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Background  ‘Zhongshanshan’ is the general designation for the superior interspecific hybrid clones of  Taxodium  species, which is widely grown for economic and ecological purposes in southern China. Growth is the priority objective in ‘Zhongshanshan’ tree improvement. A high-density linkage map is vital to efficiently identify key quantitative trait loci (QTLs) that affect growth.    Results  In total, 403.16 Gb of data, containing 2016,336 paired-end reads, was obtained after preprocessing. The average sequencing depth was 28.49 in  T. distichum  var.  distichum , 25.18 in  T. mucronatum , and 11.12 in each progeny. In total, 524,662 high-quality SLAFs were detected, of which 249,619 were polymorphic, and 6166 of the polymorphic markers met the requirements for use in constructing a genetic map. The final map harbored 6156 SLAF markers on 11 linkage groups, and was 1137.86 cM in length, with an average distance of 0.18 cM between adjacent markers. Separate QTL analyses of traits in different years by CIM detected 7 QTLs. While combining multiple-year data, 13 QTLs were detected by ICIM. 5 QTLs were repeatedly detected by the two methods, and among them, 3 significant QTLs ( q6–2 ,  q4–2  and  q2–1 ) were detected in at least two traits. Bioinformatic analysis discoveried a gene annotated as a leucine-rich repeat receptor-like kinase gene within  q4–2 .    Conclusions  This map is the most saturated one constructed in a Taxodiaceae species to date, and would provide useful information for future comparative mapping, genome assembly, and marker-assisted selection.    Electronic supplementary material  The online version of this article (10.1186/s12870-018-1493-0) contains supplementary material, which is available to authorized users.

bmc plant biology

High-density genetic map construction and quantitative trait loci identification for growth traits in (Taxodium distichum var. distichum × T. mucronatum) × T. mucronatum