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Title: Fragman: an R package for fragment analysis

Author
item COVARRUBIAS-PAZARAN, GIOVANNY - University Of Wisconsin
item DIAZ-GARCIA, LUIS - University Of Wisconsin
item SCHLAUTMAN, BRANDON - University Of Wisconsin
item SALAZAR, WALTER - University Of Wisconsin
item Zalapa, Juan

Submitted to: BioMed Central (BMC) Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/7/2016
Publication Date: 4/21/2016
Publication URL: http://handle.nal.usda.gov/10113/62385
Citation: Covarrubias-Pazaran, G., Diaz-Garcia, L., Schlautman, B., Salazar, W., Zalapa, J. 2016. Fragman: an R package for fragment analysis. BioMed Central (BMC) Genetics. 17(1):62. doi: 10.1186/s12863-016-0365-6.

Interpretive Summary: Polymerase chain reaction (PCR)-based genetic markers such as microsatellite or simple sequence repeat (SSR), amplified fragment length polymorphism (AFLP), and single nucleotide polymorphism (SNP) markers have become essential in genetic research. Traditionally, fragment analysis has been the crucial first step for genetic research such as mutation detection, linkage and QTL mapping, genetic diversity and other genetic applications using molecular markers. During fragment analysis, fluorescently-labeled PCR amplified DNA fragments, which have been denatured by a chemical reagent (i.e., formamide), are injected along with an appropriate size standard into capillaries for electrophoresis size separation. Essentially, a high voltage charge applied to the PCR fragments promotes their migration along the capillaries from cathode to anode, where smaller fragments migrate faster than larger fragments. Here, we present a new freely available and platform independent R package, Fragman, for performing fragment analysis. Fragman accurately and automatically scores DNA fragment lengths in diversity panels and biparental populations and transforms the observed lengths into formats required for further genetic analysis in other software such as GenAlEx, JoinMap and OneMap. Fragman was compared with other fragment analysis software, and we obtained similar genotyping results, but with superior automation, graphical and throughput scoring capabilities.

Technical Abstract: Determination of microsatellite lengths or other DNA fragment types is an important initial component of many genetic studies such as mutation detection, linkage and QTL mapping, genetic diversity, pedigree analysis, and detection of heterozygosity. A handful of commercial and freely available software programs exist for fragment analysis; however, most of them are platform dependent and lack high-throughput applicability. We present the R package Fragman to serve as a freely available and platform independent resource for automatic scoring of DNA fragment lengths diversity panels and biparental populations. The program analyzes fragment lengths in Applied Biosystems® (ABI) FSA files either manually or automatically by providing panels or bins. The package contains additional tools for converting the allele calls to GenAlEx, JoinMap® and OneMap software formats mainly used for genetic diversity and generating linkage maps in plant and animal populations. Easy plotting functions and multiplexing friendly capabilities are some of the strengths of this R package. Fragment analysis using a unique set of genotypes based on microsatellite markers is used to highlight the capabilities of Fragman. Fragman is a valuable new tool for genetic analysis. The package produces equivalent results to other popular software (e.g., GeneMarker®) for fragment analysis while possessing unique advantages and the possibility of automation for high-throughput experiments by exploiting the power of R.