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

breeding science

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