Scanning RNA-Seq and RAD-Seq approach to develop SNP markers closely linked to <i>MALE STERILITY 1</i> (<i>MS1</i>) in <i>Cryptomeria japonica</i> D. Don

<p><i>Cryptomeria japonica</i> 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 <i>C. japonica</i> induces pollinosis, breeding of pollen-free <i>C. japonica</i> is desired. In this study, single nucleotide polymorphism (SNP) markers located at 1.78 and 0.58 cM to a male sterility locus (<i>MS1</i>) were identified from an analysis of RNA-Seq and RAD-Seq, respectively. SNPs closely linked to <i>MS1</i> 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 <i>MS1</i>. Linkage analysis of selected SNP markers confirmed a higher efficiency of the current method to construct a partial map around <i>MS1</i>. Allele-specific PCR primer pair for the most closely linked SNP with <i>MS1</i> was developed as a codominant marker, and visualization of the PCR products on an agarose gel enabled rapid screening of male sterile <i>C. japonica</i>. The allele-specific primers developed in this study would be useful for establishing the selection of male sterile <i>C. japonica</i>.</p>