Development and characterization of 23 polymorphic microsatellite markers for banana shrimp Fenneropenaeus merguiensis
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TECHNICAL NOTE
Development and characterization of 23 polymorphic microsatellite markers for banana shrimp Fenneropenaeus merguiensis Fahui Gong1,2 • Nan Zhang1,3 • Huayang Guo1,3 • Kecheng Zhu1,3 Tiantian Liu1,2 • Shigui Jiang1,3 • Dianchang Zhang1,3
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Received: 13 November 2015 / Accepted: 7 December 2015 Ó Springer Science+Business Media Dordrecht 2015
Abstract Twenty-three polymorphic microsatellite markers were developed and characterized for Fenneropenaeus merguiensis in this study. The number of alleles varied from 3 to 16. The observed heterozygosity and expected heterozygosity ranged from 0.2188 to 1.0000 and 0.4430 to 0.8819, respectively. Four loci showed moderate polymorphism (0.25 \ PIC \ 0.5), while the rest were highly polymorphic (PIC [ 0.5). Five loci deviated from Hardy–Weinberg Equilibrium. The set of markers described here will constitute efficient tools for the conservation genetic study of F. merguiensis. Keywords Fenneropenaeus merguiensis Penaeidae Microsatellite Genetic diversity Banana shrimp (Fenneropenaeus merguiensis) is widely distributed in the Indo-West Pacific Ocean and is economically important in capture fisheries and aquaculture due to its delicious taste and rapid growth (Perez Farfante and Kensley 1997). However, the wild stocks of banana shrimp has been dramatically declined due to overfishing and environmental pollution in recent years, and genetic status of its wild population is little known so far (Nguyen & Dianchang Zhang [email protected] 1
Division of Aquaculture and Biotechnology, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Science, 231 Xingang Road West, Guangzhou 510300, Guangdong Province, China
2
School of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China
3
Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture, Guangzhou 510300, China
et al. 2014). To facilitate a better understanding of genetic diversity and population structure of banana shrimp for germplasm resource conservation, we have isolated and characterized 23 polymorphic microsatellites from banana shrimp, because microsatellites are the markers of choice for a variety of population genetic study. Total genomic DNAs were extracted from muscles of three shrimps using the QIAamp Tissue Kit (QIAGEN), and were respectively sequenced using RAD-sequencing method (Baxter et al. 2011). Total 1,483,966 reads were obtained, 115,315 microsatellites were detected among Unigenes using the MISA tool (Thiel et al. 2003). 430 putative polymorphic microsatellites were obtained by contrasting the three individuals’ microsatellites, and 58 microsatellites were selected randomly to further amplify and verify the microsatellite polymorphism in one population (32 individuals). The forward primers were labeled with a fluorescent dye and PCR conditions was following: 94 °C/5 min - (94 °C/30 s; 58–60 °C/30 s; 72 °C/ 45 s) 9 30–35 cycle; 72 °C/10 min. Amplification products were analyzed on an Applied Biosys
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