Pair-wise combinations of RAPD primers for diversity analysis with reference to protein and single primer RAPD in soybean

Annals of Agrarian Science Pub Date : 2018-09-01 DOI:10.1016/j.aasci.2018.03.002

Ramavtar Sharma , Santosh Sharma , Sushil Kumar

{"title":"Pair-wise combinations of RAPD primers for diversity analysis with reference to protein and single primer RAPD in soybean","authors":"Ramavtar Sharma , Santosh Sharma , Sushil Kumar","doi":"10.1016/j.aasci.2018.03.002","DOIUrl":null,"url":null,"abstract":"<div><p>Both RAPD and protein markers were to estimate genetic diversity present in eight varieties of soybean. Of the nineteen random primers used fourteen produced 83 bands 62 being polymorphic generating polymorphism of 74.69% level. Similar level of (72.58%) polymorphism was generated by 12 pair-wise combinations of primers. Five of the paired combinations did not generate banding patterns. Two of the paired combination (OPC-5 + OPC-15) and (OPC-5 + OPC-17) produced unique banding patterns for all the eight varieties. The bands generated by paired combinations of primers were common to one of the primers in 21% cases however 79% of them were found novel and can be used to reveal additional polymorphism. The polymorphism generated by SDS-PAGE remained very less compared to RAPD analysis. The estimation of pairwise similarity coefficient using Jaccard's similarity index based on RAPD revealed approximately 70% similarity among the genotype studied that is diversity being 30% only. Average similarity shown by SDS-PAGE was much higher (81%) than RAPD based similarity estimates. The clustering based on UPGMA analysis of RAPD profiling separated all the varieties whereas SDS-PAGE grouped three varieties together at 100% similarity. Thus, it was concluded that the material though comes from diverse sources but had narrow genetic base.</p></div>","PeriodicalId":100092,"journal":{"name":"Annals of Agrarian Science","volume":"16 3","pages":"Pages 243-249"},"PeriodicalIF":0.0000,"publicationDate":"2018-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.aasci.2018.03.002","citationCount":"12","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Annals of Agrarian Science","FirstCategoryId":"1085","ListUrlMain":"https://www.sciencedirect.com/science/article/pii/S1512188717301860","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"","JCRName":"","Score":null,"Total":0}

引用次数: 12

Abstract

Both RAPD and protein markers were to estimate genetic diversity present in eight varieties of soybean. Of the nineteen random primers used fourteen produced 83 bands 62 being polymorphic generating polymorphism of 74.69% level. Similar level of (72.58%) polymorphism was generated by 12 pair-wise combinations of primers. Five of the paired combinations did not generate banding patterns. Two of the paired combination (OPC-5 + OPC-15) and (OPC-5 + OPC-17) produced unique banding patterns for all the eight varieties. The bands generated by paired combinations of primers were common to one of the primers in 21% cases however 79% of them were found novel and can be used to reveal additional polymorphism. The polymorphism generated by SDS-PAGE remained very less compared to RAPD analysis. The estimation of pairwise similarity coefficient using Jaccard's similarity index based on RAPD revealed approximately 70% similarity among the genotype studied that is diversity being 30% only. Average similarity shown by SDS-PAGE was much higher (81%) than RAPD based similarity estimates. The clustering based on UPGMA analysis of RAPD profiling separated all the varieties whereas SDS-PAGE grouped three varieties together at 100% similarity. Thus, it was concluded that the material though comes from diverse sources but had narrow genetic base.

查看原文本刊更多论文

参考大豆蛋白质和单引物RAPD进行多样性分析的RAPD引物成对组合

利用RAPD和蛋白质标记对8个大豆品种的遗传多样性进行了评价。所用的19条随机引物中，14条产生83条条带，62条为多态性，多态性水平为74.69%。引物的12对组合产生了相似的多态性水平(72.58%)。其中5个配对组合没有产生带状图案。其中两个配对组合(OPC-5 + OPC-15)和(OPC-5 + OPC-17)在所有8个品种中均产生独特的带状图案。在21%的情况下，由一对引物组合产生的条带与其中一个引物相同，但其中79%被发现是新颖的，可用于揭示额外的多态性。与RAPD分析相比，SDS-PAGE产生的多态性仍然很少。利用基于RAPD的Jaccard相似指数估计两两相似系数，发现所研究基因型的相似度约为70%，多样性仅为30%。SDS-PAGE显示的平均相似度比基于RAPD的相似度估计高得多(81%)。RAPD图谱的UPGMA聚类分离了所有品种，而SDS-PAGE聚类将三个品种聚在一起，相似度为100%。因此，该材料来源多样，但遗传基础狭窄。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

求助全文

约1分钟内获得全文求助全文

来源期刊

Annals of Agrarian Science

自引率

0.00%

发文量