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

Genetic linkage maps were created for three apple (Malus ×domestica Borkh.) cultivars using data from two progenies (`Wijcik McIntosh' xNY 75441-67 and `Wijcik McIntosh' xNY 75441-58). The maps consist primarily of randomly amplified polymorphic DNA (RAPD) markers, but also contain six isozyme loci and four morphological markers (Rf, fruit skin color; Vf, scab resistance; Co, columnar growth habit; Ma, malic acid). Maps were constructed using a double pseudotestcross mapping format and JoinMap mapping software. An integrated `Wijcik McIntosh' map was produced by combining marker data from both progenies into a single linkage map. Homologous linkage groups from paternal maps were paired with their counterparts in the `Wijcik McIntosh' map using locus bridges composed of markers heterozygous in both parents of a progeny. The `Wijcik McIntosh' map consists of 238 markers arranged in 19 linkage groups spanning 1206 cM. The NY 75441-67 map contains 110 markers in 16 linkage groups and the NY 75441-58 map consists of 183 markers in 18 linkage groups. The average distance between markers in the maps was ≈5.0 cM.

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Rebecca Nelson Brown and James R. Myers

A molecular and morphological marker map would improve our knowledge of Cucurbita genetics, and would facilitate efforts to breed improved summer and winter squash cultivars. Random amplified polymorphic DNA (RAPD) markers were used to construct a partial map of the Cucurbita genome. The mapping population was the BC1 progeny of the Cucurbita pepo L. yellow straightneck inbred A0449 and the tropical Cucurbita moschata Duchesne ex Lam. landrace `Nigerian Local'. A0449 was the recurrent parent. This cross was chosen because of the relatively greater economic importance of summer squash, traits of value to be introgressed from the C. moschata parent, and maximized genetic variation from the interspecific cross. The map contains 148 RAPD markers in 28 linkage groups. Loci controlling five morphological traits were placed on the map. The map covers 1,954 cM, which is estimated to be 75% of the Cucurbita genome. The qualitative traits placed on the map include the B gene for fruit which turn yellow before anthesis, the M gene for silver mottling of leaves, and a locus controlling the intensity of rind color on mature fruit. Quantitative trait loci (QTL) associated with fruit shape and the depth of the indentations between primary leaf veins were identified.

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James M. Bradeen and Michael J. Havey

Commercial bulb-onion (Allium cepa L.) growers often complain that hybrids they have grown successfully for a few years fail to perform at the expected level. Inbreds used to produce hybrid-onion seed rarely have been self-pollinated for more than two generations and retain a high level of heterozygosity. Over time, selection, drift, or contamination of inbreds may contribute to disappointing hybrid performance. We identified randomly amplified polymorphic DNA (RAPD) between two inbred onion lines, demonstrated their Mendelian inheritance, and tried to distinguish among and examine changes in independently maintained, publicly released inbred lines of onion. We observed poor agreement between data sets based on genetically characterized and uncharacterized RAPD markers. Our analyses used only genetically characterized RAPD markers and revealed that contamination, in addition to-drift and/or selection, likely contributed to differences among independently maintained, publicly released inbreds. However, RAPD markers were not able to distinguish confidently among four related inbreds. RAPD markers will be useful in Allium genetics and breeding, but identifying and characterizing reliable polymorphisms is critical.

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Nnadozie C. Oraguzie, Sue E. Gardiner, Heather C.M. Basset, Mirko Stefanati, Rod D. Ball, Vincent G.M. Bus, and Allan G. White

Four subsets of apple (Malus Mill.) germplasm representing modern and old cultivars from the repository and apple genetics population of the Horticulture and Food Research Institute of New Zealand Limited were used in this study. A total of 155 genotypes randomly chosen from the four subsets were analyzed for random amplified polymorphic DNA (RAPD) variation. Nine decamer primers generated a total of 43 fragments, 42 of which were polymorphic across the 155 genotypes. Pairwise distances were calculated between germplasm subsets using the distance metric algorithm in S-PLUS, and used to examine intra-and inter-subset variance components by analysis of molecular variation (AMOVAR). A phenogram based on unweighted pair group method with arithmetic average (UPGMA) cluster analysis was constructed from the pairwise distances and a scatter plot was generated from principal coordinate analysis. The AMOVAR showed that most of the variation in the germplasm (94.6%) was found within subsets, suggesting that there is significant variation among the germplasm. The grouping of genotypes based on the phenogram and scatter plot generally did not reflect the pedigree or provenance of the genotypes. It is possible that more RAPD markers are needed for determining genetic relationships in apple germplasm. Nevertheless, the variation observed in the study suggests that the current practice of sublining populations in the first generation to control inbreeding may not be necessary in subsequent generations. If these results are confirmed by fully informative molecular markers, germplasm managers should reassess the structure of their genetics populations. There may be a need to combine sublines in order to capture the maximum genetic diversity available and to streamline breeding efforts.

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Kang Hee Cho, Seo Jun Park, Su Jin Kim, Se Hee Kim, Han Chan Lee, Mi Young Kim, and Jae An Chun

cultivars and for use in subsequent analyses. Table 2. Random amplified polymorphic DNA primers used in this study, their sequences, and the numbers of polymorphic fragments produced. Fig. 1. Random amplified polymorphic DNA profiles of 45 blueberry

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Min Wang and Irwin L. Goldman

Genetic relationships among 37 accessions of Beta vulgaris, including 21 table beet, 14 sugar beet, and two Swiss chard (Beta vulgaris ssp. cicla) accessions, were evaluated using randomly amplified polymorphic DNA (RAPD). Genetic distance was estimated based on the presence or absence of polymorphic RAPD bands. Multidimensional scaling plots of genetic distance values revealed that table beet inbred lines from the University of Wisconsin Table beet Breeding Program clustered in an intermediate position between sugar beet breeding lines and standard table beet germplasm, likely because of their origin from an introgression program designed to incorporate sugar beet genes.

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Hak-Tae Lim

The phylogenetic relationships between Korean endemic, Hanabusaya asiatica, and its allied groups, including four genera and nine species, were investigated at the DNA level using randomly amplified polymorphic DNA (RAPD) method. Ten primers out of 80 primers (10-mer) screened gave rise to very high polymorphism (99%) in all of the tested plants, producing 153 randomly amplified DNA fragments. H. asiatica was differentiated from its allied groups at the 0.62 of similarity index of RAPDs. This results were in accordance with previous classification based on palynological studies. It was confirmed that H. asiatica could be placed into Korean endemic and suggested that RAPD technique be used as an additional method of phylogenetic relationship for plant systematics.

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Guenhwa Jung, Dale T. Lindmen, and Dermot P. Coyne

Eight species and 57 selections/cultivars of Penstemon were compared for genetic variability using Random Amplified Polymorphic DNAs (RAPDs). The RAPD technique was used to help understand the genetic relationships in species and cultivars in the genus Penstemon. Ten RAPD primers (from Operon) were screened to identify polymorphisms among these eight species and 57 selections. More than 100 RAPD polymorphic bands were obtained. A principle component analysis was used to study genetic relationships. Variation among species was greater than variation among selections/cultivars within species. RAPD markers distinguished differences between most cultivars tested. DNA fingerprints generated by RAPDs should be useful to distinguish cultivars of Penstemon, as well as to assist in determining genetic relationships between species.

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Hong Xu, Diane J. Wilson, S. Arulsekar, and Alan T. Bakalinsky

Randomly amplified polymorphic DNA (RAPD) markers were generated for identifying grape (Vitis) rootstocks. Seventy-seven primers (10 bases long) were screened using CsCl-purified leaf DNA derived from several field samples of nine rootstocks sampled in successive years. Nine RAPD markers were detected from six primers and, in combination, distinguished all nine rootstocks tested. Because inconsistencies were encountered in performing the RAPD assay, sequence-specific primers were derived from cloned RAPD bands for use under more stringent amplification conditions. Southern hybridization analysis of the RAPD gels with cloned RAPD bands as probes revealed deficiencies of scoring RAPD bands based solely on ethidium bromide staining. In some cases, bands of the same size generated by the same primer in different rootstocks-normally scored as the same marker-failed to cross-hybridize, implying lack of homology between the bands. More commonly, bands scored as absent based on ethidium bromide staining were detected by hybridization. Six of the nine cloned RAPD bands were partially sequenced, and sequence-specific primer pairs were synthesized. Two primer pairs amplified a product the same size as the original RAPD band in all rootstocks, resulting in loss of polymorphism. Two other pairs of sequence-specific primers derived from the same marker failed to amplify the expected band consistently. Three of the most useful primer pairs amplified apparent length variants in some accessions and will have value as polymerase chain-reaction markers for fingerprinting.

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Kimberly J. Walters, George L. Hosfield, Mark A. Uebersax, and James D. Kelly

Three populations of navy bean (Phaseolus vulgaris L.), consisting of recombinant inbred lines, were grown at two locations for 2 years and were used to study canning quality. The traits measured included visual appeal (VIS), texture (TXT), and washed drained mass (WDM). Genotype mean squares were significant for all three traits across populations, although location and year mean squares were higher. We found a positive correlation (r = 0.19 to 0.66) between VIS and TXT and a negative correlation (r = -0.26 to -0.66) between VIS and WDM and between TXT and WDM (r = -0.53 to -0.83) in all three populations. Heritability estimates were calculated for VIS, TXT, and WDM, and these values were moderate to high (0.48 to 0.78). Random amplified polymorphic DNA markers associated with quantitative trait loci (QTL) for the same canning quality traits were identified and studied in each population. Marker-QTL associations were established using the general linear models procedure with significance set at P=0.05. Location and population specificity was common among the marker-QTL associations identified. Coefficient of determination (R2) values for groups of markers used in multiple regression analyses ranged from 0.2 to 0.52 for VIS, 0.11 to 0.38 for TXT, and 0.25 to 0.38 for WDM. Markers were identified that were associated with multiple traits and those associations supported correlations between phenotypic traits. MAS would offer no advantage over phenotypic selection for the improvement of negatively associated traits.