Design and application of a target capture sequencing of exons and conserved non-coding sequences for the rat

Target capture sequencing is an efficient way to directly identify causative mutations for genetic disorders. To apply this strategy to laboratory rats that exhibit various phenotypes, we developed a novel target capture probe set, TargetEC (Target capture for Exons and Conserved non-coding sequences), which can identify mutations not only in exonic regions but also in conserved non-coding sequences so that it can detect regulatory mutations. TargetEC covers 1,078,129 regions that consist of 146.8 Mb. We applied TargetEC to four rat inbred strains (WTC/Kyo, WTC-swh/Kyo, PVG/Seac, and KFRS4/Kyo) maintained in the National BioResource Project for the Rat in Japan, and successfully identified the mutations associated with the phenotypes, including the one observed in a conserved non-coding sequence. The method developed in this study can be an efficient way to identify regulatory mutations, which could not be covered by conventional exome sequencing, and will help to deepen our understanding of the relationships between regulatory mutations and the associated phenotypes.