Abstract
The mud shrimp Upogebia major (Crustacea, Decapoda, Gebiidea) (De Haan, 1841) is an ecological keystone species widely distributed in waters. It has contributed significantly to the maintenance of coastal benthic biodiversity as an ecosystem engineer. However, there is still a lack of effective molecular markers to effectively protect and manage this species. In this study, we used the DNeasy Blood & Tissue kit to extract DNA and Illumina HiSeq 4000 sequencing technology to obtain the SNP marker resources. A total of 177 single nucleotide polymorphism (SNP) markers were developed and characterized in U. major. The minor allele frequency ranged from 0.0500 to 0.5000. The observed heterozygosity and expected heterozygosity ranged from 0.0333 to 0.9000 and from 0.0966 to 0.5085, respectively. The polymorphic information content ranged from 0.0905 to 0.3750. The inbreeding coefficient values varied from − 0.2902 to 0.5968. Seventeen loci showed significant deviations from the Hardy–Weinberg equilibrium (P < 0.05). These polymorphic SNP markers will be helpful for the analysis of population genetic structure and the conservation of U. major.
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Acknowledgements
This work was supported by National Natural Science Foundation of China (31460562); Shandong Provincial Natural Science Foundation, China (ZR2020MD002); the Doctoral Science Research Foundation of Yantai University (SM15B01, SM19B70, SM19B28).
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Corresponding author contributed to the study conception and design. YQ, YN and ZJ helped collect samples. DS and JZ were in charge of extracting genomic DNA. SZ, ZX and SW helped collect the data. CW and YS were in charge of compiling the data. The first draft of the manuscript was written by Chenghong Wang and all authors commented on previous versions of the manuscript. Corresponding author read and approved the final manuscript.
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Wang, C., Song, Y., Zhang, J. et al. Development and characterization of 177 SNP markers in the mud shrimp Upogebia major. Conservation Genet Resour 14, 183–193 (2022). https://doi.org/10.1007/s12686-022-01252-9
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DOI: https://doi.org/10.1007/s12686-022-01252-9