One-year-old lignified hardwood was harvested from 130 backcross（BC₁）strains for hardwood cutting, and 1 672 stecklings were achieved the next year. Nine rooting-related growth traits, i.e. rooting rate, number of adventitious roots, root length (the longest root length, the second root length, the third root length and average root length of the first three roots), the diameter of the largest root, shoot length and shoot diameter of BC₁ progenies were measured. The variation law, genetic variation coefficient and the correlations among the growth traits were analyzed. Besides, the rooting ability of the 117 lines was classified according to the subordinate function values. QTL (quantitative trait loci) analysis was conducted based on the high-density genetic map of (T. distichum × T. mucronatum) ×T. mucronatum using the rQTL method. Finally, to obtain the information of candidate genes in the main QTL interval, the 2 × 100 bp sequence information of each specific-locus amplified fragment (SLAF) marker within the major QTLs was blasted with transcriptome database.

Except for the shoot diameter, the variation of the other eight phenotypic indices in BC₁ population basically conformed to the normal distribution. All the 9 growth traits were widely separated. The variation range of genetic variation coefficient was 31.14%?63.67%. The variation coefficient of shoot length was the largest, followed by the rooting rate (54.61%), and the variation range of rooting rate among individuals was 3%?73%. A significant positive correlation was found between two of the diameters of the largest root, the longest root length, the second root length, the third root length, the average root length of the first three roots, the shoot diameter and the shoot length, that is, there was a significant correlation between the radial and longitudinal growth traits of the adventitious roots and shoots. However, there was no significant correlation between rooting rate and number of the adventitious roots with other growth traits. The 117 BC₁ lines were divided into 4 groups based on the cluster result of subordinate function values. Forty seven lines were of low rooting ability type, 33 lines were of relatively low rooting ability type, 19 lines were of relatively high rooting ability type and 18 lines were of high rooting ability type. Seven major QTLs with logarithm of odds (LOD) values ≥2 located on 6 linkage groups (LG3, LG4, LG8, LG9, LG10 and LG11) were identified for the 9 growth traits, except for the diameter of the largest root and shoot diameter, and 102 SLAF markers were included. The longest root length, the second root length, the third root length and the average root length of the first three roots shared similar LOD profiles. The confidence interval of the 7 major QTLs ranged from 0 to 2.784 cM, the LOD ranged from 2.01 to 4.51, and the phenotypic variation explained (PVE) ranged from 4.24% to 12.78%. For the PVE of single QTL, the order was q3-1 (12.78%)>q10-1 (12.05%)>q4-1 (8.72%)>q9-1 (6.91%)>q11-1 (6.68%)>q3-1 (5.07%)>q8-1 (4.53%). The highest values were associated with root length and rooting rate, both of which were above 12%. Unanimously, for the cumulative PVE of total QTLs, QTLs of root length were the highest with QTLs (q3-1, q8-1 and q9-1) that totally explained 24.22% of phenotypic variation. The second was rooting rate, with two major QTLs (q3-2 and q10-1) that totally explained 17.12% of phenotypic variation. Thus, there were several strong QTLs controlling a large proportion of the genetic variation of rooting rate and root length in Taxodium. Only one QTL (q4-1) was located for number of the adventitious roots, and the PVE was 8.72%. One QTL (q11-1) was located for shoot diameter with 6.68% PVE value. Only q4-1 had a negative additive effect, and all the other six QTLs had positive additive effects. Among the 102 SLAF markers within QTLs, 25 had a high match with unigenes in transcriptome, among which encoding Ty1-copia long terminal repeat, ubiquitin binding enzyme, leucine-rich repeat extensin and GDSL lipase genes were identified, all of which participate in the root development of plants.

The genetic variations of rooting rate and adventitious root length were both significant in the BC₁ population, besides, they were both related to several strong QTLs. Thus, it is of high potential for the application of molecular marker assisted breeding in the selection and improvement of these two traits in T. ‘Zhongshanshan’.