Application of Microsatellites in Genetic Diversity Analysis and Population Discrimination of Coilia nasus from the Yangtze River

The genetic diversity and population structure of five tapertail anchovy (Coilia nasus) populations—four wild populations from the Yangtze River (Taizhou, Anqing, Shanghai, Hukou) and one cultured population from Yangzhong—were analyzed using 18 highly polymorphic microsatellite loci. All loci exhibited high polymorphism, with genetic parameters as follows: mean number of alleles = 20.567, expected heterozygosity = 13.506, Shannon information index = 2.743, and polymorphic information content = 0.9624. F-statistics ranged from 0.02898 to 0.05714, indicating varying degrees of genetic differentiation between all populations. Analysis of molecular variance revealed that 4% of the total genetic variation was attributable to differences among populations, 23% to variation among individuals within populations, and 73% to within-individual genetic variation. A UPGMA phylogenetic tree based on Nei’s genetic distance showed that the Shanghai population clustered first with Anqing, followed by Taizhou, Hukou, and finally Yangzhong. Additionally, discriminant functions developed from microsatellite data enabled accurate population assignment for all individuals. These findings provide critical insights into the genetic relationships and structure of C. nasus populations, offering valuable implications for their conservation and management.