Genetic Diversity Of Schizothorax Biddulphi Based On SSR Markers And Mt DNA Sequences

Schizothorax biddulphi is an indigenous fish only distributed in the Tarim River system in Xinjiang.At present,the resources of the S.biddulphi need to be effectively protected.In conclusion,it is necessary to study the genetic structure,genetic relationship,historical dynamics and genetic diversity of the S.biddulphi.In this experiment,Three populations of S.biddulphimk were collected from the Qarqan River,Kizilsu River,and Aksu River,respectively.The genetic diversity analysis of S.biddulphi was performed using SSR markers and mitochondrial COII and ND4 gene sequences.These marks provide some scientific basis for the rational development and utilization of S.biddulphi genetic resources and the establishment and protection of their germplasm resources.The main results are as follows:1 Features of Genomic Microsatellite and development of SSR Markers for S.biddulphiA search of the microsatellite repeats in the S.biddulphi genome revealed a total of 743,118 microsatellite sequences in 558,993 Unigene.There are mainly microsatellite types with single nucleotide,dinucleotide,trinucleotide,tetranucleotide,pentanucleotide,and hexanucleotide repeats.Among these microsatellite sequences,the number of dinucleotide repeats is the largest,accounting for about 42.74% of the total,followed by single nucleotide repeat units(39.07%),and pentanucleotide and hexanucleotide repeat types are fewer,cccounting for 0.92% and 0.24%.Among the dinucleotide repeats,the content of AC/ TG was the largest,accounting for 30.02%.In addition,the number of repetitions of the microsatellite nucleotide repeat type was highest in single nucleotides,with an average of 55.16,followed by pentanucleotide,while trinucleotide repeats are minimal.At the same time,it was found that as the number of repetitions increased,the abundance of this type of microsatellite showed a decreasing trend.In this study,genomic information was used to develop microsatellite markers in S.biddulphi,and a total of 288 pairs of primers were designed.Finally,20 pairs of primers with high polymorphism weresuccessfully screened.A total of 204 alleles were detected in eight S.biddulphi,with an average of 10.2alleles detected per primer pair.The number of effective alleles at each locus is distributed between 1.012 and 1.365,and the average number of effective alleles is 1.150.The expected heterozygosity is mainly distributed between 0.012 and 0.223,and the average expected heterozygosity is 0.104.And the average Shannon index for each locus is 0.179.It shows that 20 pairs of microsatellite locus have certain polymorphism,which meets the research requirements of population genetics.2 The study of population genetic diversity based on SSR markers for S.biddulphiThe genetic diversity of three populations of S.biddulphi was analyzed using SSR molecular markers.The results showed that 380 alleles were amplified from the three populations,and the Qarqan River(CEC)population had the highest Nei’s genetic diversity and Shannon index,which were 0.1136 and0.1936,respectively.And the Kyzylsu River(KZL)population has the highest number of effective alleles.The genetic differentiation coefficient(Fst)and genetic distance(D)between the three populations showed that a large genetic differentiation occurred between the CEC population and the other two populations,and gene flow(Nm)and genetic similarity(GS)were small.However,The Nm and GS were large between Aksu River(AKS)and KZL population.The UPGMA method was used to perform cluster analysis on individuals and groups in the S.biddulphi,and the results showed that the three groups formed two main branches.The AKS and the KZL populations are grouped together,and the CEC population is grouped separately.The results of Structure analysis further confirmed the existence of two gene banks in the three populations.That is to say,the genetic composition of the CEC population and the genetic composition of the other two populations.3 The study of population genetic diversity based on mitochondrial COII and ND4 gene sequences of S.biddulphiThe genetic diversity of three populations of S.biddulphi was analyzed using mitochondrial COII and ND4 gene sequences.The results showed that both the mitochondrial COII and ND4 gene sequences of S.biddulphi showed obvious base bias,and showed that high A + T content may also be a common phenomenon in the base composition of the mitochondrial COII and ND4 genes.And based on the genetic diversity of the two mitochondrial molecular markers,S.biddulphi belongs to high haplotypepolymorphism(Hd)and high nucleotide polymorphism(π)(Hd> 0.5,π> 0.005).It is speculated that secondary communication occurred between differently differentiation lineages of S.biddulphi.A large genetic differentiation occurred between the CEC population and the other two populations,and the D between the populations reached the level of subspecies differentiation(0.02 <D <0.2).The results of AMOVA analysis showed that the genetic variation among the populations of S.biddulphi was much larger than the genetic variation within the population,and the genetic distance NJ clustering tree showed that the CEC population was independent of the other two populations and gather alone.At the same time,the bayesian tree(BI),maximum likelihood tree(ML),and maximum parsimony tree(MP)also showed that three populations formed two groups,one group was mainly composed of the CEC population and the other was mainly composed of KZL and AKS population.The above results confirm that the S.biddulphi has formed two distinctly differentiated geographical populations.Therefore,it is suggested that the CEC population was regarded as a subspecies of S.biddulphi.