三种常用亲本分析软件效率的比较——以鹅掌楸属树种控制授粉子代亲本分析为例  

A Comparison among Three Softwares of Parentage Analysis (CERVUS, COLONY and PAPA)—A Case Study on Parentage Analysis of Control Pollination Progenies in Liriodendron

作　　者：李博[1] 潘文婷[1] 李康琴[1] 李火根[1] 

机构地区：[1]南京林业大学林木遗传与生物技术省部共建教育部重点实验室,南京210037

出　　处：《分子植物育种》2013年第2期241-248,共8页Molecular Plant Breeding

基　　金：国家自然科学基金项目(30972391;31170621);江苏省高校自然科学重大项目(10KJA220017);江苏省研究生培养创新工程(CXZZ12_0543)共同资助

摘　　要：在亲本分析中,常用基于最大似然法的软件(如CERVUS,COLONY和PAPA)进行亲本推定,但不同软件各有其特点,其分析结果与亲本推定效率有时相差较大。为比较三种常用亲本分析软件(CERVUS3.0,COLONY2.0和PAPA2.0)的效率及特点,本文以包含278个鹅掌楸潜在亲本及90个鹅掌楸已知亲本的子代群体为材料,利用13对EST-SSR位点信息,分析子代亲本并与其真实亲本进行对照,进而评价三种亲本分析软件的效率,期望为林木亲本分析软件选择提供参考。研究结果表明,13个SSR位点在实验群体中检测出的等位基因数(A)、观测杂合度(Ho)及Shannon多样性指数(I)平均值分别为5.23,0.4766和1.4636,表明该批引物多态性高,适合用于亲本分析。就亲本分析效率而言,总体上看,谱系清楚的子代远高于谱系不清的子代,单亲分析远高于双亲分析。三种软件的分析效率及特点各有差别。对于谱系不清的林下更新子代苗木,双亲分析时,三种软件的分析效率差别不大。但单亲分析时,CERVUS与COLONY软件分析效率较高,其亲本推定的准确率分别为78.87%和69.90%,高于PAPA软件的分析效率。而对于谱系清楚的控制授粉子代,双亲分析时,采用PAPA软件对异交子代亲本推定准确率为34.72%,高于CERVUS及COLONY软件;而CERVUS与COLONY软件则适合于自交子代的亲本分析,其亲本推定的准确率分别可达83.33%及81.2%,远高于PAPA软件。At present, soflwares in the basis of maximum likelihood assignment, such as CERVUS, COLONY and PAPA, were often used to analyze parentage. However, the outputs generated from different softwares were much different though applied to the same experimental population. These were mostly attributed to the different characteristics of softwares. In order to compare the power of three softwares mentioned above on parentage assigrmaent, we used 13 microsatellites to detect an experimental population of Liriodendron which includes 278 potential parents and 90 progenies whose real parents were unknown. Three softwares （CERVUS3.0, COLONY2.0, PAPA2.0） were used to assign parentage for each progeny, The power of three softwares were evaluated bychecking the assigned parentage to their real parents for each progeny. The results are as follows： the average values of number of alleles （A）, Observed heterozygosite （Ho） and Shannon diversity index （/） in this experimental population were 5.23, 0.476 6, and 1.463 6 respectively, indicating that these 13 SSR loci were high polymorphic and suitable for parentage analysis. As a whole, the power of parentage assignment for control pollination progenies was higher than that for open pollination progenies, and paternity analysis was better than parentage analysis. Each of these three soffwares had its specific characteristics. When they were applied to analyze progenies whose pedigree were not clear, no significant difference among three softwares was found when appling to parentage analysis. However, when appling to paternity analysis, the differences among three soffwares in terms of power were significant. The parentage assignment accuracy of CERVUS and COLONY were 78.87% and 69.90% respectively, much higher than that of PAPA. As for control pollination progeny whose pedigree was clear, the parentage assignment accuracy of PAPA was 34.72%, higher than other two softwares when applied to outcrossing progenies. Nevertheless, if applied to selfing progenies, the paren

关 键 词：亲本分析 CERVUS COLONY PAPA 效率 鹅掌楸属 

分 类 号：S792.21[农业科学—林木遗传育种]