Microsatellite DNA markers for paternity identification in the hermaphroditic barnacle Chthamalus challengeri Hoek

Background Simultaneously hermaphroditic animals allocate resources to both male and female reproductive functions (sex allocation). Although male reproductive success is a key factor in determining sex allocation, it is seldom evaluated in marine hermaphrodites, as it requires the development of suitable DNA markers to trace paternity. The sessile, simultaneously hermaphroditic barnacle Chthamalus challengeri Hoek, 1883 is widely found along rocky intertidal shores in the northwestern Pacific. In this report, we describe microsatellite DNA markers for C. challengeri and multiplex panels of the markers, which can be used to reveal reproductive success via paternity identification. Methods and Results We obtained 632 microsatellite sequences by using next-generation sequencing. We examined 189 primer sets, of which 11 passed our filtering criteria. Through simulation analysis, we demonstrated that these primers can be used as microsatellite markers for accurate paternity determination. Additionally, we established five multiplex panels by using all the developed markers. Conclusions We developed 11 microsatellite DNA markers for paternity analysis. These markers, which exhibited a moderate to high degree of polymorphism in a population sample, should be of great use in paternity inference. We also established multiplex panels for the markers, thus enabling low-cost and efficient analysis. These advancements will enable us to evaluate male reproductive success and contribute to a better understanding of sex allocation in C. challengeri and in hermaphroditic barnacles more broadly.