| Summary: | <p>Abstract</p> <p>Background</p> <p>High-density linkage maps facilitate the mapping of target genes and the construction of partial linkage maps around target loci to develop markers for marker-assisted selection (MAS). MAS is quite challenging in conifers because of their large, complex, and poorly-characterized genomes. Our goal was to construct a high-density linkage map to facilitate the identification of markers that are tightly linked to a major recessive male-sterile gene (<it>ms1</it>) for MAS in <it>C. japonica</it>, a species that is important in Japanese afforestation but which causes serious social pollinosis problems.</p> <p>Results</p> <p>We constructed a high-density saturated genetic linkage map for <it>C. japonica </it>using expressed sequence-derived co-dominant single nucleotide polymorphism (SNP) markers, most of which were genotyped using the GoldenGate genotyping assay. A total of 1261 markers were assigned to 11 linkage groups with an observed map length of 1405.2 cM and a mean distance between two adjacent markers of 1.1 cM; the number of linkage groups matched the basic chromosome number in <it>C. japonica</it>. Using this map, we located <it>ms1 </it>on the 9<sup>th </sup>linkage group and constructed a partial linkage map around the <it>ms1 </it>locus. This enabled us to identify a marker (hrmSNP970_sf) that is closely linked to the <it>ms1 </it>gene, being separated from it by only 0.5 cM.</p> <p>Conclusions</p> <p>Using the high-density map, we located the <it>ms1 </it>gene on the 9<sup>th </sup>linkage group and constructed a partial linkage map around the <it>ms1 </it>locus. The map distance between the <it>ms1 </it>gene and the tightly linked marker was only 0.5 cM. The identification of markers that are tightly linked to the <it>ms1 </it>gene will facilitate the early selection of male-sterile trees, which should expedite <it>C. japonica </it>breeding programs aimed at alleviating pollinosis problems without harming productivity.</p>
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