Development and characterization of 177 SNP markers in the mud shrimp Upogebia major

• Published in: Conservation genetics resources 2022-06, Vol.14 (2), p.183-193
• Main Authors: Wang, Chenghong, Song, Yunqi, Zhang, Jirui, Sun, Donghui, Qu, Ying, Ni, Yan, Jiang, Zilin, Zhang, Shukui, Xing, Zhikai, Wu, Sen, Qu, Jiangyong, Wang, Xumin, Wang, Lijun
• Format: Article
• Language: English
• Subjects: Animal Genetics and Genomics; Biodiversity; Biomedical and Life Sciences; Conservation Biology/Ecology; Ecology; Evolutionary Biology; Gene frequency; Genetic analysis; Genetic diversity; Genetic structure; Heterozygosity; Inbreeding; Keystone species; Life Sciences; Methods and Resources Article; Plant Genetics and Genomics; Polymorphism; Population; Population genetics; Single-nucleotide polymorphism; Upogebia major
• ISSN: 1877-7260; 1877-7252; 1877-7260
• DOI: 10.1007/s12686-022-01252-9

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