Development of Specific Microsatellite Markers to Analyze the Genetic Diversity in the Resident Population of Mandarin Duck (Aix galericulata)

The Mandarin Duck (Aix galericulata), traditionally breeding in northeast China, has recently expanded its range to former wintering grounds, with some populations becoming resident. This range shift necessitates adaptation to novel habitats, increasing ecological vulnerability. Alarmingly, anthropogenic pressures are accelerating wetland fragmentation and loss, threatening critical habitats. Habitat degradation disrupts connectivity, restricting gene flow and elevating inbreeding risks particularly for resident populations. Despite the urgency, genetic studies on these adapting populations remain scarce. Understanding their genetic status is vital for conservation, yet current literature fails to address this knowledge gap. To address the critical need for genetic monitoring tools in this changing landscape, we developed microsatellite markers based on fecal samples. These markers provide an essential foundation for assessing population structure, quantifying connectivity, and monitoring genetic health across the species’ expanding range. Based on fecal samples from mandarin ducks, we developed and characterized 15 microsatellite markers, of which five loci (YN042, YN054, YN055, YN081 and YN086) exhibiting null alleles were excluded from subsequent analyses. The remaining 10 polymorphic loci demonstrated moderate-to-high polymorphism levels, with expected heterozygosity (He) ranging from 0.322 to 0.742 and polymorphism information content (PIC) values between 0.29 and 0.699. Population genetic analysis of the resident Mandarin ducks in Shiqian revealed: (1) moderate genetic diversity levels, and (2) significant inbreeding signals (Fis = 0.211 > 0), highlighting the need for targeted conservation measures for this vulnerable population. The microsatellite loci identified in this study exhibit moderate-to-high polymorphism and are suitable for genetic analyses of Mandarin duck populations. These markers provide both a fundamental genetic toolkit for assessing population genetic background and valuable information for conservation management.