Genetic diversity and population structure of the endangered fish Pseudobagrus brevicorpus (Bagridae) using a newly deve
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Genes & Genomics https://doi.org/10.1007/s13258-020-00992-y
RESEARCH ARTICLE
Genetic diversity and population structure of the endangered fish Pseudobagrus brevicorpus (Bagridae) using a newly developed 12-microsatellite marker Yeong Ho Kwak1 · Kang Rae Kim1 · Moo Sang Kim2 · In Chul Bang1 Received: 14 January 2020 / Accepted: 28 August 2020 © The Genetics Society of Korea 2020
Abstract Background Pseudobagrus brevicorpus is an endangered species in Korea. The development of genetic markers and genetic information regarding the populations of this species are needed to establish conservation strategies. Objective As part of the conservation of P. brevicorpus, a 12-microsatellite marker was developed using next-generation sequencing (NGS) to provide current genetic population information. Methods Microsatellites from P. brevicorpus were identified by NGS analysis. Genetic diversity and genetic structure analysis of six populations (Seojeong Stream [SJ], Gokgang Stream [GK], Jaho Stream [JH], Daega Stream [DG], Nam River [NG], and Deokcheon River [DC]) of P. brevicorpus were conducted using the newly developed microsatellite marker. Results NGS generated 10,347,578 reads and identified 659,507 simple sequence repeats. Twelve microsatellites were successfully amplified and verified in 30 individuals of P. brevicorpus. The genetic diversity of the six P. brevicorpus populations in terms of the number of alleles ranged from 3.667 to 7.111. All populations except DG deviated significantly from Hardy–Weinberg equilibrium (HWE) at one or more loci. The genetic distances of the six populations showed the closest relationship between the SJ and GK populations (independent Stream populations), and there was a close relationship with the JH population among the Nakdong River. Structure analysis showed that P. brevicorpus is largely divided into two groups. Conclusions The developed microsatellite marker will be used to provide basic genetic data of P. brevicorpus. Genetic diversity and structure analysis of the population will provide useful information for conservation management of P. brevicorpus. Keywords Pseudobagrus brevicorpus · Next generation sequencing · Microsatellite · Genetic diversity · Populations structure
Introduction The Korean stumpy bullhead Pseudobagrus brevicorpus is an endemic species of the Nakdong River, Korea, and has been designated by the Ministry of Environment as Endangered Species Wildlife Class I and Natural Monument 455 by the Cultural Heritage Administration (Lee and Noh 2006). It is the most vulnerable species in the Nakdong River because it lives in a very restricted area covering approximately 5 km (Kang et al. 2009). However, it has recently * In Chul Bang [email protected] 1
Department of life Sciences and Biotechnology, Soonchunhyang University, Asan 31538, Republic of Korea
Digital Omics, Daejeon 34054, Republic of Korea
2
appeared in some independent Stream populations (Yoo et al. 2008, 2009). Since the 1960s, the Nakdong River has undergone many changes due to the
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