Target region amplified polymorphism (TRAP) markers were used to evaluate genetic variability among 48 accessions of spinach (Spinacia oleracea L.), an economically important leafy vegetable crop in many countries. Thirty-eight accessions collected and preserved by the USDA National Plant Germplasm System (NPGS) and 10 commercial hybrids were used in the current study. For assessing genetic diversity within accessions, DNA samples were prepared from nine to 12 individual seedlings from six germplasm accessions and two hybrids. Relatively high levels of polymorphism was found within accessions based on 61 polymorphic TRAP markers generated with two fixed primers derived from the Arabidopsis-type telomere repeat sequence and two arbitrary primers. For evaluating inter-accession variability, DNA was extracted from a bulk of six to 10 seedlings of each accession. Of the 1092 fragments amplified by 14 primer combinations, 96 (8.8%) were polymorphic and discriminated the 48 accessions from each other. The average pair-wise genetic similarity coefficient (Dice, Nei) was 57.5% with a range from 23.2 to 85.3%. A dendrogram was constructed based on the similarity matrix. It was found that the genetic relationships were not highly correlated with the geographic locations in which the accessions were collected. However, seven commercial hybrids were grouped in three separate clusters, suggesting that the phenotype-based breeding activities have effect on the genetic variability. This study demonstrated that TRAP markers are effective for fingerprinting and evaluating genetic variability of spinach germplasm.
Jinguo Hu, Beiquan Mou, and Brady A. Vick
Amnon Levi, Claude E. Thomas, Todd C. Wehner, and Xingping Zhang
Genetic diversity and relatedness were assessed among 46 American cultivars of watermelon (Citrullus lanatus var. lanatus), and 12 U.S. Plant Introduction accessions (PIs) of Citrullus sp. using 25 randomly amplified polymorphic DNA (RAPD) primers. These primers produced 288 distinct reproducible bands that could be scored with high confidence among cultivars and PIs. Based on the RAPD data, genetic similarity coefficients were calculated and a dendrogram was constructed using the unweighted pair-group method with arithmetic average (UPGMA). The cultivars and C. lanatus var. lanatus PIs differentiated at the level of 92% to 99.6% and 88% to 95% genetic similarity, respectively. In contrast, the C. lanatus var. citroides, and C. colocynthis PIs were more divergent and differentiated at the level of 65% to 82.5% and 70.5% genetic similarity, respectively. The low genetic diversity among watermelon cultivars in this study emphasizes the need to expand the genetic base of cultivated watermelon.
Lyn A. Gettys and Dennis J. Werner
Stokes aster is a herbaceous perennial native to the southeastern United States. Stokesia is a monotypic genus belonging to the tribe Vernonieae Cass. (family Asteraceae Dumont). The level of genetic diversity within the genus is unknown. The goal of this study was to determine the level of genetic diversity and relatedness among cultivars of stokes aster. The genetic relatedness among 10 cultivars of stokes aster, one accession of Vernonia crinita Raf. (syn. V. arkansana DC.), and one accession of Rudbeckia fulgida Ait. var. sullivantii (Beadle et Boynton) Cronq. `Goldsturm' was estimated using 74 randomly amplified polymorphic DNA (RAPD) primers. Similarity indices suggest that cultivars of stokes aster are very closely related, with values for all pairwise comparisons of cultivars of stokes aster ranging from 0.92 to 0.68. One cultivar, `Omega Skyrocket', had markedly lower similarity indices from the other cultivars, ranging from 0.72 to 0.68. Similarity indices between stokes aster and Vernonia and between stokes aster and Rudbeckia were 0.44 and 0.50, respectively.
The genus Actinidia contains more than 66 species and 118 taxa. The best-known species is A. deliciosa C.F. Liang et A.R. Ferguson, the commercially developed kiwifruit. The natural range of Actinidia is remarkably wide, extending from the tropics (latitude 0°0′) to cold temperate regions (500°N). However, the original distribution of most taxa of Actinidia is centered around the mountains and hills of south-central and southeast China, with the QinLing mountain as its northern boundary and the HengDuan mountain as its western boundary. Sixty-two species, 114 taxa have been found in China. Genetic variation ranging from morphological traits to DNA is discussed in here. 1) Morphological variation (mainly horticulturally important traits): fruit size varies from 2 to 100 g, fruit skin color ranges from brown to green to white to purple, fruit surface from setose to villose, and flesh color from green to purple. 2) Nutritional value and flavor: vitamin C content varies from 10 mg/100 g to 1000 mg/100 g fresh fruit, soluble solids ranges from 2% to 22%, and flavor includes variation form bitter and astringent to desirable sour-sweet. 3) Gender variation includes six phenotype/genotypes of female, inconstant female, male, fruiting male, neuter and hermaphrodite. 4) Ploidy variation is consist of 2x, 4x, 6x, 8x in both intra- and inter-taxa variation. 5) Isozyme genetic variation: high polymorphisms were detected in commercial cultivated species and 28 wild species. 6) Genetic diversity was evaluated by RAPD, SSR, PCR-RFLP of mtDNA and cpDNA, a high level of genetic diversity was found in both inter-taxa and intra-taxa. Conservation strategy for diverse genetic resources of Actinidia in China is also discussed.
Roberto F. Vieira, Peter Goldsbrough, and James E. Simon
Molecular markers were used to assess genetic diversity in basil (Ocimum L. spp., Lamiaceae). Using randomly amplified polymorphic DNA (RAPD) analysis, 11 primers generated 98 polymorphic bands, ranging from 300 to 2,000 base pairs, that discriminated among 37 accessions across nine Ocimum spp. Means of genetic similarities within Ocimum spp. showed that the domesticated species, O. minimum L. (0.887), O. basilicum L. (0.769), and O. ×citriodorum Vis. (0.711) had highest similarity indices within species, while the nondomesticated, O. americanum L. (0.580), O. gratissimum L. (0.408), and O. kilimandscharicum Guerke (0.559) showed the lowest similarity. RAPD results indicated that O. minimum should not be considered a distinct species but rather a variety of O. basilicum. Consistent clusters among all but one of the O. ×citriodorum spp., all containing citral as the major constituent, were identified using bootstrap analysis. RAPD analysis was useful in discriminating among Ocimum spp., although within species resolution will require a higher number of polymorphic bands.
Gayle Volk, Christopher Richards, Adam Henk, Ann Reilley, Nahla Bassil, and Joseph Postman
Edible European pears (Pyrus communis sp. communis L.) are thought to be derived from wild relatives native to the Caucasus Mountain region and eastern Europe. We collected genotype, phenotype, and geographic origin data for 145 P. communis individuals derived from seeds collected from wild relatives. These individuals are currently maintained in the USDA–ARS National Plant Germplasm System (NPGS) in Corvallis, Ore. Pear genotypes were obtained using 13 microsatellite markers. A Bayesian clustering method grouped the individual pear genotypes into 12 clusters. The subspecies of pears native to the Caucasus Mountains of Russia, Crimea, and Armenia could be genetically differentiated from the subspecies native to eastern European countries. Pears with large fruit clustered closely together and are most closely related to a group of genotypes that are intermediate to the other groups. Based on the high number of unique alleles and heterozygosity in each of the 12 clusters, we conclude that the genetic diversity of wild P. communis is not fully represented in the NPGS
Julie Villand, Terry Berke, Liwayway Engle, and James Nienhuis
Significant effort has been made in the collection of Capsicum germplasm throughout the world for maintenance by genebanks. The largest Capsicum germplasm collection is held by the Asian Vegetable Research and Development Center (AVRDC), consisting of 6844 accessions and eight species. The paradox of any germplasm collection is that, as the number of accessions and the probability of preserving genetic variability increases, the ability of users to efficiently utilize this resource decreases. Genetic variation can be quantified using RAPD molecular marker allele frequency and allelic variation to understand the genetic structure and variation within and among populations. The comprehensive Capsicum collection held at the AVRDC provides an opportunity to sample a range of germplasm representative of the variability that exists in available Capsicum germplasm. Accessions were sampled from the AVRDC collection to represent the range of genetic variation available in Capsicum 1) based on cluster analysis using morphological traits among 1500 accessions and 2) based on pedigree information from the Capsicum breeding program. Our objectives include understanding the structure and magnitude of genetic diversity among these AVRDC accessions and comparing the genetic diversity within sub-populations of these accessions. RAPD fingerprints of these accessions were collected using markers dispersed over numerous linkage groups based on a genetic map we have constructed. RAPD band frequencies and RAPD band diversity were used to test differences among and within sub-populations. The understanding of the distribution of genetic variation among and within these sub-populations will be useful for prioritizing collection, conservation, and sampling of these genetic resources.
Fenny Dane and Hongwen Huang
The genetic diversity within and between four geographic populations of the Ozark chinkapin was evaluated and partitioned in order to gain an understanding of the overall genetic diversity and structure of this species, which will be instrumental for its preservation and germplasm enhancement. Nuts of chinkapin trees along the natural range of the species in the Sylamore Ranger District of the Ozark National Forest in Arkansas were collected and evaluated with isozyme and RAPD markers scattered across the genome. Allozyme differences were detected among the geographic populations. Allele frequencies will be determined and subjected to genetic diversity statistics. A conservation plan will be recommended.
Kirk W. Pomper, Sheri B. Crabtree, Shawn P. Brown, Snake C. Jones, Tera M. Bonney, and Desmond R. Layne
The pawpaw [Asimina triloba (L.) Dunal.] is a tree fruit native to many areas of the southeastern and mid-western United States. Kentucky State University (KSU) is designated as a satellite repository for Asimina for the U.S. Department of Agriculture (USDA), National Plant Germplasm System (NPGS). An assessment of the level of genetic diversity in cultivated pawpaw would assist in development of the future germplasm repository collection strategies for cultivar improvement. The objectives of this study were to identify intersimple sequence repeat (ISSR) markers that segregate in a simple Mendelian fashion and to use these markers to assess genetic diversity in 19 pawpaw cultivars. Leaf samples from the 34 progeny of controlled crosses (1-7-1 × 2-54 and reciprocal) and the parents were collected, DNA was extracted, and subjected to the ISSR methodology using the University of British Columbia microsatellite primer set #9. Seven primers yielded 11 Mendelian markers with either a 3:1 or 1:1 ratio that was confirmed by chi-square analysis. Analysis of genetic diversity using 10 of the ISSR markers from 19 pawpaw cultivars revealed a moderate to high level of genetic diversity, with a percent polymorphic loci P = 80 and an expected heterozygosity He = 0.358. These diversity values are higher than those reported for cultivated pawpaw using isozyme or randomly amplified polymorphic DNA (RAPD) markers, indicating that the ISSR marker methodolgy has a higher level of discrimination in evaluating genetic diversity in pawpaw and/or pawpaw has greater levels of genetic diversity than previously found.
James Nienhuis, Julie Rodriguez, Wilber Phillips, Peter Hanson, and Liliway Engle
Worldwide, there are cuurently more than 60 germplasm banks that contain tomato (Lycopersicon esculentum) collections ranging is size from a few dozen to several thousands of accessions. In the utilization of these genetic resources sampling from only one germplasm bank may result in limiting available genetic diversity, whereas sampling from several germplasm banks may result in unnecessary redundancy. The current lack of knowledge regarding the relative magnitudes of genetic diversity contained within different collections makes it difficult to develop a core collection that maximizes genetic diversity. Two large tomato collections are housed at the Asian Vegetable Research and Development Center (AVRDC), Sanhua, Taiwan, R.O.C., and the Centro Agronomico Tropical de Investigacion y Enseoanza (CATIE), Turrialba, Costa Rica. Ninety-six accessions from CATIE and 102 accessions from AVRDC were randomly sampled from each base collection. The total of 198 accessions were charcterized for 103 polymorphic RAPD molecular marker bands. The results indicated that the two germplam banks sampled different genetic diversity. In addition, the magnitude of genetic diversity was greater in the AVRDC collection compared to CATIE.