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

Abstract

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.

Parentage Determination of Chinese Hooksnout Carp (Opsariichthys bidens) Based on Microsatellite DNA Markers

“…Using microsatellite for parentage determination could overcome the limitations of traditional physical tags. Due to their high polymorphism and codominance, microsatellite markers have been widely utilized in parentage determination of aquaculture species, such as Siniperca chuatsi, Siniperca scherzeri, Odontobutis potamophlia, Scylla paramamosain, Fenneropenaeus chinensis, Penaeus monodon, Exopalaemon carinicauda, and P. fucata [14,19,21,[34][35][36][37][38].…”

Population genetic structure of Yesso scallop (Mizuhopecten yessoensis) of Russian Far East revealed by mitochondrial and microsatellite genetic markers

“…The combined use of mitochondrial DNA (mtDNA) and microsatellite loci is now common in different studies of molecular diversity, population genetic variation, and genetic differentiation of many marine invertebrates (Cho et al 2007;Meriam et al 2015;Nie et al 2015;Sato et al 2005;Sato and Nagashima 2001;Zhang et al 2020;Zheng et al 2019). Such a combination of rapidly and slowly evolving molecular markers allows the entire illustration of ancient and recent population history.…”

Establishment and application of a microsatellite‐based parentage identification method for Oreochromis niloticus , O. aureus , and O. niloticus × O. aureus

“…The microsatellite DNA marker‐based parentage identification methods can avoid the disadvantages of traditional genetic analysis methods and it has been widely used for management of aquatic animals, such as Exopalaemon carinicauda (Zhang et al., 2020), Siniperca scherzeri (Yang et al., 2015) and O. niloticus (Zhao et al, 2016). However, no reports are available on parentage identification methods for O. aureus and O. niloticus × O. aureus .…”