show Abstracthide AbstractA strategy using mRNA-seq was used to identify polymorphisms in transcribed genes that could be used to scan the Penaeus monodon genome for markers associated with resistance to white-spot syndrome virus Whispovirus sp. Shrimp were sampled from among four landing centres around the east Indian coastline (EC), survivors of a severe WSSV infection during pond culture (SUR) and the Andaman Islands (AI). Hepatopancreas, muscle, nervous tissue, intestinal tract, heart, gonad, gills, pleopod and lymphoid organs were dissected. Equal quantities of purified RNA from tissue homogenates were combined to create AI, EC and SUR RNA pools for sequencing using the mRNA-seq protocol on the Illumina Genome Analyzer II sequencing platform.