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Michael J. Havey and Christopher von Kohn

is a slow process requiring years. Significant effort has been made to identify molecular markers that distinguish onion cytoplasms and predict genotypes at Ms . S cytoplasm is an alien cytoplasm that was introgressed into onion populations ( Havey

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Minou Hemmat, Norman F. Weeden, and Susan K. Brown

Apple scab, Venturia inaequalis (Cke.) Wint., is one of the most damaging diseases of apples. Although fungicide sprays have been used to control the disease, genetic resistance in existing commercially important varieties would be desirable. Identification of molecular marker(s) would be helpful in devising biotechnological approaches to control the disease. We used bulk segregant analysis to identify RAPD markers that cosegregate or display a tight linkage with Vf gene in Prima × Spartan cross. Using this approach, we are saturating the region around the scab resistance gene for the purpose of bracketing the locus. We have identified several markers associated with the Vf locus. The closest markers have been isolated and sequenced to be used as SCARs. The relationship and distances of the markers with the Vf locus and other previously reported markers will be discussed.

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M. Mcharo, D. LaBonte, R.O.M. Mwanga, and A. Kriegner

Molecular markers linked to resistance to sweetpotato chlorotic stunt closterovirus [SPCSV (genus Crinivirus, family Closteroviridae)] and sweetpotato feathery mottle virus [SPFMV (genus Potyvirus, family Potyviridae)] were selected using quantitative trait loci (QTL) analysis, discriminant analysis and logistic regression. Eighty-seven F1 sweetpotato [Ipomoea batatas (L.) Lam.] genotypes from a cross of `Tanzania' and `Wagabolige' landraces were used to generate DNA marker profiles for this study. Forty-five of the clones were resistant to SPCSV while 37 were resistant to SPFMV. A combination of 232 amplified fragment length polymorphism (AFLP) markers and 37 random amplified polymorphic DNA (RAPD) markers obtained were analyzed to determine the most informative markers. All three statistical procedures revealed that AFLP marker e41m33.a contributed the greatest variation in SPCSV resistance and RAPD marker S13.1130 accounted for most of the variation in SPFMV resistance. The power of discriminant and logistic analyses is that you do not need a parent-progeny population. An evaluation of these two models indicated a classification and prediction accuracy rates of 96% with as few as four markers in a model. Both multivariate techniques identified one important discriminatory marker (e44m41.j) for SPCSV and two markers (e41m37.a and e44m36.d) for SPFMV that were not identified by QTL analysis.

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Y. Gogorcena, S. Arulsekar, and D.E. Parfitt

The work reported here is an extension of studies reported in 1990. The general objective was to develop molecular markers for genotype `fingerprinting', with specific reference to possible clonal differences among `Pinot noir' clones. Leaf DNA from 8 cultivars and 9 `Pinot noir' clones were isolated. RFLP and RAPD markers were identified and used to characterize the genotypes. 65 32-P labelled cloned probes were constructed with the pUC18 plasmid and Hind-III digested `Pinot noir' DNA. The probes were tested for their ability to discriminate among the 8 cultivars. 3 probes pGAD10, pGAD15, and pGAD44 showed polymorphisms among the cultivars. pGAD15 was most useful, with 5 polymorphisms for the 8 cultivars. RAPD makers were also tested for `fingerprinting'. Several primers were tested and polymorphisms were identified among cultivars. However, significant problems with repeatability for some bands were observed. Therefore, a series of experiments were conducted to test the effect of season and extraction method. These factors did not account for the inconsistancy which seemed to be more a function of the primer used. None of these studies showed clear evidence that the `Pinot noir' clones tested were geetically different.

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Metka Sisko, Branka Javornik, Aleksander Siftar, and Anton Ivancic

about relatedness between genotypes based on phenotypic markers are not always reliable. More appropriate are molecular markers, which appear to be more stable. In the genus Pyrus , several studies have been carried out using molecular markers to

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P.W. Simon, P.A. Roberts, and L.S. Boiteux

Nematodes impart significant damage to carrot production worldwide. Genetic resistance was studied for Meloidogyne javanica, one of the three major nematodes affecting carrots in warmer climates. F2, F3, and backcross families of `Brasilia' × B6274 were evaluated for resistance in inoculated seedlings. Resistance was conditioned by one, or two linked, dominant loci. Molecular markers were also evaluated with bulked segregant analysis. Three RAPD markers and AFLPs were associated with resistance loci.

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Julie Villand, James Nienhuis, Paul Skroch, and Jan Tivang

Precise cultivar descriptions are necessary to support Plant Variety Protection and utility applications for patent protection. However, accurate discrimination among cultivars is contingent upon the dependability of the method used to delineate lines. The efficiency and reliability of Amplified Fragment Length Polymorphisms (AFLPs), Random Amplified Polymorphic DNAs (RAPDs), microsatellite polymorphisms, and phenotypic traits were studied in order to determine a method's ability to accurately predict pedigree relationships among a set of 20 California processing tomato cultivars. All molecular marker and phenotypic trait data sets were independently produced using identical cultivar seed sources. Data was reduced to a genetic distance measure and presented as a multidimensional scaling (MDS) plot. Principal component analysis using the scored quantitative phenotypic traits was computed and is compared to molecular marker data results. Experimental error, sampling variance, and independence of scored bands for each molecular marker technique are presented. These estimates should assist breeders to determine a sufficient level of characterization, determine a minimum distance considered to be unique, and defend pedigree relationships.

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Patrick J. Conner, Susan K. Brown, and Norman F. Weeden

Molecular markers (isozyme and DNA) have been used to map apple and have helped to elucidate the inheritance of some morphological traits. In this project random amplified polymorphic DNA (RAPD) and isozyme markers were used to create maps for `Wijcik McIntosh, a columnar (reduced branching) sport of `McIntosh' and NY 75441-67, an advanced selection from the multiple disease resistance breeding program. NY 75441-67 is resistant to scab source of resistance from M. floribunda) and resistant to cedar apple rust. `Wijcik McIntosh' is being used in the breeding program as a source of the dominant gene, Co, for reduced branching, but there is also interest in this genotype because of the tremendous variation in plant form observed in progenies segregating for columnar habit. Some of these form variants may be of greater commercial interest than the parental material. Morphological traits examined in this progeny included plant height, stem diameter, suckering, branching habit, spur production, and internode length. The usefulness of molecular markers to pre-select for components of plant form is being examined. Molecular markers promise to aid our understanding and manipulation of quantitative morphological traits.

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Jan Tiväng, Jim Nienhuis, and O.S Smith

The sampling method was applied to a data-set generated by RFLP molecular marker analysis, representing 37 Zea maize cultivars. A total of 251 enzyme probe-combinations were used yielding a total of 1,205 scores per genotype. Genetic distance was calculated among all 37 entries from subsets of arbitrary and increasing sample size. Each score entry in the subset was selected at random from all possible scores with replacement following each selection. The variance for genetic distance was calculated among all subsets of equal size for all possible cultivar pairs. The pooled pair variance was plotted and compared to random simulation models. Additional comparisons were made contrasting closely vs. distantly related cultivars.

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J.G. Tivang, J. Nienhuis, O.S. Smith, and J.S.C. Smith

The statistical properties associated with molecular markers are important when used to characterize germplasm. Evaluation of these properties are necessary for informed selection of one marker system over another. Five different molecular marker systems, Amplified Fragment Length Polymorphism (AFLPs), Arbitrary Primed Polymerase Chain Reaction (AP-PCR), Random Amplified Polymorphic DNA (RAPDs), Restriction Fragment Length Polymorphism (RFLPs), and Isozymes were used to evaluate 39 elite corn belt inbreds. Each system was characterized for fragment frequency distribution, and band correlation distribution as a measure of independence. A regression model estimating resolution and rate of information addition was constructed using the sampling variance. All marker systems were evaluated according to this model. The model facilitated genetic relationships among the inbreds to be compared at equivalent performance level among all marker systems. Four performance levels resulted in 10 comparisons. Pairwise test of significance were conducted using t tests where the null-distributions were obtained by the bootstrap procedure. The maker system were ranked, assisting breeders in selecting marker systems for germplasm organization.