). The genetic base of several cucumber market types has been estimated using various molecular markers, and the genetic distance (GD) among Mediterranean-types (including the Beit Alpha type) is considered relatively broad (GD = 0.09–0.55) when compared
Jack E. Staub and Isabelle Y. Delannay
Jack E. Staub and Isabelle Y. Delannay
European Long market class has the narrowest genetic diversity [genetic distance (GD) = 0.00 to 0.24] among the major commercial cucumber market classes (e.g., Mediterranean types; GD = 0.09 to 0.55; Dijkhuizen et al., 1996 ; Horejsi and Staub, 1999
James Nienhuis, Jan Tivang, Paul Skroch, and Joao B. dos Santos
Knowledge of relative genetic distance among genotypes is useful in a breeding program because it permits organization of germplasm resources. Genetic distance (GD) was estimated among 65 Phaselous lunatus L.. accessions, which included 4 large-seeded and 7 small-seeded cultivars and 54 germplasm accessions (landrace's) from the Caribbean and North, Central, and South America. Based on 125 polymorphic random amplification polymorphic DNA (RAPD) bands, two major clusters, which generally correspond in seed size and geographic region to [be Mesoamerican and Andean gene pools, were observed among the landraces (GD = 0.726 ± 0.041). Four Fordhook cultivars and a landrace from the United States formed a separate cluster that is more distantly related to the small- (GD) = 0.561 ± 0.039) than to the large-seeded cluster (GD = 0.303 ± 0.022). The mean GD between the Andean and Mesoamerican (0.726), Mesoamerican and Fordhook (0.561), and Andean and Fordhook (0.303) clusters were all significant. The significant GD between the Andean and Mesoamerican groups supports the hypothesized existence of two major gene pools in lima bean. The RAPD marker diversity of the Mesoamerican group was the largest (0.1 10), followed by the Andean (0.097) and Ford hook (0.062) groups. The plot of the relationship between the coefficient of variation (cv) and sample size (number of bands) indicates that cvs as low as 10% for estimating CD between Andean and Mesoamerican lima bean accessions can be achieved by sampling as few as 100 bands.
J.E. Staub and V. Meglic
Scientific disagreement about criteria for accurate classification of similar, if not seemingly identical, cultivars has led to spirited debate in legal and agricultural communities. The lack of universally acceptable working definitions of functional genetic distance and difference, as well as insufficient data on genetic diversity, has made it difficult to define a legal framework for cultivar discrimination. In order to satisfy the “distinctness” criterion during plant patenting, genetic diversity and difference must be described unequivocally in measurable terms. Moreover, the number of markers or other characteristics needed to identify the “nonobvious” nature of the cultigen will determine the breadth of protection under the patent. Increasingly, patent examiners must interpret novelty and distinctness in terms of molecular as well as gross phenotypic (flower color, plant habit, etc.) information. A description of difference using molecular markers may be more difficult compared to a description of function (i.e., how many markers are required to assign difference). Consequently, the effective use of molecular marker information in the legal community will require scientific agreement on the meaning of genetic distance as it relates to genetic difference.
C.L. Boehm, H.C. Harrison, G. Jung, and J. Nienhuis
Genetic differences among eleven cultivated and eight wild-type populations of North American ginseng (Panax quinquefolium L.) and four cultivated populations of South Korean ginseng (P. ginseng C.A. Meyer) were estimated using RAPD markers. Cultivated P. ginseng population samples were collected from four regions of S. Korea. Cultivated P. quinquefolium population samples were collected from three regions in North America: Wisconsin, the Southeastern Appalachian region of the United States, and Canada. Wild-type P. quinquefolium was collected from three states in the United States: Pennsylvania, Tennessee, and Wisconsin. Evaluation of germplasm with 10 decamer primers resulted in 100 polymorphic bands. Genetic differences among populations indicate heterogeneity. The genetic distance among individuals was estimated using the ratio of discordant bands to total bands scored. Multidimensional scaling of the relationship matrix showed independent clusters corresponding to the distinction of species, geographical region, and wild versus cultivated types. The integrity of the clusters was confirmed using pooled chi-square tests for fragment homogeneity.
Joseph C. Kuhl and Veronica L. DeBoer
‘German Wine’ plants with M-CTC/E-ACA and M-CAG/E-ACT resulted in 317 scored polymorphisms compared with 311 for the same two primer combinations in the larger dataset. Genetic distance analysis. Dice's similarity coefficient ( Nei and Li, 1979
Hongwen Huang, Desmond R. Layne, and R. Neal Peterson
The utility of isozyme phenotypes for identifying and determining genetic variation in pawpaw cultivars was studied using isoelectric focusing in thin-layer polyacrylamide gels. Based on a sample of 32 clones (cultivars and advanced selections) and 23 enzyme systems, 7 enzymes were found to be polymorphic, involving 9 polymorphic loci [acid phosphatase (ACP), dihydrolipoamide dehydrogenase (DDH), malic enzyme (ME), phosphoglucoisomerase (PGI), phosphoglucomutase (PGM), peroxidase (PRX), and shikimate dehydrogenase (SKD)]. Altogether these 9 loci and 32 clones yielded 28 multi-locus isozymic phenotypes useful for cultivar identification; 24 of the 32 clones were uniquely identified. The allozyme variation in these clones has the average of other long-lived woody perennials of widespread geographic range in temperate regions with insect-pollinated outcrossing breeding systems, secondary asexual reproduction, and animal-dispersed seed. Genetic differentiation among these pawpaw clones, measured by Nei's distance, D, was substantial: 496 pairwise comparisons of genetic distance among the 32 clones indicated that they differed on average of D = 0.068 ± 0.04 and ranged from 0 to 0.188. Cluster analysis (UPGMA) produced a most likely division of the 32 clones into 7 groups; however, these groups did not conform to known pedigree relations. Additional polymorphic enzymes are needed for accurate allozyme-based genetic discrimination.
Emmanouil N. Tzitzikas, Antonio J. Monforte, Abdelhak Fatihi, Zacharias Kypriotakis, Tefkros A. Iacovides, Ioannis M. Ioannides, and Panagiotis Kalaitzis
, polymorphism information content (PIC), gene diversity, genetic distances according to Nei et al. (1983) , and neighbor-joining (NJ) trees were calculated with PowerMarker 3.25 ( Liu and Muse, 2005 ). The NJ tree was plotted with MEGA 3.0 ( Kumar et al., 2004
Jaladet M.S. Jubrael, Sripada M. Udupa, and Michael Baum
Currently, the identification and characterization of date palm varieties rely on a small number of morphological traits, mainly of fruit, which are complex and greatly influenced by the environment. As a result, different varietal names may actually refer to the same variety while different varieties may have the same name. Therefore, new descriptors like molecular markers are required to identify, characterize, and estimate genetic diversity in this crop. Here we used amplified fragment length polymorphism (AFLP) markers to discriminate 18 Iraqi date palm varieties and to estimate the genetic relationship among the varieties. A total of 122 polymorphic AFLP loci were scored, with an average of 17.4 polymorphic loci per primer combination. The use of any one of the four combinations, P101(aacg)/M95(aaaa), P74(ggt)/M95(aaaa), P73(ggg)/M95(aaaa), or P100(aacc)/M95(aaaa), was sufficient to uniquely identify all the varieties. Jaccard's genetic similarity index ranged from 0.108 to 0.756, indicating moderate to diverse relationships. Estimation of average proportion of fixed recessive AFLP loci indicated that most of the loci in variety `Chipchab' were fixed, whereas most of the loci in `Jamal Al-Dean' could be heterozygous and in-between in other varieties. Unweighted pair group method with arithmatic mean (UPGMA) analysis ordered the date palm varieties first into two broad groups at 27% similarity levels. One group consisted of seven varieties and the second group consisted of the remaining 11 varieties of date palm. These results showed that the AFLP technique is an efficient method for varietal identification and estimating genetic relationships in date palm.
Joseph J. King, James M. Bradeen, and Michael J. Havey
Nuclear RFLPs were used to estimate relationships among 14 elite commercial inbreds of bulb onion (Allium cepa) from Holland, Japan, and the United States. Variability for known alleles at 75 RFLP loci and 194 polymorphic fragments revealed by 69 anonymous cDNA probes and a clone of alliinase were scored to yield genetically characterized and uncharacterized data sets, respectively. The inbred onion populations possessed more than two alleles at 20 of 43 (46%) codominant RFLP loci. Relationships among the inbreds were estimated by cluster analysis of simple-matching (genetically characterized data) and Jaccard (genetically uncharacterized data) coefficients using the unweighted pair group method and agreed with known pedigrees. RFLPs confidently distinguished among elite inbreds within and between specific market classes. RFLP profiles for virtual hybrids were computer-generated by combining gametic arrays among inbreds of the same market class and analyzed as described above. Allelic and genetically uncharacterized RFLPs confidently distinguished among these hybrids, even though heterozygosity for many markers produced a majority of monomorphic fragments. We randomly sampled decreasing numbers of RFLPs from the complete data sets and calculated simple-matching and Jaccard distances, noting the numbers of probes that were unable to distinguish any two inbreds or hybrids. As few as 10 polymorphic probe-enzyme combinations distinguished among all the inbreds and samples of 20 genetically characterized or 10 genetically uncharacterized clones distinguished all the virtual hybrids. This study demonstrated that the previously reported few RFLPs observed among open-pollinated (OP) onion populations were due to the highly heterozygous nature of the OP population.