| Chinese cabbage (Brassica rapa L.ssp pekinensis) originating from China, is a subspecies of Brassica genus that could form leaf head. It has been grown widely around China and spread all over the Asia, including Japan and Korea as well. As for the cultivar types and geographical continuity of distribution, Hebei and Shandong province of China rank the first two.Within headed Chinese cabbage, there are complex variations in morphological characters, growing and development habit and ecotypes by breeding and cultivate under different environment. Consequently, it brings on difficulty to survey and collect germplasm resources systematically.In our study, a set of 126 Chinese cabbage DH lines representing wide morphological variation and origin were collected as materials. Two different analysis method, dendrogram and structure analysis, were employed to elucidate the relatonship among phenotypic variation, geographic origin and polymorphism at DNA level using SSR and SRAP marker. And we also discussed different factors having effect on dendrogram and structure analysis. To know about the distribution and linkage relation of SSR markers which were the foundation for structure analysis, we developed a DH mapping population whose parents were selected from this set of DH lines and made SSR located in the AFLP linkage map frame. Main conclusions are listed as follows:1. Though the operation theory of structure and dendrogram analysis was totally different, the result on clustering the set of 126 Chinese cabbage DH lines was coincident. They both clustered them into six main groups (gene pools) representing erect heading type maily in Hebei province; inland overlapped type; curled inward and ovoid heading type maily in Qingdao of Shandong province; early-maturity and hot-resistence type; late-maturity type especial in Guizhou province; strong winterness and early-maturity type distributing in Jiaozhou of Shandong and Northeast China.2. Structure analysis taked advantage over dendrogram analysis special in revealing the pedigree between individuals, it was more useful to clarify the genetic relationship between species.3. Comparing the genetic distance calculated from SSR and SRAP marker in detecting the polymorphism of 31 enrolled DH lines, we suggested that combined marker data set could be utilized to construct drndrogram as reference. Dendrogram, genetic distance and polymorphic level also gave evidence that the 31 DH lines kept a wide variation of 126 DH lines set.4. Polymorphic loci number had strong effect on construct a stable dendrogram. 29 polymorphic loci could distinguish 31 DH lines, but the proper number of polymorphic loci to construct a stable dendrogram was 247 to 257.5. Differ from dendrogram, the sample number influenced the structure analysis. Few marker loci could detect population structure accurately as long as thery were not linkage closely. A DH mapping population had been developed whose parental lines (H30 and H32) were selected from the set of DH lines with highest genetic distance. SSR markers were located in our BrIVFhn linkage map that could be the foundation for structure analysis. In conclusion, dendrogram and structure analysis could supply implemental information in revealing genetic relationship. Dendrogram was influenced by polymorphic number, while structure analysis was affected by sample number; Genetic distance could be calculated in the process to construct dendrogram, while structure analysis was better to reveal pedigree between individuals.
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