Sixty-two genetically diverse modern and traditional Phaseolus vulgaris L. cultivars from Brazil, the Dominican Republic, Honduras, Mexico, the Netherlands, and the United States, representative of the Andean and Middle American gene pools, were selected to study the interaction with distinct races of Colletotrichum lindemuthianum (Sacc. & Magnus) Lams.-Scrib. Principal component and phenetic analyses were conducted on the disease reaction to inoculation with 34 races of C. lindemuthianum from Argentina, Brazil, Colombia, Costa Rica, the Dominican Republic, Honduras, Mexico, Peru, and the United States. The principal component analysis revealed four clusters in which only one cluster consisted of cultivars from both gene pools. Bean genotypes clustered based on the gene pool origin of the resistance genes present, regardless of the actual gene pool of the host genotype. Middle American genotypes in cluster A carried Andean resistance genes. Further grouping of genotypes based on overall level of resistance within each gene pool was observed. Clusters A and C consisted of the most resistant genotypes from both gene pools. The distribution of genotypes generated by the phenetic analysis, placed the most resistant and susceptible genotypes of the anthracnose differential series at the extremities of the phenogram, providing support for the range in genotypic resistance exhibited by members of the differential series. Races of C. lindemuthianum isolated from Middle American genotypes showed broad virulence on germplasm from both gene pools, whereas races with Andean reaction showed high virulence only on Andean germplasm. The reduced virulence of Andean races on Middle American genotypes suggests selection of virulence factors congruent with diversity in P. vulgaris. In addition, races of C. lindemuthianum formed two clusters corresponding to the Middle American and Andean reaction groups based on the phenetic analysis. In the principal component analysis, most races with the Andean reaction were observed in the clusters C and D, except races 15 and 23 which clustered with Middle American races in cluster B. Only races 38, 39 and 47 from the Dominican Republic showed high similarity in both multivariate analyses and clustered based on geographic origin. Races from other countries showed no geographic effect. The overlapping of specific races, however, with races from different reaction groups might indicate that this group of isolates possesses factors of virulence to both host gene pools. Data based on virulence supports variability in C. lindemuthianum structured with diversity in P. vulgaris.
R.S. Balardin and J.D. Kelly
Rozalyn Pama*, Jay Doronila, and Mari Marutani
Fifteen sweetpotato [Ipomoea batatas (L.) Lam] accessions grown on Guam were studied for morphological and genetic characteristics. Accessions, obtained from AVRDC (Asian Vegetable Research and Development Center) in Taiwan, Saipan, Rota, and Guam, were investigated for marketable yield, growth habit and characteristics of tuberous roots (color, shape, sugar content and moisture content). Results of this study were used to determine the morphological relationship of the accessions of sweetpotato. Phenetic analysis revealed four major clusters according to tuberous root characteristics. The genetic relationship of these sweetpotato accessions was also evaluated for genetic differences among accessions. DNA was extracted and went through polymerase chain reaction (PCR). PCR products were analyzed by random amplified polymorphic DNA (RAPD) fingerprinting. Result of the genetic relationship among the sweetpotatoes was compared with the morphology of accessions using UPGMA cluster analysis and principal compounds analysis.
Margaret R. Pooler and John S. Hartung
Xylella fastidiosa is a fastidious gram-negative, xylem-limited leafhopper-transmitted bacterium that has proven to be the causal agent of many economically important horticultural plant diseases, including Pierce's disease of grapevine and citrus variegated chlorosis. Genetic relationships among 11 X. fastidiosa strains isolated from mulberry, almond, ragweed, grape, plum, elm, and citrus were determined using randomized amplified polymorphic DNA (RAPD). Twenty-two 10-base primers amplified a total of 77 discrete polymorphic bands. Phenetic analysis based on a similarity matrix corresponded well with previous reports on RFLP-based similarity relationships, indicating that RAPD-PCR amplification products can be used as a reliable indicator of genetic distance in X. fastidiosa. RAPD products have been cloned and sequenced, and pairs of 21-nucleotide PCR primers have been developed that detect X. fastidiosa in general and the causal agent of citrus variegated chlorosis specifically.
Margaret Pooler and John S. Hartung
Xylella fastidiosa is a fastidious gram-negative, xylem-limited, leafhopper-transmitted bacterium that has proven to be the casual agent of many economically important diseases, including Pierce's disease of grapevine and citrus variegated chlorosis. Genetic relationships among 11 Xylella fastidiosa strains isolated from mulberry, almond, ragweed, grape, plum, elm, and citrus were determined using random amplified polymorphic DNA (RAPD). Twenty-two 10 base primers amplified a total of 77 discrete polymorphic bands. Phenetic analysis based on a similarity matrix corresponded well with previous reports on X. fastidiosa RFLP-based similarity relationships, indicating that RAPD-PCR amplification products can be used as a reliable indicator of genetic distance in X. fastidiosa. Cladistic analysis suggests the existence of five groups of X. fastidosa: the citrus group, the plum-elm group, the grape-ragweed group, the almond group, and the mulberry group.
B.S. Vivek and Philipp W. Simon
Current classifications of the genus Daucus are based on morphological and anatomical characteristics. We have used single to low copy nuclear restriction fragment length polymorphisms (nRFLPs) to describe the phylogeny and relationships of eight Daucus species including cultivated carrot (D. carota L.). Parsimony analysis of 247 characters (DNA fragments from 58 probe-enzyme combinations) yielded a tree in which accessions were grouped into three major clades and phenetic analysis using Jaccard's coefficient yielded two major clusters. The phylogenetic relationships from the nuclear RFLP data generally agreed with an earlier morphological classification. Resolution and placement of D. guttatus and D. muricatus were not consistent with the morphological classifications. Molecular variation among carrot inbreds was large.
R.L. Jarret and K.V. Bhat
Fifty-seven accessions of Musa including cultivated clones Of 6 genomic groups (AA, AB, AAA, AAB, ABB, ABBB), M. balbisiana (BB), M. acuminata ssp. banksii (AA), M. acuminata ssp. malaccensis (AA) and M. velutina were examined for random amplified polymorphic DNA (RAPD) genetic markers using PCR with sixty 10-mer random primers. Forty-nine of 60 tested primers gave reproducible DNA amplification patterns. The number of bands resolved per amplification was primer dependent and varied from 1 to a maximum of 24. The size range of the amolification products also differed with the select& primer sequence/genotype and ranged from 0.29 to 3.0 kb. RAPD data were used to generate Jaccard's similarity coefficients which were analyzed phenetically. Phenetic analysis separated clones into distinct groupings that were in agreement with clusterings revealed when data were subsequently analyzed by principal coordinate analysis (PCO). In both the phenetic and the PCO analyses, previously unclassified cultivars grouped with cultivars previously classified for their genomic group based on morphological keys. The implications of RAPD analysis for Musa germplasm classification, clonal identification, and management are discussed.
Anna L. Hale, Mark W. Farnham, and Monica A. Menz
Breeders of cole crops (Brassica oleracea L.) have an interest in utilizing current and emerging PCR-based marker systems to differentiate elite germplasm. However, until efficiency and cost-effectiveness are determined, most breeders are hesitant to change methods. In this study, our goal was to compare simple sequence repeat (SSR), amplified fragment-length polymorphism (AFLP), and sequence-related amplified polymorphism (SRAP) marker systems for their effectiveness in differentiating a diverse population of 24 elite broccoli (B. oleracea Italica Group) inbreds. Published SSR primer sequences for Brassica L. species were used along with AFLP and SRAP primer combinations. Several SSR primers failed to amplify DNA in the broccoli population, but all AFLP and SRAP primer combinations produced multiple bands. Twenty-nine percent of the SSR primers were monomorphic, while most of the remaining primers detected only one or two differences among inbreds. AFLP and SRAP methods produced multiple differences per primer in almost every case. Phenetic analysis revealed that the type of marker affected the classification of the genotypes. All three marker systems were able to successfully differentiate between the 24 elite inbreds, however, AFLPs and SRAPs were more efficient, making them better alternatives than SSRs over other established methods for fingerprinting B. oleracea inbreds.
Joseph C. Kuhl and Veronica L. DeBoer
was dropped due to low dye signal. Data analysis. Phenetic analysis was conducted using NTSYS-pc (version 2.20e; Applied Biostatistics, Setauket, NY). Distance matrices (SIMQUAL) were generated using Dice (1945) estimate of genetic similarity
Innocenzo Muzzalupo, Francesca Stefanizzi, and Enzo Perri
(94% of the cultivars analyzed). Therefore, synonyms characterization is very important to avoid genotype redundancy to maximize genetic diversity in the Italian olive germplasm collection. Phenetic analysis of the genetic polymorphism carried out by
Mark K. Ehlenfeldt, Joseph Kawash, and James Polashock
, S.P. Dickinson, T.A. 1992 The taxonomy of Vaccinium section Hemimyrtillus Bot. Mag. Tokyo 105 601 614 Vander Kloet, S.P. Dickinson, T.A. 2005 RAPD typification: Phenetic analysis of Vaccinium inflorescences Bot. J. Linn. Soc. 148 445 457