Background: Acute Hepatopancreatic Necrosis Disease (AHPND) is one of the most significant challenges facing the Pacific white shrimp (Litopenaeus vannamei) farming industry, causing widespread mortality and substantial economic losses. The identification of genetic markers associated with resistance to this disease can play a crucial role in Marker-Assisted Selection (MAS) breeding programs.
Objective: This study aimed to investigate the association of the SNP locus g.657G/T within the PEN2-1 gene with resistance to AHPND in Pacific white shrimp. The results of this study will contribute to the development of breeding programs for resistance to this disease.
Methodology: In this study, 149 L. vannamei shrimp samples (susceptible shrimp (n = 74) and resistant shrimp (n = 75)) were collected from farms affected by AHPND in Bushehr city, Iran. Genotyping of the target SNP was performed using the ARMS-PCR technique, and the amplified products were resolved by agarose gel electrophoresis. To confirm the PCR results, Sanger sequencing of the amplified fragment was performed, and the results were compared using the BLASTn tool against the NCBI database. Allele and genotype frequencies were calculated, and Hardy-Weinberg equilibrium was assessed. Furthermore, the association of genotypes with disease resistance was evaluated using binomial logistic regression within a Generalized Linear Model (GLM). All statistical analyses were conducted using SAS software version 9.4.
Results: The results showed that the frequencies of the GG, GT, and TT genotypes were 38.7%, 62.92%, and 0%, respectively. The frequencies of the G and T alleles were calculated as 0.5369 and 0.4631, respectively. Sequencing of the amplified gene fragment confirmed 99% identity with the reference PEN2-1 gene sequence of Pacific white shrimp (DQ206401.1). The Hardy-Weinberg equilibrium test revealed a highly significant deviation from equilibrium (P < 0.05). Chi-square test results indicated a significant as
