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Here single nucleotide polymorphisms (SNPs) were associated with white spot syndrome virus (WSSV) resistance in black tiger shrimp  Penaeus monodon . SNPs were identified by single-strand conformation polymorphism (SSCP) screening and DNA sequencing of shrimp sampled from 3 families (100 shrimp per family) challenged with WSSV. Shrimp that died over the 14 d challenge trial were designated susceptible, with those remaining alive on Day 14 designated resistant. To compare SNPs, 10 samples from the susceptible and resistant groups, each comprising DNA pooled from 3 shrimp, were amplified by polymerase chain reaction (PCR) using primers to 12 selected genes and screened by SSCP. SNPs were only identified in the anti-lipopolysaccharide factor 3 (ALFPm3) gene product. Analysis of complete ALFPm3 gene sequences confirmed the existence of 3 SNPs (g.934C&gt;G, g.1186A&gt;G, and g.1898C&gt;G) that were polymorphic between the susceptible and resistant groups. Further analyses using specific tetra-primer amplification refractory mutation system PCR primer sets associated these 3 SNPS, and particularly the g.1186A&gt;G SNP, with WSSV resistance. This SNP thus has potential for use as a DNA marker to select for WSSV resistance in  P. monodon  breeding programs.

Association between ALFPm3 single nucleotide polymorphism and white spot syndrome virus resistance in black tiger shrimp Penaeus monodon