Christopher S. Cramer and Michael J. Havey
Michael J. Havey
Although always among the top five vegetables in value, little genetic information has been published on the bulb onion. Genetic and molecular analyses are hampered by the plant's biennial nature, severe inbreeding depression, and huge genome. Research is underway to construct a low-density genetic map of onion based on RFLPs, AFLPs, and RAPDs. Among open-pollinated populations (OPPs), levels on DNA polymorphisms were in agreement with those of other outcrossing diploid species. However, we identified little putative-allelic diversity among the OPPs (1.9 polymorphic bands per polymorphic probe–enzyme combination) supporting a bottleneck during the domestication of onion. Our segregating family is from the cross of two diverse inbreds and will be used to map quantitative trait loci conditioning phenotypically correlated production (maturity, storability, and firmness), consumer-preference (pungency, flavor, and bulb shape), and health-enhancing (anti-platelet aggregation) attributes of onion. We are also attempting to tag chromosome regions controlling relatively simply inherited traits that are difficult or expensive to characterize classically.
F. Sanz-Cortés, M.L. Badenes, S. Paz, A. Íñiguez, and G. Llácer
Forty olive (Olea europaea L.) cultivars from Valencia, Spain, were screened using random amplified-polymorphic DNA (RAPD) markers. Eighteen selected decamer primers produced 34 reproducible amplification fragments that were then used as polymorphic markers. The resulting combinations of these RAPD markers were used to discriminate 40 cultivars. Results were analyzed for similarity among cultivars and the relatedness of polymorphisms obtained between cultivars agreed with previous results using isozymes. Unweighted pair group method cluster analysis of their similarity values revealed two main groups divided according to geographic origin within Valencia. A third group, which included two Spanish cultivars from regions outside of Valencia, was clustered separately from the Valencian cultivars. RAPD technology proved useful in discriminating closely related cultivars. There was no apparent clustering of cultivars by fruit size or other morphological traits.
Michael J. Havey, Joseph J. King, James M. Bradeen, and Ockyung Bark
Leigh K. Hawkins, Fenny Dane, and Thomas L. Kubisiak
Morphological traits were examined in an F3 generation derived from a cross between C. lanatus var. lanatus [(Thunb.) Matsum. & Nakai] and C. lanatus var. citroides. At least three genes, C (yellow) vs. c (red), i (inhibitory to C) vs. I (non-inhibitory to C), and y (yellow) vs. yw (white), with epistatic and inhibitory actions were found to govern the inheritance of fruit flesh color. The high frequency of yellow-fleshed fruit and low frequencies of white and red fruits can be explained by the presence of a new allele (yw recessive to y) in the multiple allele series at the Y locus. The low frequency of tan colored seeds in segregating populations could be explained by at least three genes governing inheritance of seed-coat color. Single factor analysis of variance was conducted for each pairwise combination of random amplified polymorphic DNA (RAPD) locus and fruit or seed characteristics. Several RAPD loci were identified to be loosely linked to morphological characteristics.
Hongwen Huang, Desmond R. Layne, and Thomas L. Kubisiak
Thirty-four extant pawpaw [Asimina triloba (L.) Dunal] cultivars and advanced selections representing a large portion of the gene pool of cultivated pawpaws were investigated using 71 randomly amplified polymorphic DNA (RAPD) markers to establish genetic identities and evaluate genetic relatedness. All 34 cultivated pawpaws were uniquely identified by as few as 14 loci of eight primers. Genetic diversity of the existing gene pool of cultivated pawpaws, as estimated by Nei's gene diversity (He), was similar to that of wild pawpaw populations. The genetic relatedness among the cultivated pawpaws examined by UPGMA cluster analysis separated 34 cultivars and selections into two distinct clusters, a cluster of PPF (The PawPaw Foundation) selections and a cluster including a majority of the extant cultivars selected from the wild and their derived selections. The results are in general agreement with the known selection history and pedigree information available. The consensus fingerprint profile using the genetically defined RAPD markers is a useful and reliable method for establishing the genetic identities of the pawpaw cultivars and advanced selections. This also proved to be an improved discriminating tool over isozyme markers for the assessment of genetic diversity and relatedness. RAPD profiling of data presented in this study provides a useful reference for germplasm curators engaged in making decisions of sampling strategies, germplasm management and for breeders deciding which parents to select for future breeding efforts.
Minou Hemmat, Norman F. Weeden, Herb S. Aldwinckle, and Susan K. Brown
Bulked segregant analysis was used to identify RAPD markers that display tight linkage to the Vf gene in apple (Malus sp.) that confers resistance to five races of apple scab [Venturia inaequalis (Cke.) Wint.]. We identified several new RAPD markers linked to Vf. The most tightly linked marker in the test population, S52500, was cloned and sequenced. A linkage map of the Vf region was developed using these markers, RAPD markers previously described by other laboratories, and the isozyme locus Pgm-1. An assay was developed for Vf by multiplexing the two markers closely flanking the Vf locus. This assay has a theoretical `escape' value (discarding a resistant plant) of 3% and an error rate (selection of a susceptible plant) of 0.02%.
Five edible mountain vegetables (Saussurea sp., Aster tataricus, A. scaber, Synurus deltoides, Ligularia fischeri) were investigated on the basis of amplified DNA polymorphisms resulted from PCR–polymerase chain reaction analysis. The sampled plants consisted of 38 individuals in five taxa. Only 10 primers out of 62 [60 random (10-mer) primers, one 15-mer-M13 core sequence, and (GGAT)4 sequence] tested gave rise to polymorphisms in all of the tested plants, producing 176 DNA fragments amplified randomly and specifically. Intraspecific polymorphisms found in each taxa showed intra-variety constancy (31.1% to 40.9%) in the banding patterns of individual plants—Saussurea sp., 31.1%, 15 bands; Aster tataricus, 40.9%, 18 bands; A. scaber, 38.5%, 15 bands; Synurus deltoides, 34.7%, 17 bands; Ligularia fischeri, 38.9%; 22 bands, respectively. All five species were well-differentiated from each other at the 0.93 level of similarity index value. Genetic relationships among intraspecific and interspecific variations were closely related at the levels ranging from 0.62 to 0.99. Based on these results, our PCR analyses support the previous data derived from external morphology of the five edible mountain vegetables, but very low levels of intraspecific variations were detected in all of these taxa.
Antonio Figueira, Jules Janick, Morris Levy, and Peter Goldsbrough
Genetic similarities among eight Theobroma and two Herrania species, including 29 genotypes of T. cacao, were estimated by rDNA polymorphism. A phenogram based on these genetic similarities significantly separated two clusters: one cluster included all Herrania and Theobroma species, except T. cacao, while the second contained 28 of 29 T. cacao genotypes. There was no clear distinction between Herrania and Theobroma species. Separation of 29 T. cacao genotypes, representing all races and various origins, had no congruency with the conventional classification into three horticultural races: Criollo, Forastero, and Trinitario. Genetic similarities in T. cacao, estimated with RAPD markers, indicated continuous variation among the generally similar but heterogeneous genotypes. The wild genotypes formed an outgroup distinct from the cultivated genotypes, a distinction supported by the rDNA data. The phenograms constructed from RAPD and rDNA data were not similar within the wild and cultivated cacao subsets.
Majid R. Foolad
In tomato, Lycopersi conesculentum Mill., currently there are >285 known morphological, physiological and disease resistance markers, 36 isozymes, and >1000 RFLPs, which have been mapped onto the 12 tomato chromosomes. In addition, currently there are >162,000 ESTs, of which ∼3.2% have been mapped. Several tomato genetic maps have been developed, mainly based on interspecific crosses between the cultivated tomato and its related wild species. The markers and maps have been used to locate and tag genes or QTLs for disease resistance and other horticultural characteristics. Such information can be used for various purposes, including marker-assisted selection (MAS) and map-based cloning of desirable genes or QTLs. Many seed companies have adopted using MAS for manipulating genes for a few simple morphological characteristics and several vertical disease resistance traits in tomato. However, MAS is not yet a routine procedure in seed companies for manipulating QTLs although it has been tried for a few complex disease resistance and fruit quality characteristics. In comparison, the use of MAS is less common in public tomato breeding programs, although attempts have been made to transfer QTLs for resistances to a few complex diseases. The potential benefits of marker deployment to plant breeding are undisputed, in particular for pyramiding disease resistance genes. It is expected that in the near future MAS will be routine in many breeding programs, taking advantage of high-resolution markers such as SNPs. For quantitative traits, QTLs must be sought for components of genetic variation before they are applicable to marker-assisted breeding. However, MAS will not be a “silver bullet” solution to every breeding problem or for every crop species.