Open Access Research article

The construction of a high-density linkage map for identifying SNP markers that are tightly linked to a nuclear-recessive major gene for male sterility in Cryptomeria japonica D. Don

Yoshinari Moriguchi1, Tokuko Ujino-Ihara1, Kentaro Uchiyama1, Norihiro Futamura2, Maki Saito3, Saneyoshi Ueno1, Asako Matsumoto1, Naoki Tani4, Hideaki Taira5, Kenji Shinohara2 and Yoshihiko Tsumura1*

Author affiliations

1 Department of Forest Genetics, Forestry and Forest Products Research Institute, Tsukuba, Ibaraki 305-8687, Japan

2 Department of Molecular and Cell Biology, Forestry and Forest Products Research Institute, Tsukuba, Ibaraki 305-8687, Japan

3 Toyama Prefectural Agricultural Forestry and Fishieries Research Center, Forestry Research Institute, Yoshimine 3, Tateyama-cho, Nakashinkawagun, Toyama 930-1362, Japan

4 Forestry Division, Japan International Research Center for Agricultural Sciences, Ohwashi, Tsukuba, Ibaraki 305-8686, Japan

5 Graduate School of Science and Technology, Niigata University, Igarashi 2-nocho, Niigata 950-2101, Japan

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Citation and License

BMC Genomics 2012, 13:95  doi:10.1186/1471-2164-13-95

Published: 16 March 2012

Abstract

Background

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 (ms1) for MAS in C. japonica, a species that is important in Japanese afforestation but which causes serious social pollinosis problems.

Results

We constructed a high-density saturated genetic linkage map for C. japonica 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 C. japonica. Using this map, we located ms1 on the 9th linkage group and constructed a partial linkage map around the ms1 locus. This enabled us to identify a marker (hrmSNP970_sf) that is closely linked to the ms1 gene, being separated from it by only 0.5 cM.

Conclusions

Using the high-density map, we located the ms1 gene on the 9th linkage group and constructed a partial linkage map around the ms1 locus. The map distance between the ms1 gene and the tightly linked marker was only 0.5 cM. The identification of markers that are tightly linked to the ms1 gene will facilitate the early selection of male-sterile trees, which should expedite C. japonica breeding programs aimed at alleviating pollinosis problems without harming productivity.