In recent years, some new Qi-Nan clones of Aquilaria sinensis, which have the characteristics of easily induced and high-quality agarwood, have been selected and propagated by grafting seedlings. To date, research on the grafting of Qi-Nan seedlings is limited. In this study, the effects of grafting on physiological characteristics and endophytic fungi of seedlings within a short period after grafting were studied by means of histochemical observations, physiological index determinations and Illumina sequencing. The results showed that the grafting healing time of ordinary A. sinensis was at least 10 days shorter than that of Qi-Nan, according to the degree of lignification of callus, and the tissue basis for the healing was the interxylary phloem. The MDA content of Qi-Nan peaked earlier than that of ordinary A. sinensis. The contents of JA and ABA peaked earlier in ordinary A. sinensis, and the SA content was significantly higher than that of Qi-Nan at 20–40 days; on average, it was 17.33% higher than that of Qi-Nan. A total of 5 phyla, 28 classes, 84 orders, 197 families, 489 genera and 842 species of endophytic fungi were identified before and after grafting. After grafting, the abundance and diversity of endophytic fungi in ordinary A. sinensis and Qi-Nan decreased, and the endophytic fungi were significantly different before and after grafting. In ordinary A. sinensis, before grafting, Dothideomycetes was the dominant class, and after grafting, Sordariomycetes was the dominant class. The dominant class of Qi-Nan before and after grafting was Dothideomycetes. The dominant genus of ordinary A. sinensis before grafting was Devriesia, and after grafting, it was Fusarium; that of Qi-Nan before grafting was Hyweljonesia and after grafting was Arthopyrenia. Functional genes of the endophytic fungi were mostly related to carbohydrate metabolism and energy metabolism, which may be the reason why endophytic fungi promote agarwood formation in Aquilaria trees. The findings suggest that the healing of the grafting interface in A. sinensis seedlings was the result of multiple factors, and endophytic fungi of Qi-Nan scion changed after grafting.

In recent years, some new “Qi-Nan” clones of Aquilaria sinensis with the characteristics of easy induction and high-quality agarwood have been obtained, through the cultivation and propagation of grafted seedlings. These clones are used for the intensive production of high-quality agarwood. The speed of resin formation and yield are crucial for the development of the agarwood industry. The differences in yield and chemical composition among different Qi-Nan clones and induction times are worth investigating. While the chemical composition differences between Qi-Nan and ordinary A. sinensis have been extensively studied, the effects of induction time coupled with different Qi-Nan clones on the chemical composition of Qi-Nan agarwood remain insufficiently explored. This study compared the changes in the chemical composition of four “Qi-Nan” clones of A. sinensis after 6, 12, and 24 months of induction through GC-QTOF-MS, the chemical composition and structure types of the four “Qi-Nan” clones were mainly 2-(2-phenylethyl)chromone derivatives (PECs) and Sesquiterpenoids (SESs), with the prolongation of induction time, the content of SESs increased, while the content of PECs decreased. Both the differences among clones and the induction time of “Qi-Nan” agarwood influence its chemical composition, which in turn affects the quality of the agarwood. Among these factors, induction time has a greater impact on the production of PECs in agarwood. The prolongation of induction significantly enhanced the yield of “Qi-Nan” agarwood and exhibited an inducing effect on the production of 2-(2-phenylethyl) chromone and 2-(2-4 phenylethyl)chromone. Compared with the agarwood obtained after 6 and 12 months of induction, the agarwood of “Qi-Nan” after 24 months of induction exhibited superior quality. The induction time for high-quality agarwood from the XGY clone was shorter (12 months) compared to the RH, YYZ, and AS clones (24 months). The study underscores that optimizing induction time and selecting suitable “Qi-Nan” clones can significantly enhance agarwood yield, quality, and production efficiency.

In recent years, plantations of Aquilaria sinensis in China have been dominated by Qi-nan, yet there remains limited research on the growth evaluation and breeding of these clones. In this study, a multi-point joint variance analysis, an additive main effect and multiplicative interaction (AMMI) model, a weighted average of absolute scores (WAASB) stability index, and a genotype main effect plus a genotype-by-environment interaction (GGE) biplot were used to comprehensively analyze the yield, stability, and suitable environment of 25 3-year-old Qi-Nan clones from five sites in southern China. The results showed that all the growth traits exhibited significant differences in the clones, test sites, and interactions between the clones and test sites. The phenotypic variation coefficient (PCV) and genetic variation coefficient (GCV) of the clones’ growth traits at the different sites ranged from 16.56% to 32.09% and 5.24% to 27.06%, respectively, showing moderate variation. The medium–high repeatability (R) of tree height and ground diameter ranged from 0.50 to 0.96 and 0.69 to 0.98, respectively. Among the clones, Clones G04, G05, G10, G11 and G13 showed good growth performance and could be good candidates for breeding. Environmental effects were found to be the primary source of variation, with temperature and light primarily affecting growth, while rainfall influenced survival and preservation rates. Yangjiang (YJ) was found to be the most suitable experimental site for screening high-yield and stable clones across the different sites, whereas the tree height and ground diameter at the Chengmai (CM) site were significantly higher than at the other sites, and the Pingxiang (PX) and Zhangzhou (ZZ) sites showed poor growth performance. The findings suggest that Qi-nan clones are suitable for planting in southern China. There were also abundant genetic variations in germplasm resources for the Qi-nan clones. The five selected clones could be suitable for extensive planting. Therefore, large-scale testing is necessary for determining genetic improvements in Qi-nan clones, which will be conducive to the precise localization of their promotion areas.