Analysis of genetic diversity among six dojo loach (Misgurnus anguillicaudatus) populations in the Pearl River Basin based on microsatellite and mitochondrial DNA markers

Due to environmental pollution and overfishing, the germplasm resources of wild loach (Misgurnus anguillicaudatus) have been degraded. To explore the genetic diversity of different geographical populations of loach in the Pearl River Basin, a total of 184 M. anguillicaudatus individuals from six dojo loach natural populations sampled from Yingde (Beijiang), Qingyuan (Beijiang), Liannan (Beijiang), Nanxiong (Dongjiang), Meizhou (Dongjiang), and Liuzhou (Liujiang) were investigated based on microsatellite DNA markers and mitochondrial DNA markers (cytb and D-loop). The results showed that a total of 71 alleles (Number of alleles, Na) were amplified in the six M. anguillicaudatus populations by 10 pairs of microsatellite primers. The average observed heterozygosity (Ho), expected heterozygosity (He), and polymorphic information content (PIC) among were 0.3892, 0.5101, and 0.4781, respectively. The average genetic differentiation coefficient (Fst) and number of migrants per generation (Nm) of the six M. anguillicaudatus populations were 0.3395 and 0.4863, respectively, indicating a low level of genetic exchange among the six populations and a high degree of genetic differentiation. Moreover, based on cytb, the number of haplotypes (h), the haplotype diversity (Hd), and nucleotide diversity (π) of the six M. anguillicaudatus populations were 34, 0.925, and 0.0539, respectively, and were 36, 0.879, and 0.0160 based on D-loop sequences. The Fst values among the six populations were 0.4963 (cytb) and 0.4833 (D-loop), and they all showed a high degree of genetic differentiation. The above results indicate that there is abundant genetic diversity of M. anguillicaudatus in the Pearl River Basin in China, and the fish could be used as excellent materials for breeding. The study provides a theoretical basis for the protection and utilization of M. anguillicaudatus natural resources in the Pearl River Basin of China.