Scanning RNA-Seq and RAD-Seq approach to develop SNP markers closely linked to () in D. Don.

is a major forestry tree species in Japan. Male sterility of the species is caused by a recessive gene, which shows dysfunction of pollen development and results in no dispersed pollen. Because the pollen of induces pollinosis, breeding of pollen-free is desired. In this study, single nucleotide polymorphism (SNP) markers located at 1.78 and 0.58 cM to a male sterility locus () were identified from an analysis of RNA-Seq and RAD-Seq, respectively. SNPs closely linked to were first scanned by a method similar to MutMap, where a type of index was calculated to measure the strength of the linkage between a marker sequence and . Linkage analysis of selected SNP markers confirmed a higher efficiency of the current method to construct a partial map around . Allele-specific PCR primer pair for the most closely linked SNP with was developed as a codominant marker, and visualization of the PCR products on an agarose gel enabled rapid screening of male sterile . The allele-specific primers developed in this study would be useful for establishing the selection of male sterile .