Abstract
The blue swimming crab (Portunus pelagicus) is one of most important crab fishery resources in China. In this study, we first isolated and characterized a set of 91 SNP loci in P. pelagicus. A total of 8426 bp long high quality DNA sequences were obtained, from which 91 SNP loci were identified and well genotyped. The average frequency of SNP loci was one locus every 93 base pairs in P. pelagicus genome. Of these 91 SNP loci, each had bi-alleles with the minor allele frequency ranging from 0.0167 to 0.5000. The observed heterozygosity per locus ranged from 0.0333 to 1.0000, while the expected heterozygosity per locus was from 0.0333 to 0.5085. Forty-four loci showed significant deviation from Hardy–Weinberg equilibrium. The SNP markers developed herein will be helpful for elucidating population genetic diversity, population dynamics, and conservation genetics of P. pelagicus and other related crab species.
References
Bryars S, Adams M (1999) An allozyme study of the blue swimming crab, Portunus pelagicus (Crustacea: Portunidae), in Australia: stock delineation in southern Australia and evidence for a cryptic species in northern waters. Mar Freshwater Res 50:15–26
Cui Z, Hui M, Liu Y, Song C, Li X, Li Y, Liu L, Shi G, Wang S, Li F, Zhang X, Liu C, Xiang J, Chu KH (2015) High-density linkage mapping aided by transcriptomics documents ZW sex determination system in the Chinese mitten crab Eriocheir sinensis. Heredity 115:206–215
Du ZQ, Ciobanu DC, Onteru SK, Gorbach D, Mileham AJ, Jaramillo G, Rothschild MF (2010) A gene-based SNP linkage map for pacific white shrimp, Litopenaeus vannamei. Anim Genet 41:286–294
Feng NN, Ma HY, Ma CY, Xu Z, Li SZ, Jiang W, Liu YX, Ma LB (2014) Characterization of 40 single nucleotide polymorphism (SNP) via Tm-shift assay in the mud crab (Scylla paramamosain). Mol Biol Rep 41:5467–5471
Ikhwanuddin M, Hayimad T, Ghazali A, Halim SSA, Abdullah SA (2016) Resistance test at early larval stage of blue swimming crab, Portunus pelagicus. Songklanakarin J Sci Technol 38:83–90
Jeffery NW (2012) The first genome size estimates for six species of krill (Malacostraca, Euphausiidae): large genomes at the north and south poles. Polar Biol 35:959–962
Johnston D, Harris D, Caputi N, Thomson A (2011) Decline of a blue swimmer crab (Portunus pelagicus) fishery in Western Australia-History, contributing factors and future management strategy. Fish Res 109:119–130
Klinbunga S, Khetpu K, Khamnamtong B, Menasveta P (2007) Genetic heterogeneity of the blue swimming crab (Portunus pelagicus) in Thailand determined by AFLP analysis. Biochem Genet 45:725–736
Klinbunga S, Yuvanatemiya V, Wongphayak S, Khetpu K, Menasveta P, Khamnamtong B (2010) Genetic population differentiation of the blue swimming crab Portunus pelagicus (Portunidae) in Thai waters revealed by RAPD analysis. Genet Mol Res 9:1615–1624
Lai JCY, Peter KLN, Peter JFD (2010) A revision of the Portunus pelagicus (L., 1758) species complex (Crustacea: Brachyura: Portunidae), with the recognition of four species. Raffles B Zool 58:199–237
Ma HY, Yang JF, Su PZ, Chen SL (2009) Genetic analysis of gynogenetic and common populations of Verasper moseri using SSR markers. Wuhan Univ J Nat Sci 14:267–273
Ma HY, Ma QQ, Ma CY, Ma LB (2011) Isolation and characterization of gene-derived single nucleotide polymorphism (SNP) markers in Scylla paramamosain. Biochem Syst Ecol 39:419–424
Morin PA, Aitken NC, Rubio-Cisneros N, Dizon AE, Mesnick S (2007) Characterization of 18 SNP markers for sperm whale (Physeter macrocephalus). Mol Ecol Notes 7:626–630
Ren GJ, Miao GD, Ma CY, Lu JX, Yang XL, Ma HY (2016) Genetic structure and historical demography of the blue swimming crab (Portunus pelagicus) from southeastern sea of China based on mitochondrial COI gene. Mitochondr DNA. doi:10.1080/24701394.2016.1261855
Song L, Bian C, Luo Y, Wang L, You X, Li J, Qiu Y, Ma X, Zhu Z, Ma L, Wang Z, Lei Y, Qiang J, Li H, Yu J, Wong A, Xu J, Shi Q, Xu P (2016) Draft genome of the Chinese mitten crab, Eriocheir sinensis. GigaScience 5:5
Wu XG, Zhou B, Cheng YX, Zeng CS, Wang CL, Feng L (2010) Comparison of gender differences in biochemical composition and nutritional value of various edible parts of the blue swimmer crab. J Food Compos Anal 23:154–159
Yap ES, Sezmis E, Chaplin JA, Potter IC, Spencer PBS (2002) Isolation and characterization of microsatellite loci in Portunus pelagicus (Crustacea: Portunidae). Mol Ecol Notes 2:30–32
Yeh FC, Yang RC, Boyle T (1999) POPGENE version 1.31. Microsoft window-based freeware for population genetic analysis. University of Alberta and the Centre for International Forestry Research. http://www.ualberta.ca/~fyeh/
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This study was supported by the National Program for Support of Top-Notch Young Professionals.
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Guidong Miao and Hongyu Ma have contributed equally (co-first authors) to this study.
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Miao, G., Ma, H., Yang, X. et al. Isolation and characterization of 91 single nucleotide polymorphism (SNP) markers for the blue swimming crab (Portunus pelagicus). Conservation Genet Resour 9, 549–556 (2017). https://doi.org/10.1007/s12686-017-0720-6
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DOI: https://doi.org/10.1007/s12686-017-0720-6