Lineage specific detection of the scaly form of the pen shell Atrina spp. by a loop-mediated isothermal amplification method

Abstract

Taxonomy of the pen shell (genus Atrina) in East Asia has been confused because of the plasticity of the shell morphology and lack of unified morphological characteristics. We analyzed the mitochondrial cytochrome c oxidase subunit I (COI) sequence of the pen shell sampled from Ariake Bay and Seto Inland Sea, western Japan. All individuals were identified as the scaly form based on external morphology; however, their COI sequences were comprised of two distinct lineages. The sequence divergence between the two was 8.3%, indicating the high possibility that they are different species. The scaly form of the pen shell in Japan is one of the target species for resource enhancement, therefore COI lineage identification of broodstock individuals is critically important to avoid producing hybrid seed. We developed a loop-mediated isothermal amplification method that enables specific detection of the two lineages. This method can contribute to reducing the cost and time required for genotyping broodstock individuals prior to seed production.