Genetic Diversity And Population Structure Of The Oriental River Prawn(Macrobrachium Nipponense) In China

Macrobrachium nipponense is a commercially important fishery species in China,and distributed largely over the East Asian regions including China,Japan,Korea,Vietnam and Myanmar.It has very high economic efficiency and the annual freshwater aquaculture production of this species is estimated to more than 270,000 tonnes and annual output valued about 20 billion Yuan(RMB).Therefore,it is of great significance to study the genetic diversity and population structure of M.nipponense for the protection,development and utilization of the germplasm resources.The study of genetic variation(polymorphism)is very inevitable in all living organisms this is because of mutation caused by normal cellular interaction with the environment.Polymorphism enhances living organisms to adapt with the environment changing and it is necessary for the survival of the species.Evolutionary forces such as genetic variation,genetic drift and selection occurs between individuals leading to differentiation at the level of higher order of taxonomic groups,population and even within specie.Genetic molecular markers are the powerful tools used to detect polymorphism between population,individuals or species.There are numbers of common molecular markers that are used in aquaculture,such as RAPD,AFLP and S SR.Mitochondrial DNA(mtDNA)D-loop sequence is widely used in population genetic analysis.Mitochondrial DNA shows more divergence than nuclear DNA.Additionally,the mtDNA has faster rate of mutation due to lack of repair mechanism during replication.Moreover,mtDNA is characterized by small effective population size due to maternal inheritance of the haploid mitochondrial genome.Control regions of mtDNA are the rapidly evolving regions.Non-coding parts like the D-loop region shows elevated levels of variation compared to coding sequences such as the cytochrome b gene.In this study,mitochondrial DNA(D-Loop)marker was used to systematically analyze the genetic diversity and population structure of 8 M.nipponense populations from different latitudes from south to north in China.The collected populations include:Songhua River population(SHJ)in Fu Yuan city,Yellow River population(HH)in Ji Yuan city,Yangtze River population(YZ)in Wuhan city,Zhujiang River population(ZJ)in Guangzhou city,Weishan Lake(WSH)population in Weishan county,Taihu Lake(TH)population in Wuxi city,Bosten Lake(BH)population in Bohu county and Wanquan River(WQH)population in Qionghai city.Mitochondrial D-loop genes in 168 samples from 8 populations were analyzed.The total DNA of each individual was extracted,and mitochondrial DNA D-loop gene fragment were amplified and the products were sequenced.A total of 144 samples were successfully sequenced.An 1130 bp sequences were used for further analysis after comparison and manual proofreading.Genetic diversity of the oriental river prawn(M nipponense)population from the selected sites in China.The results obtained from this study indicated that in the 1130-bp D-loop region,239 sites were variant,contributing to 73 haplotypes.The results exhibited a higher content of A+T(79.04%)than C+G(20.95%)this make a confirmation that the D-loop is higher in A+T region than in C+G region of the mitochondrial genome.The population haplotype diversity(h)of the population was ranked as follows:WQH(0.9810)>YZ(0.9571)>WSH(0.9429)>ZJ(0.8901)>SHJ(0.8791)>HH(0.8693)>TH(0.8667)>BH(0.3684);the nucleotide diversity(π)was ranked as:WQH(0.0607)>YZ(0.0299)>SHJ(0.0236)>WSH(0.0221)>TH(0.0132)>ZJ(0.0131)>HH(0.0118)>BH(0.0011).The results indicated that the genetic diversity of BH population was very low,and the genetic diversity of the other 7 populations was very high,especially the diversity of WQH population was the highest.Additionally,the genetic distances ranged from 0 to 0.06 within the populations and from 0.014 to 0.102 between the populations.Genetic differentiation index(FST)value between two populations showed that there was no significant differentiation between WSH group and TH,HH and ZJ populations(P>0.05).The FST values in other pair populations reached extremely significant level(P<0.01).The gene flow(Nm)results proved that gene exchange between WSH and TH(11.057),HH(7.226)and ZJ(6.255)were abundant.Phylogenetic analysis and population structure of the oriental river prawn(Macrobrachium nipponense)from the selected sites in China.Studying on micro evolutionary process that generates population genetic structure of aquatic organism is very important for improving our understanding of the mechanisms of their adaptive divergence and speciation.The phylogeny and population structure of M.were analyzed in this study.The maximum likelihood(ML)phylogenetic tree indicated that a distinct distribution of phylogenetic structure existed among the analyzed haplotypes.Seventy-three haplotypes were divided into two different branches(Clades),each with different small branches.Only the haplotypes of BH population were clustered together,and the haplotypes of other populations were dispersed in different lineages,which indicated that BH population had a low genetic diversity,but a high diversity was observed in other populations.Network results were consistent with phylogenetic tree results.The analysis of mismatch distribution showed that all 8 populations presented multimodal distribution.Fu’s Fs test and Tajima’s D tests were applied to find out the population expansion.All the 8 populations showed non-significant negative values and we supposed that M.nipponense population may not have experienced population expansion.This study systematically investigated the genetic diversity and genetic structure of M.nipponense in China from south to north.The results can provide a strong basis for the protection and development of M nipponense germplasm resources.