Development Of Novel Microsatellites Markers And Population Genetics Study For Scatophagus Argus

The spotted scat?Scatophagus argus?is an economically important farmed fish species on the southeast coast of China.As a candidate for artificial breeding with a great potential for aquaculture,due to its omnivorous nature and displaying resistance to stresses.Carrying out genetic diversity research is a necessary prerequisite for the conservation and utilization of germplasm resources and a key means to improve the genetic traits of species.In this study,we analyzed distribution patterns of microsatellites and the development of polymorphic markers in Scatophagus argus aided by genome survey sequencing.Then,mitochondrial cytochrome b?Cyt b?and control region?D-Loop?sequences as well as genomic microsatellite markers were used to analyze the genetic diversity,genetic structure,and population history of nine Scatophagus argus populations.The main content and results are as follows:?1?The MIcro SAtellite?MISA?identification software was employed to mine and isolate the microsatellites loci in S.argus.A total of 390 967 microsatellites loci were identified in the genome of S.argus,with a relative abundance of 653/Mb.There are249 902 Di-to Hexa-nucleotides repeats SSR,of which Di-is the most?52.64%?.A total of 23 pairs of polymorphic markers were obtained,capillary electrophoresis of 7of them,and the genetic diversity of 30 wild individuals from Zhanjiang was detected.A total of 58 alleles were identified,per locus ranged from 4 to 11.The expected and observed heterozygosity?H_O and H_E?ranged from 0.431 to 0.859 and from 0.417 to0.861,respectively.The polymorphism information content ranged from 0.389 to 0.830.After Bonferroni correction,five loci were consistent with the Hardy-Weinberg equilibrium and showed no linkage disequilibrium;one marker belongs to the mid-frequency null allele and should be used with caution in subsequent studies;one marker belongs to the high-frequency null allele,not applicable to follow-up studies.Five of the 12 pairs of markers from the literature are polymorphic and can be used for subsequent research.These microsatellite markers can be used for studies of genetic variation and genetic population structure,as well as to support conservation efforts.?2?A total of 149 alleles were detected in 9 S.argus populations by 11 SSRs.The mean values of H_O and H_E was 0.746 and 0.812,respectively,with the highest and minimum value of H_O and H_E observed in LR?0.769?and SY?0.713?,respectively.The range of the Shannon index?I?was 1.6289-2.2940.The largest distribution of the number of private alleles and the number of alleles is TW population,0.609,and 8.705,respectively.But the BH is the least,0.128 and 7.387,respectively.AMOVA results showed that 87.65%of the variation was related to within individuals and only 3.29%belonged to between population.The mean F_ST value of 0.0663 indicates a low level of population differentiation.UPGMA cluster and structure analysis identified non-significant phylogeographic structures,ZJ,ZH,and YQ clustered into one group as well as the remaining six groups clustered into another group.The analysis of population historical dynamics showed that all populations had not experienced genetic bottleneck.?3?A total of 34,162,and 174 haplotypes were detected in the Cyt b,D-Loop,and Combine?Cyt b+D-Loop?,respectively.The highest and minimum value of haplotype diversity observed in HK?0.998?and TW?0.963?,respectively.The largest distribution of the number of nucleotide diversity is TW population,0.03808,and the SY is the least,0.00856.The TW population also has the most variable sites?182?,parsimony information sites?155?,and the average number of nucleotide differences?58.7933?,with the highest genetic diversity.Pairwise F_ST statistics suggested that TW population and the other eight populations existed a high level of differentiation.Neighbor-joining?NJ?tree and median-joining?MJ?network analysis divide S.argus into three lineages and identified non-significant phylogeographic structures.AMOVA for both markers revealed that the genetic variation occurred within populations is greater than the genetic variation occurred among populations.Neutral test and mismatch distribution suggest that the S.argus populations expansion occurred in the late Pleistocene.