Abstract
Neotrypaea japonica (Ortmann 1891) is a burrowing shrimp that lives in tidal flats. In this study, 123 SNP markers were isolated and characterized from N. japonica. The frequency range of minor alleles varied from 0.2500 to 0.4833, the observed heterozygosity ranged from 0.4333 to 0.9000, and the expected heterozygosity ranged from 0.4944 to 0.6503. The polymorphic parameter and inbreeding value varied from 0.3680 to 0.5651 and − 0.2768 to 0.1045, respectively. Significant departures from Hardy–Weinberg equilibrium after Bonferroni correction (P < 0.05) were observed for 16 loci. The study of polymorphic SNPs will provide an important theoretical basis for further population genetic diversity analysis and species conservation of N. japonica.
References
Baird NA, Etter PD, Atwood TS, Currey MC, Shiver AL, Lewis ZA, Selker EU, Cresko WA, Johnson EA (2008) Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLoS ONE 3(10):e63376. https://doi.org/10.1371/journal.pone.0003376
Dworschak PC (2000) Global diversity in the Thalassinidea (Decapoda). J Crustac Biol 20:238–245
Felder DL (2001) Diversity and ecological significance of deep-burrowing macrocrustaceans in coastal tropical waters of Americas (Decapoda: Thalassinidea). Interciencia 26:440–449
Kaikai L, Hong Y, Qi L (2018) Development and characterization of 108 SNP markers in the Iwagaki oyster, Crassostrea nippona. Conserv Genet Resour 11(4):437–442. https://doi.org/10.1007/s12686-018-1047-7
Kalinowski ST, Taper ML, Marshall TC (2007) Revising how the computer program CERVUS accommodates genotyping error increases success in paternity assignment. Mol Ecol 16:1099–1106. https://doi.org/10.1111/j.1365-294X.2007.03089.x
Kim S, Ahn DH, Park JK, Kim SJ, Choi HG, Min GS (2013) The complete mitochondrial genome of the Japanese ghost shrimp Nihonotrypaea japonica (Crustacea, Decapoda, Axiidea). Mitochondrial DNA 24(3):243–245. https://doi.org/10.3109/19401736.2012.752480
Mukai H, Koike I (1984) Behavior and respiration of the burrowing Shrimps Upogebia major (de Haan) and Nihonotrypaea japonica (de Haan). J Crustac Biol 4(2):191–200
Posey MH, Dumbauld BR, Armstrong DA (1991) Effects of a burrowing mud shrimp Upogebia pugettensis (Dana), on abundances of macro-infauna. J Exp Mar Biol Ecol 148:283–294. https://doi.org/10.1016/0022-0981(91)90088-E
Qu JY, Wang SS, Cui YT, Guo XY, Wang YY (2020) Development and characterization of 26 SNP markers in Nipponacmea schrenckii. Conserv Genet Resour 12(2):195–198. https://doi.org/10.1007/s12686-019-01095-x
Vignal A, Milan D, SanCristobal M, Eggen A (2002) A review on SNP and other types of molecular markers and their use in animal genetics. Genet Sel Evol 34:275–305. https://doi.org/10.1186/1297-9686-34-3-275
Acknowledgements
This work was supported by National Natural Science Foundation of China (No. 31460562), Natural Science Foundation of Shandong Province (ZR2020MD002) and the Doctoral Science Research Foundation of Yantai University (2215001, 2219013).
Author information
Authors and Affiliations
Corresponding author
Ethics declarations
Conflict of interest
The authors declare that they have no competing interests.
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
Sun, X., Zhang, J. & Che, Z. Development and characterization of 123 SNP markers in Neotrypaea japonica (Ortmann 1891). Conservation Genet Resour 13, 395–403 (2021). https://doi.org/10.1007/s12686-021-01223-6
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s12686-021-01223-6