Development and characterization of 50 SNP markers in three watersheds populations of Xenocypris davidi

• Published in: Conservation genetics resources 2023-06, Vol.15 (1-2), p.29-47
• Main Authors: Su, Chaoqun, Tan, Chenxi, Zhao, Liangjie, Peng, Xinliang, Liu, Jun, Li, Haolong, Guo, Xusheng
• Format: Article
• Language: English
• Subjects: Animal Genetics and Genomics; Biodiversity; Biomedical and Life Sciences; Conservation; Conservation Biology/Ecology; Ecology; Evolutionary Biology; Fish; Fishing; Genetic analysis; Genetic diversity; Genetic markers; Life Sciences; Plant Genetics and Genomics; Polymorphism; Population genetics; Rivers; Single-nucleotide polymorphism; Technical Note; Transcriptomes; Water pollution; Watersheds; Xenocypris davidi
• ISSN: 1877-7260; 1877-7252; 1877-7260
• DOI: 10.1007/s12686-023-01300-y

Xenocypris davidi is an ecologically important fish species that is widely distributed in China. However, the natural genetic diversity of X. davidi has dramatically declined in recent years owing to over-harvesting and water pollution. Data regarding the genetic markers in this species are scarce. In this study, 50 single nucleotide polymorphism (SNP) markers of X. davidi were newly developed using the snapshot method based on transcriptome data and were identified and characterized among three X. davidi populations. For the Huaihe River watershed population, 39 SNPs were polymorphic; for the Yangtze River watershed population, 38 SNPs were polymorphic; and for the Pearl River watershed population, 34 SNPs were polymorphic. Nine, ten, and seven loci significantly deviated from the Hardy–Weinberg equilibrium in the Huaihe River, Yangtze River, and Pearl River populations, respectively. These novel polymorphic SNPs would be useful for further population genetic analyses and natural resource conservation.