sharing distance matrix and PCA for flowering dogwood demonstrated high genetic diversity for the loci analyzed. Allele sharing distances ranged from 0.44 to 0.94 and most of the values were greater than 0.70 ( Table 3 ). Principal coordinate analysis
Phillip A. Wadl, Xinwang Wang, Andrew N. Trigiano, John A. Skinner, Mark T. Windham, Robert N. Trigiano, Timothy A. Rinehart, Sandra M. Reed, and Vincent R. Pantalone
Jose A. Oliveira, Ana B. Monteagudo, Suleiman S. Bughrara, Jose L. Martínez, Ana Salas, Esther Novo-Uzal, and Federico Pomar
coordinate analysis based on genetic similarity matrices was performed with the DCENTER and EIGEN options of the NTSYS-pc Version 2.1 to identify the number of groups based on eigenvectors. The principal coordinate analysis result was displayed by the Mod3D
Weisheng Liu, Dongcheng Liu, Aimin Zhang, Chenjing Feng, Jianmin Yang, Jaeho Yoon, and Shaohua Li
Chinese plum-types that reflected their geographic origins. Fig. 3. Two-dimensional plot of 104 plum and related accessions generated by ISSR data using principal coordinate analysis (PCoA) based on the Jaccard coefficients of similarity; • = P
José López Medina, Patrick P. Moore, Carl H. Shanks Jr., Fernando Flores Gil, and Craig K. Chandler
Genotype × environment interaction for resistance to the twospotted spider mite (Tetranychus urticae Koch) of eleven clones of Fragaria L. sp. (strawberries) grown in six environments throughout the United States was examined using two multivariate analysis techniques, principal coordinate analysis (PCA) and additive main effect and multiplicative interaction (AMMI). Both techniques provided useful and interesting ways of investigating genotype × environment interaction. PCA analysis indicated that clones X-11 and E-15 were stable across both low and high environments for the number of spider mites per leaflet. The initial AMMI analysis showed that the main effects of genotype, environment, and their first-order interaction were highly significant, with genotype × environment interaction due mainly to cultivar `Totem' and environment FL94. A second AMMI analysis, which excluded `Totem' and FL94, showed that the main effects of the remaining genotypes, environments, and genotype × environment interaction were also highly significant. AMMI biplot analysis revealed that FL93 and GH93 were unstable environments, but with opposite interaction patterns; and GCL-8 and WSU2198 were unstable genotypes with similar interactions that were opposite those of WSU 2202.
Jasmina Muminović, Andrea Merz, Albrecht E. Melchinger, and Thomas Lübberstedt
Twelve amplified fragment length polymorphism (AFLP) primer combinations and 10 inter-simple sequence repeat (ISSR) primers were applied to estimate genetic diversity among 68 varieties of cultivated radish (Raphanus sativus L.). The material consisted of open-pollinated varieties, inbred lines, diploid and a few tetraploid hybrid varieties of garden radish [R. sativus var. sativus DC. convar. radicula (DC.) Alef.] and black radish [R. sativus var. niger (Mill.) Pers.]. Two accessions of uncultivated relatives of radish that as weeds cause serious contamination during the process of hybrid radish production were added to the analyses. Polymorphic fragments were scored for calculation of Jaccard's coefficient of genetic similarity (GS). Substantial level of genetic variability (average AFLP-based GS = 0.70; average ISSR-based GS = 0.61) was detected in the available germplasm of cultivated radish. Cluster analyses separated two weedy species from the cultivated germplasm. Within cultivated material, black radish and french breakfast radish types formed separate clusters. Based on AFLP data, a principal coordinate analysis (PCoA) and model-based approach revealed the genetic structure within cultivated radish germplasm and indicated the existence of divergent pools. Although the model-based approach did not separate black radish from french breakfast radish varieties, it offered a clear sub-division within garden radish germplasm. The results of this study may be relevant for hybrid radish breeding.
M.C. Scott, G. Caetano-Anollés, and R.N. Trigiano
DNA amplification fingerprinting (DAF) was used to study genetic relationships between closely related chrysanthemum cultivars (Dendranthema grandiflora Tzvelev.). Twenty-one cultivars were examined that belonged to the Anne, Blush, Boaldi, Charm, Davis, and Pomona series (families). The genetic variability of cultivars within and between series was evaluated using eleven arbitrary octamer primers. A few polymorphic characters uniquely identified closely related cultivars within each of the series. In contrast, many DNA polymorphisms were observed between members of the different series. Phenetic patterns were established by unweighted pair group cluster analysis using arithmetic means (UPGMA) and principal coordinate analysis (PCO). The average distance between series was 10-fold greater than between cultivars within a series. DNA from all cultivars belonging to a series were also bulked to generate profiles containing unique amplified products for each series. Cluster analysis and PCO of bulked DNA clearly grouped Charm and Pomona together. However, series grouping did not correspond to morphology of inflorescence types. The results demonstrate the utility of the DAF technique in distinguishing clonal materials and its potential use for patent protection, phylogenetic studies, and for identifying useful markers in breeding applications.
Nnadozie C. Oraguzie, Sue E. Gardiner, Heather C.M. Basset, Mirko Stefanati, Rod D. Ball, Vincent G.M. Bus, and Allan G. White
Four subsets of apple (Malus Mill.) germplasm representing modern and old cultivars from the repository and apple genetics population of the Horticulture and Food Research Institute of New Zealand Limited were used in this study. A total of 155 genotypes randomly chosen from the four subsets were analyzed for random amplified polymorphic DNA (RAPD) variation. Nine decamer primers generated a total of 43 fragments, 42 of which were polymorphic across the 155 genotypes. Pairwise distances were calculated between germplasm subsets using the distance metric algorithm in S-PLUS, and used to examine intra-and inter-subset variance components by analysis of molecular variation (AMOVAR). A phenogram based on unweighted pair group method with arithmetic average (UPGMA) cluster analysis was constructed from the pairwise distances and a scatter plot was generated from principal coordinate analysis. The AMOVAR showed that most of the variation in the germplasm (94.6%) was found within subsets, suggesting that there is significant variation among the germplasm. The grouping of genotypes based on the phenogram and scatter plot generally did not reflect the pedigree or provenance of the genotypes. It is possible that more RAPD markers are needed for determining genetic relationships in apple germplasm. Nevertheless, the variation observed in the study suggests that the current practice of sublining populations in the first generation to control inbreeding may not be necessary in subsequent generations. If these results are confirmed by fully informative molecular markers, germplasm managers should reassess the structure of their genetics populations. There may be a need to combine sublines in order to capture the maximum genetic diversity available and to streamline breeding efforts.
Alice Le Duc, Robert P. Adams, and Ming Zhong
Van Melle (1947) proposed that juniper cultivars of the Pfitzer Group were of hybrid origin and ascribed the name Juniperus ×media Melle. This purported hybrid of J. chinensis L. × J. sabina L. has not been accepted unanimously by the horticultural community. Random amplified polymorphic DNAs (RAPDs) were used to analyze and establish new evidence for the hybrid origin of the Pfitzer Group, using both parents and seven cultivars of the Pfitzer Group. Principal coordinate analysis (PCO) of 122 RAPD bands demonstrated that samples of J. chinensis cluster tightly together, as do the J. sabina samples. Cultivars of the Pfitzer Group lacked affinity with either species, but stood apart as a distinct cluster. The data support Van Melle's conclusion that the Pfitzer Group is separate from J. chinensis and indicate hybrid origin from parents J. chinensis and J. sabina. We recognize Juniperus ×pfitzeriana (Späth) Schmidt [Pfitzer Group] as the correct name for cultivars of Pfitzer junipers. Juniperus ×media, proposed by Van Melle, was rendered illegitimate because of the earlier name J. media V.D. Dmitriev.
Salih Kafkas, Yıldız Doğan, Ali Sabır, Ali Turan, and Hasbi Seker
performed to construct a dendrogram. The similarity matrix data were also subjected to principal coordinate analysis (PCoA) using the NTSYSpc program. The cultivars were plotted first on three dimensions using the G3D procedure of the Statistical Analysis
Hussam S.M. Khierallah, Saleh M. Bader, Michael Baum, and Alladin Hamwieh
with 100 bootstrap. Principal coordinate analysis (PCA) was performed according to Euclidean similarity index using the PAST software. Results The 33 primer pairs of Akkak et al. (2009) and Billotte et al. (2004) were tested for their ability to