Characteristic analysis of simple sequence repeats in the ridgetail white prawn Exopalaemon carinicauda genome and its application in parentage assignment

The ridgetail white prawn, Exopalaemon carinicauda is one of the most valuable marine resources in China, but few studies have been conducted to describe the characteristics of the simple sequence repeats (SSRs) for this species. The present study provides a genome-wide view to SSRs in E. carinicauda. A total of 3,243,071 SSRs were detected in the whole genome sequences, while the mononucleotide SSR was the most abundant type. Adenine and Thymine (AT)-rich SSRs were more abundant than guanine and cytosine (GC)-rich SSRs. These SSR resources will be very useful for genetic studies such as parentage assignment, genetic diversity evaluation, and marker-assisted selection. Sustainable development of E. carinicauda aquaculture requires improved breeding stocks and systematically family-based selective breeding that relies on accurate pedigree information for estimating genetic merits. Therefore, eight highly polymorphic SSRs were selected for parentage assignment analysis. A total of 180 individuals from the offspring of four full-sib and two half-sib families were used to examine the efficacy of parentage analysis of those SSRs. The results showed that 98% of the offspring were unambiguously assigned to their female parent. The high efficacy of parentage assignment showed that the developed polymorphic SSR markers could be used for selective breeding in E. carinicauda.