基于微卫星标记的地理群体仿刺参遗传结构判别分析模型的建立

通过主成因判别分析法(discriminant analysis of principal component,DAPC)建立仿刺参个体水平地理亚群体来源的判别模型。实验运用了20个微卫星引物,对俄罗斯海参崴(RS)和中国大连两个亚群(CN1、CN2)3个仿刺参地理群体进行了产物扩增和标记分型,获得3个地理群体分子标记表型数据。开创性地运用主成因分析和判别分析法建立判别模型,以研究不同群体仿刺参个体水平上遗传背景及其群体来源。结果显示,运用20对微卫星引物在仿刺参不同地理群体中稳定扩增的136个等位基因位点数据建立的判别模型可以准确判别刺参个体的群体来源。用75%的原有数据集建立模型,剩余的25%数据对模型的准确度进行验证,3个群体时模型准确率大于80%,2个群体时模型准确性超过90%。传统的遗传多样性和遗传结构分析显示,刺参的3个地理群体间存在中度的遗传分化,且遗传距离较近(D1=0.18,D2=0.159)。传统分析方法和新方法结果良好的一致性表明,利用DAPC和微卫星等位基因信息建立的刺参地理群体判别模型,可以很好地用于未知遗传背景刺参种质的来源鉴别。

Linear discriminant model construction based on microsatellite alleles for geographic distant populations of sea cucumber(Apostichopus japonicus)

A Discriminant Analysis of Principal Components(DAPC)method was adopted to construct a germplasm resource prediction model at individual level,for the sea cucumber Apostichopus japonicus.One hundred and thirty six alleles generated by twenty microsatellite markers were used as the raw data input.Three populations were sampled from Vladivostok,Russia(RS,131.55 E,43.08 N)and Dalian,China(CN1,CN2).Principal Component Analysis(PCA)and Discriminant Analysis(DA)were carried out sequentially.Linear Discriminant functions were constructed with the two China subpopulations as one overall CN population and two separated populations respectively.The results showed that with 75% individuals as training set and the remaining 25% as test set,the accuracy of constructed model reached up to about 80% for the three-pop model and over 90% for the two-pop model.Conventional genetic diversity and genetic structure analysis showed moderate genetic differentiations among the three geographic populations of sea cucumber,and relatively close genetic distances(D₁=0.18,D₂=0.159).Nice accordance of results of conventional analysis and our novel analysis indicated that the current method can be practically well applied on prediction and discrimination on germplasm resource at individual level.To our knowledge,this is the first application of DAPC with molecule marker information to genetic study.The novel method built in the current study can be well applied to the practical breeding project in future.