A SIMPLE pipeline for mapping point mutations

Abstract

A forward genetic screen is one of the best methods for revealing the regulatory functions of genes. In plants, this technique is highly efficient since it is relatively easy to grow and screen the phenotypes of hundreds or thousands of individuals. The cost-efficiency and ease of data production afforded by next-generation sequencing techniques have created new opportunities for mapping induced mutations. The principles of genetic mapping remain the same. However, the details have changed, which allows for rapid mapping of causal mutations. Current mapping tools are often not user-friendly and complicated or require extensive preparation steps. To simplify the process of mapping new mutations, we developed a pipeline that takes next generation sequencing fastq files as input, calls on several well-established and freely available genome-analysis tools, and outputs the most likely causal DNA change(s). The pipeline has been validated in Arabidopsis and can be readily applied to other species.