New linkage maps for the Cupressaceae species Chamaecyparis obtusa and Thujopsis dolabrata var. hondae and comparison with the linkage map of Cryptomeria japonica

ABSTRACT

Comparative mapping studies, which can determine whether the genome structure differs among genera, have yet to be conducted in Cupressaceae. This study analyzed three important forestry species in Japan: Cryptomeria japonica, Chamaecyparis obtusa, and Thujopsis dolabrata var. hondae. To date, linkage maps have only been constructed for C. japonica. We constructed the first linkage maps for C. obtusa and T. dolabrata var. hondae using double digest restriction-site associated DNA sequencing (ddRAD-Seq) data, expressed sequence tag-derived simple sequence repeat (EST-SSR) markers, and single-nucleotide polymorphism (SNP) markers designed from homologous unigenes obtained from RNA-seq data. The lengths of the linkage maps were 1,835 cM (1,981 markers) for C. obtusa and 1,833 cM (1,295 markers) for T. dolabrata var. hondae. A total of 11 distinct linkage groups were identified in these maps, corresponding to the haploid number of Cupressaceae. Using four published linkage maps for C. japonica, we then constructed a composite linkage map with 7,784 markers. Finally, the three linkage maps were compared using 207 SNP markers designed from homologous unigenes. Although most markers were mapped to the same LG despite representing different species, indicating strong synteny. The high level of interspecific and intergeneric synteny and macro-collinearity detected in Cupressaceae were similar to those of other trees. We also detected three major chromosomal rearrangements between but not within subfamilies, which may have been caused by the taxonomic distance. This is the first example of comparative mapping for Cupressaceae species.

KEYWORDS:

• Conifer
• RNA-seq
• chromosomal rearrangement
• translocation
• Cupressaceae

Acknowledgements

The authors would like to thank Yukiko Bamba and Yukiko Ito (Niigata Prefectural Forest Research Institute) for providing samples, Yoshiaki Sato (Niigata Prefectural Forest Research Institute) for artificial crossing, and Shinji Itoo for the kind advice on an artificial crossing. We also thank Nozomi Ohmiya (FFPRI) for her help in RNA extraction and Yasuyuki Komatsu (FFPRI) for his help in DNA analyses. Analysis of sequence data was conducted in part by the supercomputer of AFFRIT, MAFF, Japan.

Consent for publication

The authors give consent for the publication.

Data availability statement

The datasets used and/or analyzed in this study are available from the corresponding author up-on reasonable request.

Disclosure statement

No potential conflict of interest was reported by the authors.

Author contribution

Conceived and designed the experiments, YM, SU and AM; performed the experiments and analyzed the data, GD, SU, RS, YH, and AM; plant material preparation, HS, SH; methodology, YM, SU; funding acquisition, YM; writing – original draft, GD, YM and SU; writing – review and editing, YM, GD, SU, AM and YH. All authors have read and agreed to the published version of the manuscript.

Supplemental material

Supplemental data for this article can be accessed online at https://doi.org/10.1080/13416979.2024.2314829.

Additional information

Funding

This work was supported by KAKENHI Grant Number 18H02234 to YM and Japanese Government.