Elsevier

Gene

Volume 751, 15 August 2020, 144763
Gene

Research paper
Population genetic diversity of mud crab (Scylla paramamosain) from southeast coastal regions of China based on mitochondrial COI gene sequence

https://doi.org/10.1016/j.gene.2020.144763Get rights and content

Highlights

  • Significant genetic differentiation was only observed between BA and SHCM population.

  • All of the populations showed high haplotype diversity (>0.5) except NHF1.

  • Nucleotide diversity and haplotype diversity were all highest in Shanghai and lowest in Hainan.

  • 99.68% of total genetic variation occurred within populations.

Abstract

Mud crab (Scylla paramamosain) is a native and economically important species in East Asia. In order to provide a comprehensive genetic background for the resource protection and management in this species, the genetic diversity and population structure of S. paramamosain were analyzed based on mitochondrial cytochrome oxidase subunit I (COI) gene sequence. Totally, 599 individuals were sampled from 20 populations, including 18 wild and two cultured populations from five provinces along southeastern coast of China. After the sequencing of a 638 bp fragment of COI gene, 84 variable sites were found and no insertion or deletion was detected. The H2 (haplotype 2) was the dominant hapolotye shared by 301 individuals (50.3% of all individuals) and existed in all localities. In addition, a high percent of unique haplotypes (53 of 93 haplotyoes) was found. The average nucleotide diversity (π) of all populations was 0.00194, ranging from 0.00010 (NHF1) to 0.00305 (SHCM). The haplotype diversity (h) ranged from 0.067 (NHF1) to 0.876 (CM) with an average 0.738. All of the populations showed high h (>0.5) except NHF1. Genetic distance ranged from 0.00063 to 0.00337 between populations and from 0.00010 to 0.00374 within populations. The molecular variance analysis (AMOVA) showed that the total genetic variation mainly occurred within populations (99.68%) and only 0.32% was contributed by among populations variation. No significant genetic differentiation was observed among all wild populations except that between BA and SHCM (Fst = 0.0.05707, P < 0.05), indicating a low level of genetic differentiation among localities. It is worth to note that two progeny population (HNF1 and NHF1) showed significantly different genetic variation, which suggested that a large quantity of parents could help to improve the genetic diversity of progeny populations.

Introduction

Scylla paramamosain is a kind of mud crab which is commonly consumed and widely distributed in Southeast Asia countries, including China, Vitenman, Janpan, Cambodia, Singapore and Indonesia. In China, S. paramamosain was previously referred as a congeneric species, S. serrata (Ma et al., 2006). It is distributed along the southeastern coastal regions and is an important crab resource for fishing and aquaculture, which has been aquacultured for>100 years (Shen and Lai, 1994). However, due to over-fishing and sea water pollution, S. paramamosain resource has decreased significantly.

A better understanding of genetic diversity and population genetic structure is of crucial importance and provide clues for the management and protection of a commercially important species (Ma et al., 2009; Ortega-Villaizan Romo et al., 2006). It can also guide how to conserve the resource and breed the important species (Zhan et al., 2009, Fuji et al., 2007, Ortega-Villaizan Romo et al., 2006). To date, genetic analysis of the population structure of S. paramamosain in China has also been conducted by mtDNA, SSR and other molecular markers (Cai et al., 2011, Lu et al., 2009, Ma et al., 2011, Ma et al., 2012, He et al., 2010, Song et al., 2010, Song et al., 2012, Shu et al., 2011, Sun et al., 2012). Most of those researches were focused on S. paramamosain individuals collected from certain areas, such as Beibu Gulf (Cai et al., 2011, Song et al., 2010, Song et al., 2012, Sun et al., 2012;) and Hainan Island (Ma et al., 2011). Contrastingly, a larger scale of sampling and genetic analysis were less reported (Lu et al., 2009, He et al., 2010, Ma et al., 2012). Based on the current available studies, a low level of genetic differentiation of S. paramamosain from southeastern China were showed, while the high level and low level of their genetic diversity were both reported. The conflicting conclusions may result from the different sampling locations, and the small sample size of some wild S. paramamosain populations (<10 individuals), which might not be large enough to provide a representative data. Moreover, it is worth noting that all those studies were performed before 2012, the general situation of genetic diversity and population structure of S. paramamosain in China could be changed in the past few years, as the over-exploitation, habitat destruction, water pollution, and artificial breeding activities could have dramatically influenced natural resources of this species.

Therefore, aimed to provide a comprehensively understanding of the genetic background of S. paramamosain distributed along the southeastern sea of China, the genetic diversity and population structures of 599 individuals from 18 wild and two breeding populations of this crab from five provinces (Hainan, Guangdong, Fujian, Zhejiang and Shanghai) were analyzed using mitochondrial COI gene in present study. The expected results will also help to the conservation and management of wild resources of this species.

Section snippets

Ethics statement

The sampling location of experimental animals is not protected or privately-owned, and the field sampling did not involve protected or endangered species. All experiments and sampling animals were handled according to national laws and the guidelines of the animal care and use policy set by the ECSFRI (East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China).

Sample collection and DNA extraction

A total of 557 wild individuals of S. paramamosain were collected by fishermen from 18 different

Characteristics of COI sequence and genetic diversity of S. Paramamosain

The length of fragment of mtDNA COI gene was 638 bp, which was amplified from 599 individuals of S. paramamosain. The average nucleotide frequencies among all sequences were 38.1% T, 17.7% C, 28.8% A and 15.4% G, respectively. The A/T content (66.9%) was significantly higher than the C/G content (34.1%). There were 84 variable sites being found and no insertion or deletion was detected.

Among the 599 sequences, a total of 93 different haplotypes were defined. In Hainan province, 68 haplotypes

Discussion

mtDNA was widely used for studying the genetic diversity of many crustacean animals such as Feneropenaeus chinensis (Li et al., 2009), Eriocheir sensu stricto (Wang et al., 2008), S. serrata (Fratini et al. 2010), S. paramamosain (Lu et al., 2009, He et al., 2010, Ma et al., 2011) and Portunus sanguinolentus (Ren et al., 2017). In this study, the genetic diversity of S. paramamosain in the East China Sea and South China Sea was investigated based on mitochondrial COI gene sequences. A total of

CRediT authorship contribution statement

Wei Wang: Conceptualization, Methodology, Software, Resources, Writing - original draft, Writing - review & editing, Funding acquisition. Chunyan Ma: Methodology, Software, Writing - original draft. Wei Chen: Resources, Investigation. Zhongwen Jin: Resources, Funding acquisition. Ming Zhao: Resources, Investigation. Fengying Zhang: Conceptualization. Zhiqiang Liu: Conceptualization, Resources. Lingbo Ma: Conceptualization, Methodology, Funding acquisition.

Declaration of Competing Interest

The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

Acknowledgements

This work was supported by grants from the Special Program on Agricultural Aspect of Science and Technology Commission of Ningbo (2016C11003), Shanghai Agriculture Applied Technology Development Program, China (2018-02-08-00-07-F01550), the Basic Research Fund for State-level Nonprofit Research Institutes of ESCFRI (2014Z01) and China Agriculture Research System-48 (CARS-48).

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