本研究利用RAPD（逢機擴增多型性DNA）方法分析形態有變異的紅檜之間的遺傳關係。在15個紅檜外表形態變異種，篩選到8個RAPD引子，共擴增出109個條帶，其中74個條帶為多型性（佔總條帶數的67.5%）；每個引子所擴增的條帶數介於13~15個條帶之間，平均為13.6。此結果顯示紅檜各不同基因型間存在高度遺傳變異。UPGMA與PCA兩者的群團分析都將紅檜變異種分成5群；根據UPGMA歸群結果，AMOVA分析所顯現之遺傳變異與各外表型群團有著高度一致性，顯示紅檜變異種在園藝用途上有相當的潛力。如以紅檜樹幹分支來做外表形態的分群，與以AMOVA的分析結果作對照，並未發現遺傳上的關連；影響紅檜樹幹分支可能是透過遺傳與環境的交互作用，因此可能需透過數量性狀基因座的研究才能有比較清楚的解答。
RAPD (random amplified polymorphic DNA) markers were used to analyze the genetic relationships of morphological variants of Chamaecyparis formosensis. Fifteen Chamaecyparis genotypes including one from natural stand were under investigation. RAPD analysis from 8 primers revealed a total of 109 bands, of which 74 were polymorphic (67.5% polymorphism). The range of RAPD bands observed was 13~15 and the average bands per primer was 13.6. The analysis of molecular variance revealed large genetic diversity among Chamaecyparis genotypes investigated. Both UPGMA and PCA analysis found five clusters in the grouping of morphological variants of C. formosensis. AMOVA analysis according to the grouping of UPGMA revealed great genetic variability unique to individual genotypic clusters indicating potential use for horticultural purpose. Grouping of morphological variants of C. formosensis with trunk branching patterns and analyzed by AMOVA analysis found that patterns of trunk Branching is not genetically related. However, factor(s) that effect the generation of trunk branching possibly via genetic and environmental interaction that could only be resolved by quantitative trait loci (QTL) analysis.
