Multiplex panels of SNP markers based on single-base primer extension in the west Pacific pen shell Atrina lischkeana (Clessin, 1891)

As part of stock enhancement programs for marine fishery species, the stocking of hatchery-produced seedlings into sea areas has been implemented worldwide. DNA markers are vital for responsible stock enhancement practices that aim to conserve the genetic diversity of recipient wild populations. We report novel single-nucleotide polymorphism (SNP) markers and multiplex SNP panels developed for the west Pacific pen shell Atrina lischkeana (Clessin, 1891), a large bivalve that is expected to be a subject of stock enhancement activity as the natural resource has dwindled, especially in Japan.

On the basis of single-base primer extension combined with MALD-TOF/MS analysis, we developed 218 SNP markers across eight multiplex SNP panels, which allowed genotyping of specimens from two wild A. lischkeana populations. However, our parentage analysis for a captive-bred population sample revealed that 21 of the 218 markers exhibited non-Mendelian patterns of allelic transmission in parent–offspring trios. We verified that the inheritance of undetectable null alleles caused almost all the aberrant allelic transmissions.

The developed markers will be of significant use in dealing with issues related to the stock enhancement of A. lischkeana, such as the monitoring of genetic diversity of hatchery stocks and the evaluation of impacts of stocking upon the genetic makeup of recipient wild populations, although caution is warranted especially when the 21 markers with unexpected patterns of allelic segregation are applied to field samples. Additionally, the markers can be analyzed in other targeted genotyping platforms.