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Development and Validation of Tetranucleotide Repeat Microsatellite Markers at the Whole-Genome Level in the Yangtze Finless Porpoise

Mengting Tang,Denghua Yin,Jianglong Que,Danqing Lin,Congping Ying,Jie Liu,Fangning Liu,Pan Wang,Wenwen Li,Jinxiang Yu,Kai Liu

Published 2025 in Animals

ABSTRACT

Simple Summary The Yangtze finless porpoise (Neophocaena asiaeorientalis asiaeorientalis) serves as a key flagship species for evaluating the effectiveness of fishing bans and assessing the ecological health of the Yangtze River ecosystem, China. To provide stable and reliable molecular markers for population genetic studies, this study utilized high-quality chromosome-level genomic data of the Yangtze finless porpoise along with resequencing data from 12 individuals to identify highly variable microsatellite loci. By integrating PCR amplification with capillary electrophoresis technology, this study successfully validated a total of 19 tetranucleotide repeat microsatellite loci that exhibit stable amplification, high polymorphism, and low genotyping error rates. Using these molecular markers, a genetic diversity analysis was performed on the Poyang Lake population to assess their functional advantages and applicability. The microsatellite markers developed in this study serve as a critical tool for future accurately identifying genetic relationships among Yangtze finless porpoises and reliably predicting population dynamics.

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