Analysis of genetic diversity of Siniperca scherzeri 

population in Qingshui River based on 

mitochondrial Cytb and D-Loop sequences

Abstract: Qingshui River is located in the northern part of the eastern section of Miaoling Mountain range, which is the slope of the transition from the YunnanGuizhou Plateau to the hills of Hunan and Guangxi, and it is the upper reaches of Yuanjiang River in Dongting Lake Water System of the Yangtze River basin, and it is also the second largest river in Guizhou Province. In order to analyze the genetic diversity and population genetic structure of wild Siniperca scherzeri population in Qingshui River basin, and to provide a theoretical basis for conservation management of the wild resources, we have set up a total of ten sampling sites in the upper, middle and lower reaches of Qingshui River and collected 287 individuals of wild Siniperca scherzeri. Genetic diversity and phylogenetic relationshihs of 287 wild Siniperca scherzeri were investigated based on mitochondrial cytochrome b (Cytb) and control region (DLoop) sequences. The completed mt DNA Cytb gene sequence (1 141 bp) and partial DLoop control region sequence (840841 bp) of wild Siniperca scherzeri were PCR amplified, sequenced, and analyzed. The preliminary findings were as follows: 1) The average contents of A, T, G and C in Cytb sequences were 24.3%, 27.3%, 15.5% and 32.4%, respectively, and the corresponding contents off our bases in DLoop sequences were 34.0%, 30.1%, 15.8% and 20.1%, respectively. Meanwhile, the average content of A+T was 51.6% (Cytb) and 64.1% (DLoop) respectively, both higher than the average C+G content of 48.4% (Cytb) and 35.9% (DLoop), and the proportion of base G was the lowest, respectively, the data showed a bias against G, and the proportion of A to T in Cytb and DLoop gene sequence was a little different. In addition, 23 variation sites were detected in Cytb gene sequences, of which 16 were parsimony informative sites and 7 were singleton variable sites, no base insertions or deletions, and a base conversion/reversal ratio of 4.60. While 44 variation sites were detected in DLoop gene sequences, of which 39 were parsimony informative sites and 5 were singleton variable sites, no base insertions or deletions, 3 base deletions, no base insertions and a base conversion/reversal ratio of 10.19. 2) 25 haplotypes were defined in Cytb gene sequences, the haplotype diversity of 3 populations (UQ, MQ and LQ) ranged from 0.793±0.037 to 0.829±0.024, and the nucleotide diversity ranged from 0.0019±0.0001 to 0.0021±0.0001, the average haplotype diversity and nucleotide diversity were 0.821 ± 0.018 and 0.0020 ± 0.0001, respectively, the average number of nucleotide differences was 2.311. At the same time, 43 haplotypes were identified in DLoop gene sequences, the haplotype diversity of 3 populations (UQ, MQ and LQ) ranged from 0.884±0.031 to 0.921±0.017, and the nucleotide diversity ranged from 0.0074±0.0005 to 0.0091±0.0004, the average haplotype diversity and nucleotide diversity were 0.919±0.009 and 0.00831 ± 0.00025, respectively, the average number of nucleotide differences was 6.968. The genetic diversity of 3 populations showed a decreasing trend of UQ>MQ>LQ in DLoop gene, while Cytb gene had the highest genetic diversity in MQ, with the order of size being MQ>LQ>UQ.3) Within populations, the genetic distance decreased from 0.0092±0.0017 to 0.0074±0.0015 within UQ, MQ and LQ populations in DLoop gene, and the degree of genetic variation became progressively lower. However, Cytb gene had the highest variation in MQ, with the same degree of variation in UQ and LQ. Among populations, the greatest genetic differences were found between UQ and MQ in DLoop gene, and the smallest between MQ and LQ, while Cytb gene differed to a similar extent between the two populations of three populations. And the mean genetic distances within the population were 0.0021 and 0.0087 in DLoop and Cytb genes, respectively. Fst values among 3 populations were not significant both in Cytb and DLoop genes. The level of gene flow between UQ and LQ of Qingshui River was higher，and the individuals’exchanges were frequent. Analysis of molecular variance (AMOVA) demonstrated that variation in individuals within the population accounted for 97.54% (Cytb) and 97.32%(DLoop) of total variation, genetic differentiation among populations was not significant. 4) The results of phylogenetic analysis and haplotype evolution network showed that the haplotypes of both Cytb and DLoop genes clustered into two branches, and haplotypes of both branches distributed in the upper, middle and lower reaches of the river, there was no clear geographical pattern of distribution. And it had the closest evolutionary relationship with Siniperca scherzeri from Yangtze River (Dongting Lake water system) according to Cytb phylogenetic study. 5) Tajima’ s D and Fu’ s Fs values of wild Siniperca scherzeri were -0.9553 and showed extremely significant difference (P<0.01) in Cytb gene, and mismatch distribution analysis showed a poisson distribution, the results of neutral test and nucleotide mismatch analysis in Cytb gene showed that there had been a significant population expansion event recently, the equation estimated that the population expansion of wild Siniperca scherzeri population in Qingshui River occurred 0.176 million years ago. In contrast, the DLoop gene was consistent with the hypothesis of neutral evolution and no population expansion was detected. In summary, these findings indicated that wild Siniperca scherzeri population in Qingshui River showed no obvious genetic differentiation among populations, and had higher genetic diversity, as high haplotype diversity and low nucleotide diversity. The results can complement basic genetic diversity background of wild Siniperca scherzeri in Yangtze River basin, and will be usefully applied to scientific strategies for the protection, sustainable development and commercial utilization of germplasm resources of wild Siniperca scherzeri in Qingshui River.

Keywords: Siniperca scherzeri; genetic diversity ; Cytb; DLoop