPs were found to be significantly associated with the resistance of the shrimp against V. parahaemolyticus infection (false discovery rate corrected at P < 0.05). Three SNPs were further validated by individual genotyping in all samples of population 1. Our study illustrated that target sequencing and pooling sequencing were effective in identifying the markers associated with economic traits, and the SNPs identified in this study could be used as molecular markers for breeding disease-resistant shrimp.

Comparison of Gene Expression Between Resistant and Susceptible Families Against VPAHPND and Identification of Biomarkers Used for Resistance Evaluation in Litopenaeus vannamei

“…In 2018, 95 full-sib families with an average body weight of 2.10 g were selected for evaluation of resistance. For the challenge experiment, VP AHPND was prepared according to the method described by Zhang Q. et al (2019). About 100 healthy shrimp from each family were subjected to VP AHPND immersion infection.…”

“…So far, several genes associated with disease resistance have been reported in aquatic animals. Polymorphism of LvALF and TRAF6 was reported to be associated with the resistance to WSSV in shrimp (Wang et al, 2011;Liu et al, 2014b;Liu et al, 2014a;Yu et al, 2017;Zhang Q. et al, 2019). A major quantitative trait locus (QTL) for the resistance of Atlantic salmon (Salmo salar) against infectious pancreatic necrosis (IPN) was discovered, which has been already applied in marker-assisted breeding of IPN-resistant fish (Houston et al, 2008;Moen et al, 2009;Woldemariam et al, 2020).…”

A Superior Contiguous Whole Genome Assembly for Shrimp (Penaeus indicus)

“…In shrimp, the role of SNPs was demonstrated for use in construction of linkage maps (Baranski et al, 2014;Yu et al, 2015;Jones et al, 2017) trait-specific association studies (Robinson et al, 2014;Santos et al, 2018;Zhang Q. et al, 2019;Janpoom et al, 2020), genetic characterization (Perez-Enriquez et al, 2018;Vu et al, 2020) and parentage testing (Henshall et al, 2014;Sellars et al, 2014). In this study, we report 2,572 nonsynonymous SNPs, of which 46 might have potential to impact the functions of coding proteins.…”

Shrimp immune response: A transcriptomic perspective

“…However, the modification of genes needs full understanding of their functions and the functional networks that can be affected before the edition strategy can be tested. As example of the appli- Molecular markers based on single nucleotide polymorphisms (SNPs) have been recently implemented for selecting for growth performance, 113,114 resistance to V. parahaemolyticus in P. vannamei, 111,115 parvovirus in P. mergulensis 116 or even different stressors such as nitrite concentration. 117 Recently, Pooljun et al 118 have found an association between a SNP in the anti-lipopolysaccharide factor 3 (ALF3) and resistance to WSSV in P. monodon.…”