Abstract:

Aims: Understanding genetic diversity and population structure of Pleuronichthys cornutus is essential for the sustainable conservation of threatened fishery resources. This study aims to compare the feasibility and effectiveness of different markers in analyzing genetic diversity and population structure of P. cornutus, and to elucidate the molecular mechanism of genetic differentiation between the populations of P. cornutusin the coastal water of China and Japan.

Methods: A total of 200 individuals of P. cornutus from seven localities in coastal waters of China and Japan were sequenced to assess the genetic diversity and population structure based on three markers of control region (CR, 549 bp), cytochrome b (Cytb, 1,008 bp), and NADH subunit 2 (ND2, 1,044 bp).

Results: CR analysis showed seven populations of P. cornutus in the coastal water of China and Japan had a high haplotype diversity (H_d= 0.9699) and low nucleotide diversity (π = 0.0061), a low and not significant F_ST values (-0.0197-0.0184, P> 0.05), and a high variation within populations (99.17%), indicating that there was no genetic differentiation between the populations, and the haplotype network did not show a clear geographic clustering and genealogical structure among populations. Further analysis of five populations of P. cornutus was done by comparing the Cytb and ND2 genes with CR sequences, respectively. The analysis of genetic diversity (H_d= 0.9683-0.9829, π= 0.0050-0.0063), haplotype distribution, and AMOVA (> 98.39%) by Cytband ND2 genes were consistent with the results of the above analysis of CR sequence. Only the F_STvalue (F_ST= 0.0302, P< 0.05) among populations based on the analysis of the ND2 gene revealed a significant differentiation between the Jieshi population in China and the Akashi population in Japan. The neutrality tests and mismatch analyses based on CR, Cytb, and ND2 sequences, respectively, estimated that P. cornutus may have experienced a recent demographic population expansion event. The expansion was occurred in the late Middle Pleistocene of the Quaternary, which dated from about 319,300 to 95,800 years ago (CR), 275,300 to 220,200 years ago (Cytb), and 269,900 to 187,500 years ago (ND2), respectively.

Conclusion: In summary, high genetic diversity and insignificant genetic differentiation were found in P. cornutusby investigating CRsequences and Cytb and ND2genes, except for a low but significant differentiation between the Jieshi and the Akashi populations in ND2. Hence, ND2 was more suitable than CR and Cytb for the study of population structure of P. cornutus.The presence of two separate refuges during the ice age and the geographical distance were likely to be the main causes of the genetic divergence. The combination of multiple genetic markers in future studies can effectively compensate for the limitations of a single genetic marker for the analysis of population genetic diversity. It provided a theoretical basis for the conservation and sustainable use of the germplasm resources of P. cornutus in the coastal water of China and Japan.

Key words: Pleuronichthys cornutus, genetic diversity, control region, cytochrome b genes, NADH dehydrogenase subunit 2 genes