Abstract:Abstract 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 multi-peak 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.
[1]郭瑞星, 刘小红, 荣廷昭, 等.植物标记的发展及其在遗传育种中的应用[J].玉米科学, 2005, 13(2):8-11
[2]王凤格, 杨扬, 易红梅, 等.中国玉米审定品种标准指纹库的构建[J].中国农业科学, 2017, 50(1):1-14
[3]王凤格, 易红梅, 赵久然, 等.毛细管电泳荧光检测中的异常电泳类型及原因分析[J].分子植物育种, 2007, 5(6):890-894
[4]王凤格, 易红梅, 赵久然, 等.玉米品种鉴定技术规程 SSR标记法[S]., 2014, :-
[5]Antonella P, Di G, Maria M, et al.A Set of Microsatellite Markers with Long Core Repeat Optimized for Grape Genotyping[J].BMC Plant Biology, 2008, 8(1):127-
[6]Binladen J, Gilbert M T, Campos P F, et al.Tailed Sequencing Primers Improve Sequencing Quality of PCR Products[J].Biotechniques, 2007, 42(2):174-
[7]Buel E, Schwartz M B, Lafountain M J.Capillary Electrophoresis STR Analysis Comparison to Gel-based Systems[J].Journal of Forensic Sciences, 1998, 43(1):164-170
[8]Chambers G, Macavoy E.Microsatellites: Consensus and Controversy[J].Comp Biochem Physiol B Biochem Mol Biol, 2000, 126(4):455-476
[9]Curriefraser E, Shah P, True S.Data Analysis Using GeneMapper? V41: Comparing the Newest Generation of GeneMapper Software to Legacy Genescan? and Genotyper? Software[J].Journal of Biomolecular Techniques, 2010, 21(3 Suppl):S31-
[10]Flores-Rentería L, Krohn A.Scoring Microsatellite Loci[J].Methods in Molecular Biology, 2013, 1006:319-336
[11]Flores-Rentería L, Whipple A.A New Approach to Improve the Scoring of Mononucleotide Microsatellite Loci[J].American Journal of Botany, 2011, 98(3):51-53
[12]Ghosh S, Karanjawala Z, Hauser E, et al.Methods for Precise Sizing,Automated Binning of Alleles,and Reduction of Error Rates in Large-Scale Genotyping Using Fluorescently Labeled Dinucleotide Markers[J].Genome Research, 1997, 7(2):165-178
[13]Guichoux E, Lagache L, Wagner S, et al.Current Trends in Microsatellite Genotyping[J].Molecular Ecology Resources, 2011, 11(4):591-611
[14]Hill C R, Butler J M, Vallone P M.A 26plex Autosomal STR Assay to Aid Human Identity Testing[J].Journal of Forensic Sciences, 2009, 54(5):1008-1015
[15]Holland M M, Parson W.GeneMarker? HID: A Reliable Software Tool for the Analysis of Forensic STR Data[J].Journal of Forensic Sciences, 2011, 56(1):29-35
[16]Li L, Fang Z, Zhou J, et al.An Accurate and Efficient Method for Large-Scale SSR Genotyping and Applications[J].Nucleic Acids Research, 2017, 45(10):e88-
[17]Li Y, Korol A, Fahima T, et al.Microsatellites: Genomic Distribution,Putative Functions and Mutational Mechanisms a Review[J].Molecular Ecology, 2002, 11(12):2453-
[18]Olejniczak M, Krzyzosiak W J.Genotyping of Simple Sequence Repeats--Factors Implicated in Shadow Band Generation Revisited[J].Electrophoresis, 2006, 27(19):3724-3734
[19]Rajwantk K, Manojk R, Sanjay K, et al.Microsatellite Markers: An Overview of the Recent Progress in Plants[J].Euphytica, 2011, 177(3):309-334
[20]Schl?tterer C.The Evolution of Molecular Markers-Just a Matter of Fashion[J].Nature Reviews Genetics, 2004, 5(1):63-
[21]Schumm J W, Gutierrez-Mateo C, Tan E, et al.A 27-Locus STR Assay to Meet All United States and European Law Enforcement Agency Standards,[J].Journal of Forensic Sciences, 2013, 58(6):1584-1592
[22]Sun X, Liu Y, Lutterbaugh J, et al.Detection of Mononucleotide Repeat Sequence Alterations in a Large Background of Normal DNA for Screening High-Frequency Microsatellite Instability Cancers[J].Clinical Cancer Research An Official Journal of the American Association for Cancer Research, 2006, 12(2):454-459
[23]Thompson R, Zoppis S, Mccord B.An Overview of DNA Typing Methods for Human Identification Past, Present, and Future[J][J].Methods in Molecular Biology, 2012, 830:3-16
[24]Vieira M, Santini L, Diniz A, et al.Microsatellite Markers: What they Mean and Why they are so Useful[J].Genetics & Molecular Biology, 2016, 39(3):312-328
[25]Wheeler G, Dorman H, Buchanan A, et al.A Review of the Prevalence,Utility,and Caveats of Using Chloroplast Simple Sequence Repeats for Studies of Plant Biology[J].Applications in Plant Sciences, 2014, 2(12):---
[26]Willems T, Gymrek M, Highnam G, et al.The Landscape of Human STR Variation[J].Genome Research, 2014, 24(11):1894-1904
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