Development And Application Of Software Package For Adding Genes In Manhattan Plot Of Genome-Wide Association Studies

With the development of genotyping technology,cost reduction and advanced data analysis methods,genome-wide association studies(GWAS)has become one of the main methods for genetic profiling of quantitative traits,which is widely used in the genetic analysis of quantitative traits in animals and plants and complex human diseases.Complex traits tend to be associated with multiple genetic loci,and the technique measures millions of gene loci simultaneously,ultimately looking for significant sites associated with complex traits.Due to the large number of scanning sites,the results of GWAS are often more complex.Saving analysis results in file format can be tedious,so we usually use Manhattan plots to visualize the final analysis results.However,the commonly used Manhattan plot only has the probability P result of the whole genome scan,and the target gene cannot be directly presented.In response to this problem,R was used to add known or candidate genes to the Manhattan diagram.1)The software uses the powerful mapping function of R language,firstly,use ggplot2 to draw the background scatter map of each chromosome in the Manhattan diagram,take the locus of each chromosome as a reference,make the coordinates of the X axis,and the P-Value of the site takes-log(10)as the left Y-axis data,which comes from the results of the first whole genome scan.Secondly,the double Y axis of the Manhattan plot is plotted by the method of axis mapping,and the right axis data is the LOD value in the second step.Finally,the gene is automatically added using the ggrepel package,and various details of the Manhattan map are layered.The software relies on Windows 10 and is available by installing the R package Manhattan Mark.2)Association analysis is applied to the Manhattan plot to add known and candidate gene R software.Firstly,203 inbred lines of maize 876306 SNP markers were correlated with maize plant height by 3Vmr MLM method,and 88 QTNs and 14 QEIs were detected.Secondly,around these significant loci,one known genes phy A1 and thirteen candidate genes GRMZM2G046070,GRMZM2G077621,GRMZM2G378586,GRMZM2G078077,GRMZM2G365166,GRMZM2G004590,GRMZM2G378586,GRMZM2G150098,GRMZM2G135498,GRMZM2G056424,GRMZM2G058244,GRMZM2G065194 and GRMZM2G136889;Finally,the newly developed software Manhattan Mark was used to add known and candidate genes to the Manhattan map.This software can automatically add genes to the corresponding sites of the Manhattan map,and automatically detect duplicates when a large number of genes are made,effectively avoiding redundant duplication of added genes;At the same time,the user interaction is good,and the user can set various details such as LOD threshold size,chromosome color of the Manhattan map,color and size of genes,etc.,to make the Manhattan map more beautiful.In order to reduce the storage memory,you can choose to remove points with a P-value value greater than 0.1,which has no effect on the results.More importantly,this software is not limited to the results of 3Vmr MLM,but can also draw beautiful Manhattan maps in the results analyzed by other methods.