适于二碱基重复类型SSR引物指纹分析的连续多峰算法  

Continuous Multi-peak Algorithm Fitting for Fingerprint Analysis of SSR Primers with Dinucleotide Repeat Sequences

作　　者：王凤格[1] 李欣 易红梅[1] 江彬 任洁[1] 王璐[1] 霍永学 王蕊[1] 葛建镕[1] 杨杨 赵久然[1] WANG Feng-Ge;LI Xin;YI Hong-Mei;JIANG Bin;REN Jie;WANG Lu;HUO Yong-Xue;WANG Rui;GE Jian-Rong;YANG Yang;ZHAO Jiu-Ran(Maize Research Center, Beijing Academy of Agriculture ＆ Forestry Sciences, Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing 100097, China;Beijing TodaySoft Inc., Beijing 100083, China)

机构地区：[1]北京市农林科学院玉米研究中心、玉米DNA指纹及分子育种北京市重点实验室,北京100097 [2]北京华生恒业科技有限公司,北京100083

出　　处：《农业生物技术学报》2018年第6期1004-1013,共10页Journal of Agricultural Biotechnology

基　　金：国家重点研发计划(No.2017YFD0102001); 国家科技支撑计划(No.2015BAD02B02)

摘　　要：二碱基重复类型的SSR引物容易出现连续多峰的峰型,对指纹的正确采集造成影响。为提高此类引物指纹分析的准确性和自动化水平,本研究进行了连续多峰指纹采集算法的开发,并测试连续多峰算法与邻峰过滤、N+1峰识别、高低峰过滤和二倍体过滤等其他峰处理算法的相互作用。结果表明,连续多峰算法提高了对二碱基重复类型SSR引物的指纹读取准确性和分析效率,峰的识别和定位更加准确,峰高估值更加真实反映引物扩增情况,连续多峰峰错误识别率由50%以上降低到1%以内,识别精度由2~4 bp提高到1 bp以内,整体分析时间缩短了30%以上;通过调整参数等方式,保证了连续多峰算法与其他峰处理算法的相互协调。连续多峰算法解决了连续多峰的识别、定位及峰高估计的问题,改善了二碱基重复类型的SSR引物的指纹采集效果,消除了基因组上多态性最高、应用最广泛的二碱基重复类型SSR引物的应用限制,为SSR引物在实践中更好的应用提供了重要技术支撑。SSR primers with dinucleotide repeat sequences are prone to continuous multi-peak,which influences the accurate collection of fingerprints.In order to improve the accuracy and automation of fingerprint analysis of such primers,an algorithm for the collection of fingerprints with continuous multi-peak was developed,and interactions between the continuous multi-peak algorithm and algorithms for other peaks including adjacent peak filtration,N＋1 peak recognition,high-low peak filtration and diploid filtration were tested.Results demonstrated that the continuous multi-peak algorithm improved the accuracy and efficiency of fingerprint reading for SSR primers with dinucleotide repeat sequences,increased the accuracy of peak identification and location,and facilitated the estimation of peak height to truly reflect primer amplification.The error recognition probability of the continuous multi-peak peak was reduced from 50% to less than 1%,the recognition accuracy was increased from 2~4 bp to less than 1 bp,and the overall analysis time was shortened by more than 30%.By adjusting parameters,the intercoordination between the continuous multipeak algorithm and algorithms for other peaks was guaranteed.The continuous multi-peak algorithm solves the identification and location of continuous multi-peak and the estimation of peak height,improves the efficacy of fingerprint collection of SSR primers with dinucleotide repeat sequences,eliminates the restriction in the application of SSR primers with dinucleotide repeat sequences that have the highest polymorphism in genomes and the most widely application,and provides important technical support for the better application of SSR primers in practice.

关 键 词：SSR 二碱基重复 连续多峰 指纹分析 算法开发 

分 类 号：S18[农业科学—农业基础科学] Q75[生物学—分子生物学]