Genetic Divisity For The Odontobutis Sinensis In Yangtze River And The Pearl River

1.Genetic diversity analysis and population genetic structure analysis of the Odontobutis Sinensis population in the Yangtze River and the Pearl River Basin,based on the mitochondrial Cytb gene.Mitochondrial Cyt b genes were obtained and amplified from 108 individuals within 9 areas of YD,DY,JZ,HH,YT,GL,DTH,QZ,XT and so on.After removing the sequencing errors at the ends and comparing the missing data,1127 bp were selected for genetic analysis.The results are as follows:In this study,the genetic diversity of 9 wild Odontobutis sinensis populaitons in Yangtze River and Pearl River was analyzed based on Cyt b gene.The main results were as follows:(1)The total Cyt b gene length was 1 127 bp and 29 hapotypes were obtained from 108 individuals collecting from the nine populations.The average haplotype diversity(Hd)and nucleotide(π)was 0.929 0 and 0.009 41,respectively,indicating high genetic diversity and low nucleotide diversity.(2)The FST values and k2-P distances were 0.110 6~0.998 8(P<0.01)and 0.002~0.022,respectively,showing significant differentiation among the nine populations.Moreover,most of the Nm vales between populations were lower than 1(P>0.05),and it proved limited gene exchange among populations in O.sinensis.(3)Neutrality tests and network analysis suggest population expansion existed in GL and DTH for O.sinensis.We inferred that the gene exchange direction would be from YZ River to Pear River in the population of O.sinensis.Through the above research,it provides scientific theoretical basis for protection,development and utilization of resources of O.sinensis.2.Genetic Diversity and Genetic Structure of Populations Based on EPICsIn this study,we cloned the EPICs-55305E1 gene for the analysis of genetic diversity and genetic structure.(1)Sequence analysis.In this study,1070 bp of 55305E1 gene were selected to genetic diversity analysis.Among these bases,there were 178 mutations,accounting for 16.7%,of which the singleton variable sites were 105,59% of the total variations,and the simple information locus was 63,35% of the total variations.The average content of the base was T 32.6%,C 18.4%,A 31.7%,G17.7%.A + T(64.3%)> G + C(36.1%),indicating that the mitochondria and nuclear genes in O.sinensis were both showing A-T preference.(2)Genetic diversity analysis.The total haplotype diversity of the nine populations was 0.99330 with the variation of 0.6 to 1.The nucleotide diversity was 0.01370,with the variation of 0.0035 to 0.0132.(3)Population Genetic Relationship and Genetic Structure Analysis.There were 82 haplotypes detected from the 108 individuals of 9 populations.Each population had multiple haplotypes,of which the haplotypes of DTH were the most(19),while those of GL were the least.H3 and H14 were the shared haplotypes of GL and QZ,and H13 was the shared haplotype of GL,QZ and XT,and the other haplotypes were unique to the water systems.The phylogenetic tree,constructed according to the genetic distance between populations,found that O.sinensis in the Yangtze River and the Pearl River Basin were divided into two major groups: one was YD population,and the other group consists of the rest of the 8 populations which were GL,DTH,XT,QZ,YD,JZ,HH,YT population.GL and QZ in the Pearl River Basin were clustered at first and then clustered with XT and DTH.The haplotype network structure showed that the nine populations were not clustered according to the geographical location,indicating that the O.sinensis populations were in a stage of lineage sorting.AMOVA was the best grouping method to analyze O.sinensis,that is,YD population serves as one group,and the other populations were put together as the other group.This grouping method presents the highest genetic differentiation index.(4)Detection of History Development of O.sinensis PopulationsThe value of Tajima’s D and Fu’s Fs,less than 0(P <0.05),and the haplotype-minimum mesh pattern showed the characteristics of stellate dispersal,indicating that O.sinensis in the Yangtze River and the Pearl River Basin might have experienced expansion events.3.Genetic diversity and population structure of the O.sinensis Based on microsatellite marker.In this paper,13 pairs of microsatellite primers were used to analyze the genetic diversity and genetic structure of the above nine populations.The main results are as follows:(1)Population genetic diversity.The value of NA was 6,and XT has most alleles,while the least for YD.QZ has the highest allele richness(AR)and the lowest for YD.The observed heterozygosity(Ho)of all populations was 0.347 and the expected heterozygosity(HE)was 0.601.The Ho of GL was the highest(0.471),while the Ho of DY was the lowest(0.212).The HE of GL was the highest(0.588),the lowest of XT(0.398).The inbred line FIs of these populations is in the range of 0.713-0.745,which indicates that there is some differentiation among the nine populations and the total genetic diversity of the population is high.(2)Population genetic diversity analysisThe overall genetic distance of the population is a bit large.The genetic distance of DY and YT was 0.0458,while the minimum(0.101)was distance of GL and QZ.AMOVA analysis of different populations showed,regardless of whether grouping groups by geographic distance or phylogenetic tree branching,The genetic differences among the populations were greater than the genetic differences within the population.Indicating that the main difference comes from the populations.NJ tree display that GL,QZ,XT,DTH are clustered into one class,and JZ,HH,YT,DY,YD are clustered into one kind,which shows the characteristics of clustering according to geographical location.(3)Population principal component analysisGL,QZ,XT and DTH were grouped together,while JZ,HH,YT,DY and YD were grouped together.PC1 was 34.94% and PC2 was 20.87%.Structure shows the best grouping when K = 2.(4)The bottleneck effect of the populationWe can determine whether the population experienced a bottleneck effect according to the heterozygosity.Of population,(Sign test and Wilcoxon’s test)detection model showed that GL,DY,JZ populations experienced significant bottleneck effect.