Genetic similarities were calculated among 89 Brassica oleracea L. genotypes, which included 62 broccolis (var. italica), 16 cauliflowers (var. botrytis), and 11 cabbages (var. capitata). These entries represented a wide range of commercially available germplasm, including open-pollinated cultivars, commercial hybrids, the inbred parents of several hybrid cultivars, and 27 entries that were provided as unknowns. Sixteen random genomic clones were used as probes in Southern hybridizations to detect restriction fragment length polymorphism (RFLP). From each of the random probes, an average of four polymorphic bands were classified as to their presence or absence for each genotype. The genetic similarity between ail pairs of genotypes was calculated. A multidimensional scaling (MDS) plot indicated that the broccoli, cauliflower, and cabbage groups were clustered with very little overlap. Within groups, genetic similarity corresponded to relationships based on available pedigree information. Comparison of banding patterns between hypothetical and actual hybrids was used to correctly identify the parents of several parent-hybrid combinations. The RFLP pattern of a hybrid and one of the parents (female) were used to predict the genotype and identity of the other parent (male).
James Nienhuis, Mary K. Slocum, Dawn A. DeVos, and Roger Muren
Daniel J. Bell, Lisa J. Rowland, John Stommel, and Frank A. Drummond
spatial genetic structure among clones within fields ( Bell et al., 2009 ). In the present study, our goal was to test whether genetic similarity levels affect yield and also whether other genetic factors such as self-fertility and/or combining abilities
Jianping Ren, Warren F. Lamboy, lames R. McFerson, Stephen Kresovich, and Jianping Ren
Fifty-two germplasm accessions of Chinese vegetable Brassicas were analyzed using 112 random amplified polymorphic DNA (RAPD) markers. The array of material examined spanned a wide range of morphological, geographic, and genetic diversity, and included 30 accessions of Brassica rapa (Chinese cabbage, pakchoi, turnip, broccoletto), 18 accessions of B. juncea (leaf, stem, and root mustards), and 4 accessions of B. oleracea ssp.alboglabra (Chinese kale). The RAPD markers unambiguously identified all 52 accessions. Net and Li genetic similarities were computed and used in UPGMA cluster analyses. Accessions and subspecies clustered into groups corresponding to the three species, but some accessions of some subspecies were most closely related to accessions belonging to another subspecies. Using genetic similarities, it was found that Chinese cabbage is more. likely to have been produced by hybridization of turnip and pakchoi, than as a selection from either turnip or pakchoi alone. RAPD markers provide a fast, efficient technique for diversity assessment that complements methods currently in use in genetic resources collections.
Antonio Figueira, Jules Janick, and Peter Goldsbrough
RAPD markers were used to examine genetic similarity in cacao. DNA from 30 cacao cultivars amplified using 15 arbitrary oligonucleotide primers, produced a total of 112 fragments, of which 88% were polymorphic. A phenogram was developed which illustrates the genetic relationships among the cacao cultivars representing the four major geographic groups of cacao (Criollo, Trinitario, Forastero Lower Amazonian, and Forastero Upper Amazonian). The phenogram indicated a general separation of the four groups into three clusters. Criollos and Trinitarios (supposedly hybrids between Forastero and Criollos types) appeared in a single cluster. Lower Amazonian cultivars (mainly selections made in Bahia, Brazil) appeared in a separate cluster. The third cluster consisted of the Upper Amazonian cultivars, which were originally collected from the region believed to be the center of origin of this crop. This cluster displayed the furthest genetic distance from the others. Crosses between Upper Amazon germplasm and local selections have shown heterosis in clonal crosses, which has been exploited in all genetic improvement programs for cacao. We propose that genetic distances based on RAPD markers can be potentially used as a criterion to select parents capable of producing superior hybrids and populations. Genetic relationships can also be useful to define germplasm collections and conservation strategies. Studies are underway to compare phenograms derived from RAPD markers and ribosomal RNA gene polymorphisms.
John E. Bowers and Carole P. Meredith
RFLP data were used to assess genetic similarity among 33 Vitis vinifera L. cultivars and one interspecific cultivar. A similarity matrix was constructed on the basis of the presence or absence of 49 bands generated by eight RFLP probes and cluster analysis was performed. The mean similarity index for all pairwise comparisons was 0.696 and ranged from 0.444 between `St. Emilion' and the interspecific hybrid `Salvador' to 0.952 between `Chenin blanc' and `Semillon'. Mean similarity among all V. vinifera cultivars was 0.705. Several groupings of similar cultivars are consistent with historical reports and presumed geographic origins: `Chardonnay' and `Melon', `Colombard' and `Folle blanche', `Gewürztraminer' and `Trousseau', `Cabernet franc' and `Cabernet Sauvignon', `Mission' and `Palomino'. The similarity between `Mission' and `Palomino' is the first genetic evidence to support the putative Spanish origin of `Mission'. Some groupings are unexpected (`Sauvignon blanc' and `Gewürztraminer', `Chenin blanc' and `Semillon') because the cultivars are not thought to have originated in the same regions. While some relationships suggested by this study may be artifacts of RFLP analysis or of the statistical method, they raise questions for further genetic inquiry into the origins of grape cultivars.
Salih Kafkas, Yıldız Doğan, Ali Sabır, Ali Turan, and Hasbi Seker
for analysis. Scores for all three types of markers, polymorphic and monomorphic, were analyzed using the NTSYSpc 2.11V program (Exeter Software, Setauket, NY) ( Rohlf, 2004 ). Genetic similarities between hazelnut cultivars were calculated using
Eric T. Stafne, John R. Clark, and Kim S. Lewers
A tetraploid blackberry population that segregates for two important morphological traits, thornlessness and primocane fruiting, was tested with molecular marker analysis. Both randomly amplified polymorphic DNA (RAPD) and simple sequence repeat (SSR) markers were used to screen a population of 98 genotypes within the population plus the two parents, `Arapaho' and `Prime-Jim' (APF-12). RAPD analysis averaged 3.4 markers per primer, whereas SSR analysis yielded 3.0 markers per primer pair. Similarity coefficient derived from the Dice index averaged over all individuals was 63% for RAPD markers, 73% for SSR markers, and 66% for RAPD and SSR markers together. The average similarity coefficients ranged from a high of 72% to a low of 38% for RAPD markers, 80% to 57% for SSR markers, and 73% to 55% for both. Comparison of the parents indicated a similarity of 67% for RAPD markers, 62% for SSR markers, and 67% for both. This is similar to a previous study that reported the similarity coefficient at 66%. Although inbreeding exists within the population, the level of heterozygosity is high. Also, evidence of tetrasomic inheritance was uncovered within the molecular marker analysis. This population will be used to identify potential markers linked to both morphological traits of interest. Further genetic linkage analysis and mapping is needed to identify any putative markers.
Karen L. Burgher, Andrew R. Jamieson, and Xuewen Lu
Twenty-six genotypes of lowbush blueberry (Vaccinium angustifolium Aiton) representing four geographical zones (Maine, United States; New Brunswick, northern Nova Scotia, and western Nova Scotia, Canada) were selected to obtain DNA fingerprints and to estimate genetic similarity by randomly amplified polymorphic DNA analysis. The genotypes were either native accessions or selections from crosses involving native accessions as parents or grandparents. Thirty 10-base RAPD primers were initially screened; 11 proved to be polymorphic, resulting in 73 consistent RAPD bands. All 26 genotypes could be distinguished by their unique RAPD banding patterns and three unlabeled samples were correctly identified. The RAPD band data set was analyzed with Genstat5 to calculate similarity and distance matrices. Average similarity across all genotypes was 56%. Results from average linkage cluster analysis were used to construct a dendogram which demonstrated six main clusters with an average similarity linkage of 70%. The selection `Fundy' and its parent `Augusta' clustered at 77% similarity. The corresponding principal coordinate analysis supported the clusters and identified two distinct outliers. There was a small association by geographic grouping for five genotypes from Maine. It was concluded that RAPD analysis is a useful tool for genotypic identification and estimates of genetic similarity in lowbush blueberry.
Roger J. Sauve, Suping Zhou, Yingchun Yu, and Wolfram George Schmid
A randomly amplified polymorphic DNA (RAPD) technique was used to identify and determine the phylogenetic relationships of 37 hosta accessions representing the major subgenera, sections and groups in the genus Hosta. Results of this study show that RAPD markers were able to differentiate not only the main groups, whose plants shared many genetic traits, but also cultivars within a species. Some accessions were identified by a single primer while others had high intercross linkage and required many markers for their separation. The phylogenetic clustering showed that H. plantaginea, the only night-blooming species, and H. ventricosa, the only known natural tetraploid, are unique and should be classified separately. The four species in the subgenus Bryocles, section Lamellatae H. venusta, H. minor, H. capitata, and H. nakaiana have very low genetic similarity since they do not share many amplified fragments. The other accessions were classified into four main clusters; cluster 1: H. venusta, H. tardiva, H. pycnophylla, H. tsushimensis `Ogon', H. montana, H. tibae, H. montana f. macrophylla, H. kikutii `Kikutii', H. longissima `Longifolia', H. rectifolia `Rectifolia', H. takahashii and H.`Undulata'; cluster 2: H. laevigata, H. sieboldiana, H. pycnophylla × H. longipes f. latifolia, H. longipes `Urajiro' and H. ibukiensis; cluster 3: H. capitata, H. kikutii `Polyneuron', H. nigrescens, H. kikutii `Yakusimensis', H. pachyscapa, H. kikutii `Caput-Avis', H. longipes f. latifolia, H. hypoleuca, H. okamotoi, H. densa and H. takiensis; and cluster 4: H. aequinoctiiantha, H. rupifraga, H. `Amanuma', H. minor and H. kikutii `Densa'.
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.