| As an introduced species,along with the adaptation and localization of P.yessoensis in China is that the fact that lots of problems have appeared during the several decades' aquafarming,such as the low survival rate,high morbidity and the slow-growing.Is this associated to the small effective population which will have inbreeding exist during the production process? Or will it lead to it will lead to some degree of decline in the level of genetic diversity after many generations breeding? Due to the difference of the method,the number of samples and sampling scope,and there are differences between the results have been published.So it is very important to carry out comprehensive and accurate phylogenetic analysis and germplasm evaluation in the main aquaculture areas of China.First of all,the paper reviews the achievement in the culture of P.yessoensis,including growth,biological characteristics,genetic diversity,reproductive development.The problems in its artificial breeding and culture are also analyzed.It is concluded that the breeding period of the Chinese group was during March to May,and the temperature of the breeding peak is about 5.0-7.0?,which has a certain degree of change compared with Japanese group.The optimal temperature for larval growth of Chinese group is about 15?,which is similar to Japanese group.In feeding,according to preliminary studies have concluded that Chinese group mainly fed on diatoms.The growth status of Chinese colonization was also affected by the density of the breeding population.It was concluded that the optimum culture density was 10 per layer in a cylindrical cage with a diameter of 30 cm and a height of 12 cm.As for the bottom culture,the seeding rate should be determined according to the specific ecological capacity of the local waters.In the aspect of population genetics,a comprehensive analysis of existing research reports can lead to the conclusion that the genetic diversity of Chinese group was decreased compared with its native Japanese group,but there was no uniform opinion and conclusion until now.Secondly,for a comprehensive understanding of the distribution and frequency of microsatellite in P.yessoensis genome,in this study,the microsatellite sequences in P.yessoensis genome were analyzed by establishing and sequencing an RAD library.The sequences were assembled,and SSRs were detected by bioinformatics method.The total length of the DNA sequences obtained from P.yessoensis genome is 92551435 bp and 3618 contigs were detected to contain SSR sequences from all the filtered 259535 contigs.Among these loci,the trinucleotide repeats?45.87%?were the most frequently microsatellites,although the AT repeat?14.91%?was the dominant motif.The PCR products of 47 primer pairs?78.3 %?from 60 primer pairswere successfully amplified using genomic DNA from 6 samples as templates,while other 13 primer pairs?21.7%?failed to produce visible,weak or multiple PCR bands.27 polymorphic SSR markers from above 47 primer pairs were further verified using genomic DNA from 48 samples.The number of alleles?Na?per locus varied from 2 to 6.The observed heterozygosity?Ho?and expected heterozygosity?He?ranged from 0.0883 to 0.9792 and 0.2945 to 0.7454,respectively.Fourteen locus show a high polymorphism?PIC>0.5?,while elven locus show moderate polymorphism?0.5>PIC>0.25?,and two locus show a low polymorphism?PIC<0.25?.Five loci showed significant deviation from Hardy– Weinberg expectations.Cross-species amplification was successful in different degrees?Table 2?,while 20 of 27 in A.irradias and 17 of 27 in C.farreri were successfully amplified.This indicated that there are high potential for use of these loci in studies of population genetics with scallops.This study described the isolation and characterization of microsatellites from P.yessoensis using RAD-sequencing by next-generation sequencing.They will be useful for describing the genetic diversity and population structure across the distribution range of P.yessoensis.These SSR markers also showed a relatively high level of polymorphism for other related scallop species.Furthermore,in order to elucidate the changes in the genetic diversity of Chinese and Japanese groups,and to carry out the genetic diversity research about P.yessoensis in main mariculture area of China.In this study,the mitochondrial cytochrome b?Cyt b?gene sequencing techniques was used to analyze the genetic diversity and variation of six stocks of P.yessoensis?the bottom sowing cultured stock of Changdao,Haiyangdao and Zhangzidao,the natural stock of Lvshun and Japan,and the artificial selected stock of Zhangzihong?.The results were as follows: A total of 20 haplotypes were found among 120 sequences of Cyt b gene from six stocks of P.Yessoensis,however,the minimum number of haplotypes was found in “Zhangzihong” artificial breeding stock,the maximum number occurred in Japan Aomori Mutsu Bay stock,with the haplotype diversity?Hd?0.100 and 0.884,respectively.By the analysis of molecular variance?AMOVA?,the percentage of variation between the Japanese and Chinese group was 15.34%,which was significantly higher than when as one genetic pool.For Chinese group,83.41% of the genetic variations came from within stocks,and only 1.52% of the variation among stocks within the group,indicating that the genetic variation between individual of China group is higher than between stocks.Fst analysis showed that there was a moderate level of genetic variance among Japanese stock and Chinese stock(0.07455 0.17895,Fst > 0.05).The genetic distance between 6 stocks of P.yessoensis was calculated based on Tamura-Nei model,the maximum genetic distance was found between Japan Aomori Mutsu Bay stock and Haiyangdao bottom sowing cultured stock,the minimum genetic distance was found between Zhangzidao bottom sowing cultured stock and “Zhangzihong” artificial breeding stock.The UPGMA phylogenetic tree was constructed based on the genetic distance from 6 stocks of P.yessoensis,which showed that the 5 Chinese groups clustered into a genetic branch,and then together with the Japanese stock.According to the results,it could be concluded that there were obvious genetic differentiation between the scallop from China stock and Japan stock.And the genetic diversity of P.yessoensis from China stock was lower,compared with which of the Japanese stock.The results of this study would be very important and useful for making scientific strategy for protection and sustainable development and utilization of scallop germplasm resources.In order to clarify the relationship between the Chinese and the Japanese groups,in this study,we sampled from six bottom sowing cultured stocks,one nature stock and one artificial selected stock of China,and also one nature stock of Japan,a total of 251 samples.The GBS library was constructed by the next-generation-sequencing method,a large amount of SNP data was obtained by high throughput sequencing,and then the phylogenetic tree analysis,principal component analysis and population genetic structure analysis were carried out based on these SNPs.The main results are as follows: The total sequencing amount was 95.73 G,and the average raw data of each individual was 381.4M.After a rigorous filtration,a total of 95.72 G of clean data was obtained,and the average clean data for each individual was 381.34 M.Q20?93%,Q30?85%,GC distribution was normal,and the sequencing quality was high.A total of 38251 shared SNP sites were obtained after a rigorous filtration and screening.Through analysis,there was a certain degree of genetic differentiation between Chinese and Japanese groups,although the degree of differentiation between various stocks of China is not high,but there was a higher degree of genetic homogeneity between "Zhangzidao Red" artificial breeding stock and Zhangzidao 2014 sowing stock.In view of the origin of the natural population of Lvshun,this study testifies to the results of the early physical index release from the molecular level,which was that the natural seeds of Lvshun were mainly from the waters near Zhangzidao,but there was little possibilities from Changdao.The study reveals the relationship between the different stocks about P.yessoensis,which can provide a theoretical basis for the rational development and utilization of resources of P.yessoensis,and also for the breeding works. |
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