Software Improvement And Online Platform Construction For Pooled QTL Mapping

Bulked segregant analysis(BSA)combined with the next-generation sequencing technology(abbreviated as BSA-Seq)has proven to be a very efficient approach for rapid mapping of quantitative trait loci(QTLs),which is likely to become a mainstream approach of QTL mapping soon.Recently,our group has developed a new statistical analysis method for QTL mapping using BSA-Seq,named as block regression mapping(BReM).The method can not only estimate QTL positions and confidence intervals,but also first time realizes the estimation of the heritability of an individual QTL(i.e.,the proportion of phenotypic variation explained by the QTL),providing a complete solution for QTL mapping based on BSA-Seq.Therefore,it can be expected that the method will be widely utilized.Moreever,QTL-Seq is another popular BSA-Seq approach and also applied in many species because of its simplicity.The source code of QTL-Seq software can be downloaded from web.For the above two software of BSA-Seq,we perform the following two aspects of work in this paper.1)To facilitate the use of BReM method by experimental researchers,an online platform for BReM analysis was constructed in this study using the Joomla system.Using this platform,only with simple inputting and submission of a data file containing the information of marker position,polymorphism,and depth etc.,as well as a text file with length of each chromosome,users can directly acquire all the results of BReM analysis,including various figures and tables generated during the analysis process and the final table of detailed information about the candidate QTLs mapped,which includes QTL position,confidence interval,significance level,and heritability etc..It has been tried to visualize the results as better as possible,making them more intuitive and understandable.In particular,the figures produced by the platform are generally of high quality,meeting the requirement for publication,and therefore can be used directly.2)We use two data(from rice and yeast respectively)to test QTL-Seq,and find some shortcomings of QTL-Seq software.To solve these shortcomings,we have made some improvements to the source code of QTL-Seq software.We added new function to the software for setting a custom window size and step when running QTL-Seq.Therefore,this improved function make QTL-Seq more easily applying to other species,and optimized window size can be more easily selected by testing QTL-Seq.We also have made software work efficiency is improved obviously after optimizing the source code.