Bulk segregation analysis mapping is a widely used approach in functional genomics, especially now that low sequencing costs make mapping-by-sequencing realistic. However, the huge data processing required is not trivial. To help in this regard, we utilized our population of maize kernel mutants to develop a new mapping-by-sequencing analysis software tool, (MSA), to identify causative genes based on the DNA and RNA level variations in mutant pools. It is designed to identify the association regions, which show linkage disequilibrium to causative mutations, and place linkage peaks on the chromosomes. The method involves the comparison of mutant and normal pools of F2 individuals, and the parents for F2s can be also used alongside the two pools. It allows simultaneous analysis of multiple mutants and multiple normal samples, which can reduce the noise.
