Abstract
The three-spot swimming crab (Portunus sanguinolentus) is one of the most important large size economic crabs in China. In this study, we first isolated and characterized a set of 84 SNP loci in P. sanguinolentus. PCR products from ten pairs of primers were sequenced and a total of 3181 bp high-quality DNA sequences were obtained. After genotyping, 84 polymorphic SNP loci were identified. The average frequency of SNP loci was one locus per 38 base pairs in P. sanguinolentus genome. Of these 84 SNP loci, each had bi-alleles with the minor allele frequency ranging from 0.0167 to 0.5000. The observed heterozygosity varied from 0.0333 to 0.7143, while the expected heterozygosity ranged from 0.0333 to 0.5085 per locus. 51 loci showed low variation (HO ≤ 0.3) and 14 SNP loci showed high variation (HO ≥ 0.5). Among 84 SNP loci, 11 loci showed significant deviation from Hardy–Weinberg equilibrium. The developed SNP markers herein will provide valuable information for elucidating population genetic diversity, population dynamics, and conservation genetics of this germplasm resource and other related crab species.
This is a preview of subscription content, log in via an institution to check access.
References
Campbell GR, Fielder DR (1986) Size at sexual maturity and occurrence of ovigerous females in three species of commercially exploited portunid crabs in S.E. Queensland. Proc R Soc Qld 97:79–87
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. https://doi.org/10.1038/hdy.2015.26
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. https://doi.org/10.1007/s12686-017-0720-6
Huang RF (1993) Studies on the taxonomy and distribution of the portunid crabs (Crustacea: Decapoda: Brachyura) in Taiwan. Doctoral Dissertation, National Taiwan Ocean University, Keelung, Taiwan, p 235 (In Chinese)
Hultgren KM, Jeffery NW, Moran A, Gregory TR (2018) Latitudinal variation in genome size in crustaceans. Biol J Lin Soc 123(2):348–359. https://doi.org/10.1093/biolinnean/blx153
Jacob R, Prasad PN, Kusuma MS (1990) Maturity and dimensional studies in female crabs of Portunus Sanguinolentus and P. pelagicus (decapoda, portunidae). Indian J Mar Sci 19:221–223
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. https://doi.org/10.1007/s00300-011-1137-4
Jin S, Zhao Q, Wang CL, Chen YE (2004) RAPD genetic markers in six species of marine crab. Zool Res 25(2):172–176. https://doi.org/10.3321/j.issn:0254-5853.2004.02.016
Lee H-H, Hsu C-C (2003) Population biology of the swimming crab Portunus Sanguinolentus in the waters of Northern Taiwan. J Crustac Biol 23(3):691–699. https://doi.org/10.1651/C-2358
Lu S, Li R, Wang C, Mu C, Song W (2021) Development of expressed sequence tag-single nucleotide polymorphism markers in swimming crab, Portunus trituberculatus. Pak J Zool. https://doi.org/10.17582/journal.pjz/20181220171259
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. https://doi.org/10.1016/j.bse.2011.05.024
Ma HY, Ma CY, Zhu JJ, Ren GJ, Wang W, Chen W, Ma LB (2016) Characterization of the complete mitochondrial genome and phylogenetic relationships of the three-spot swimming crab (Portunus sanguinolentus). Genet Mol Res 15(3):gmr.15038580. https://doi.org/10.4238/gmr.15038580
Meng X, Jia F, Zhang X, Liu P, Li J (2016) Complete sequence and characterization of mitochondrial genome in the swimming crab Portunus sanguinolentus (Herbst, 1783) (Decapoda, Brachyura, Portunidae). Mitochondrial DNA Part A 27(4):3052–3053. https://doi.org/10.3109/19401736.2015.1063130
Miao G, Ma H, Yang X, Wang S, Wu Q, Shi X, You C (2017) Isolation and characterization of 91 single nucleotide polymorphism (SNP) markers for the blue swimming crab (Portunus pelagicus). Conserv Genet Resour 9(4):549–556. https://doi.org/10.1080/24701394.2016.1177040
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. https://doi.org/10.1111/j.1471-8286.2006.01654.x
Rasheed S, Mustaquim J (2010) Size at sexual maturity, breeding season and fecundity of three-spot swimming crab Portunus sanguinolentus (Herbst, 1783) (Decapoda, Brachyura, Portunidae) occurring in the coastal waters of Karachi, Pakistan. Fish Res 103(1–3):56–62. https://doi.org/10.1016/j.fishres.2010.02.002
Ren G, Ma H, Ma C, Wang W, Chen W, Ma L (2017) Genetic diversity and population structure of Portunus sanguinolentus (Herbst, 1783) revealed by mtDNA COI sequences. Mitochondrial DNA Part A 28(5):740–746. https://doi.org/10.1080/24701394.2016.1177040
Soundarapandian P, Varadharajan D, Boopathi A (2013) Reproductive biology of the commercially important portunid crab, Portunus sanguinolentus (Herbst). J Mar Sci 3(2):1–9. https://doi.org/10.4172/2155-9910.1000124
Stephenson W, Campbell B (1959) The Australian portunids (Crustacea: Portunidae). III. The genus Portunus. Aust J Mar Freshw Res 10:84–124. https://doi.org/10.1071/MF9590084
Sumpton WD, Smith GS, Potter MA (1989) Notes on the biology of the Portunid crab, Portunus sanguinolentus (Herbst), in subtropical Queensland waters. Aust J Mar Freshw Res 40:711–717. https://doi.org/10.1071/MF9890711
Williams MJ, Primavera JH (2001) Choosing tropical portunid species for culture, domestication and stock enhancement in the Indo-Pacific. Asian Fish Sci 14:121–142. https://www.researchgate.net/publication/285312865_Choosing_tropical_portunid_species_for_culture_domestication_and_stock_enhancement_in_the_Indo-Pacific
Yang J, Li Y, Zhu S, Chen W, Li J, Xue H, Li X (2020) Development and characterization of 26 SNP markers in Ochetobius elongatus based on restriction site-associated DNA sequencing (RAD-seq). Conserv Genet Resour 12(1):53–55. https://doi.org/10.1007/s12686-018-1075-3
Zhang Y, Miao G, Wu Q, Lin F, You C, Wang S, Ma H (2018) Transcriptome sequencing and molecular markers discovery in the gonads of Portunus sanguinolentus. Sci Data 5(1):1–10. https://doi.org/10.1038/sdata.2018.131
Acknowledgements
This study was supported by Natural Science Foundation of Guizhou Province (No. [2017]7021), Doctoral Research Fund Project of Xingyi Normal University for Nationalities (No. 16XYBS16), Key Cultivation Discipline of Ecology in Guizhou Province (ZDXK[2016] 32), the National Program for Support of Top-Notch Young Professionals, National Innovation and Entrepreneurship Project for College Students (202010666016), Guizhou Training Program of Innovation and Entrepreneurship for Undergraduates (S202010666081, 201710666011).
Author information
Authors and Affiliations
Corresponding authors
Additional information
Publisher's Note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Rights and permissions
About this article
Cite this article
Miao, G., Wang, F., Guo, J. et al. Development of 84 single nucleotide polymorphism (SNP) markers for the three-spot swimming crab (Portunus sanguinolentus) by using RAD approach. Conservation Genet Resour 14, 19–26 (2022). https://doi.org/10.1007/s12686-021-01236-1
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s12686-021-01236-1