Amplified Fragment Length Polymorphism Bands Research Articles

Molecular characterization of eliminated chromosomes in Hessian fly (Mayetiola destructor (Say))

Like other cecidomyiid Diptera, Hessian fly has stable S chromosomes and dispensable E chromosomes that are retained only in the germ line. Amplified fragment length polymorphisms (AFLP), suppressive subtractive hybridization (SSH), fluorescent in-situ hybridization (FISH), and sequencing were used to investigate similarities and differences between S and E chromosomes. More than 99.9% of AFLP bands were identical between separated ovary and somatic tissue, but one band was unique to ovary and resembled Worf, a non-LTR retrotransposon. Arrayed clones, derived by SSH of somatic from ovarian DNA, showed no clones that were unique to ovary. FISH with BAC clones revealed a diagnostic banding pattern of BAC positions on both autosomes and both sex chromosomes, and each E chromosome shared a pattern with one of the S chromosomes. Sequencing analysis showed that E chromosomes are nearly identical to S chromosomes, since no sequence could be confirmed to belong only to E chromosomes. There were a few questionably E-specific sequences that are candidates for further investigation. Thus, the E chromosomes appear to be derived from S chromosomes by the acquisition or conversion of sequences that produce the negatively heteropycnotic region around the centromere.

Phenotypic and genetic characterization of “Aglione della Valdichiana”: Population structure and genetic relationship analysis of a white gentle giant

“Aglione della Valdichiana” (Allium ampeloprasum var. holmense) is a landrace of Great Headed Garlic (GHG), an historical and healthy vegetable that has been recently rediscovered and registered in the National and Regional catalog of local varieties. It is grown in small fields in a region between Tuscany and Umbria, Italy, and due to its high market value, it is at risk of commercial frauds. The morphological traits and molecular profile of 9 local populations were evaluated together with 36 accessions of leek, garlic, wild relatives and other GHGs of different geographic origins and used as controls. The 39 morphological descriptors were able to distinguish the 9 accessions from leek and garlic, but unable to distinguish among them. The 549 AFLP (Amplified Fragment Length Polymorphism) amplicons obtained from nine primer combinations were able to clearly distinguish Aglione accessions from all the others, both by UPGMA (Unweighted Pair Group Method with Arithmetic mean) clustering and by STRUCTURE analysis, and this is due to several private AFLP bands, most from M+AGC/E+CTG primer combination. Despite its vegetative propagation, the within accession variability of Aglione is higher than expected and most likely due to somatic mutations. The genetic relationships are discussed, including the closer relationship found between Aglione and garlic vs. Aglione and leek.

Genetic relationship among 12 Trapa species/varietas from Yangtze River Basin revealed by AFLP markers

Abstract Trapa species are floating-leaved aquatic plants with significant economic and ecological values. However, the genetic relationship within Trapa genus is unclear. Here, we evaluated the genetic relationship of 12 Trapa species/varietas and 155 individuals collected from the Yangtze River Basin (China), one of the species diversity centers of the genus. With 264 AFLP (amplified fragment length polymorphism) bands, the NJ analysis showed that all the individuals were clearly divided into groups according to their taxonomic positions and geographic origins. Both PCoA and NJ analysis further demonstrated that the two small-seed species (T. incisa and T. maximowiczii) were initially separated from the other taxa with large seeds, indicating the basal classification status of the two species. Three clustering approaches (NJ tree, STRUCTURE and PCoA) consistently exhibited a close relationship among T. bispinosa, T. quadrispinosa and T. bicornis var. cochinchinensis, which suggested that T. bicornis var. cochinchinensis, the cultivated taxon, might be of hybrid origin between T. bispinosa and T. quadrispinosa; as for T. quadrispinosa group, T. quadrispinosa var. quadrispinosa and its two variants shared the same genetic group and should be treated as one species; compared with T. japonica as a single genetic cluster, four taxa (T. natans var. pumila, T. octotuberculata, T. macropoda and T. mammillifera) were closely related, and the four taxa shared thick husks and exaggerated or deformed tubercles on seeds. This study is of great implication to provide molecular proof for phylogeny within Trapa genus, which will facilitate the utilization of natural germplasm of Trapa.

Macroscopic-microscopic characteristics and AFLP fingerprint for identification of Erythroxylum novogranatense, E. cambodianum and E. cuneatum endemic to Thailand

Erythroxylum novogranatense (Morris) Hieron, E. cambodianum Pierre and E. cuneatum (Miq.) Kurz in family Erythroxylaceae was traditionally used as an antipyretic, general stimulant and gastrointestinal diseases. Due to their morphological similarity, the correct identification was necessary for the quality control in herbal medicine. E. novogranatense (Morris) Hieron, E. cambodianum Pierre and E. cuneatum (Miq.) Macroscopic and microscopic characteristics evaluated Kurz endemic to Thailand according to WHO standard guideline and amplified fragment length polymorphism (AFLP) fingerprint. Morphological characters of E. novogranatense, E. cambodianum and E. cuneatum were similar in their flower, fruit and seed but different in stem and leaf. Microscopic characteristics from these three species, including constant leaf numbers, showed individual values. The stomata were classified as paracytic type. The midrib transverse section showed distinct characters of the epidermis, palisade cell, stomata, spongy cell, parenchyma, xylem vessel, phloem tissue and collenchyma. AFLP fingerprint showed highly polymorphisms 97.42% with the number of bands (349 bands) ranging between 50-750 bands. Primer E+ACG/M+CTT had the highest number of AFLP band (91 bands). The dendrogram generated from UPGMA could separate these three species. In summary, the combination of morphological characteristics, microscopic investigation and AFLP fingerprinting can be used to identify plant species and determine the genetic relationship among three Erythroxylum species.

Genetic diversity of Indigofera kirilowii Maxim. ex Palibin using AFLP makers

The present studies were conducted to assess the genetic diversity and to infer population structure of 220 individuals of Indigofera kirilowii from 8 natural populations of Shandong province, north China, using amplified fragment length polymorphism (AFLP) markers. A total of 1589 AFLP bands were produced, of which 99.87% were polymorphic. High genetic diversity was considered (H = 0.1401; I = 0.2346), with high genetic differentiation (GST = 0.1058), while estimates of gene flow (Nm) were high in all analysis. No correlations were observed between geographic location and genetic diversity (r = –0.0901; p = 0.3293). Based on the results, here a strategy for the conservation of I. kirilowii germplasm was proposed.

Genetic diversity of Solanum elaeagnifolium, an invasive problematic weed in Jordan

SummarySolanum elaeagnifolium (silverleaf nightshade) is a problematic weed that is common in Jordan and difficult to control. The weed exhibits distinct morphological variations in growth habit, leaf shape, leaf margins, flower colour and presence or absence of spines between individuals among and within populations suggesting genetic differences. Genetic variations among 61 samples of S. elaeagnifolium collected from heavily infested sites in the central Jordan Valley were investigated using six simple sequence repeat (SSR) markers and eight amplified fragment length polymorphism (AFLP) primer combinations. Results showed that 111 out of 675 AFLP bands were polymorphic generating polymorphism information content (PIC) of 38.0%, while 23 SSR polymorphic alleles were detected generating a PIC of 30.8%. Phylogenetic analysis using RaxML software identified four major clades with a clear clustering of the samples with their collection sites. Genetic analysis using both techniques revealed high level of genetic diversity among S. elaeagnifolium samples collected from a small geographical area indicating that a range of genetic diversity may be detected in weed populations across the country that may complicate its management.

Genetic diversity and relationship of sainfoin (Onobrychis viciifolia Scop.) germplasm as revealed by amplified fragment length polymorphism markers

Sainfoin (Onobrychis viciifolia Scop.) is a perennial forage legume widely distributed in the northern temperate regions of the world. Its genetic improvement has been relatively slow due, in part, to the lack of genetic information including molecular characterization of sainfoin germplasm. An attempt was made to evaluate genetic diversity and relationships among 38 sainfoin accessions collected from different regions of the world using amplified fragment length polymorphism (AFLP) markers. Five AFLP primer pairs were used to assess 367 individual plants, which produced 1042 polymorphic AFLP bands. The frequencies of the scored bands in all assayed individuals ranged from 0.003 to 0.973, with a mean value of 0.165. The analysis of molecular variance revealed higher within-accession (84.3%) genetic variation than among accessions (15.7%). The genetic distance based on inter-accession distance matrices was significant for most accessions but was not significant for accessions sharing similar parents. A dendrogram of the collected accessions showed two clusters at an inter-accession genetic distance coefficient of 0.36. The revealed information on genetic distance and genetic diversity of the sainfoin accessions is useful for selecting genetically diverse germplasms for sainfoin genetic improvement efforts.

Screening for single nucleotide polymorphisms in highly degraded DNA by using the amplified fragment length polymorphism technique

Short tandem repeat (STR) analysis is generally used for human identification of forensic samples; however, standard STR analysis sometimes fails to generate full profiles since DNA is frequently degraded by various environmental factors. Recently, single nucleotide polymorphism (SNP) analysis has attracted attention for human identification since the shorter amplicons are better suited for degraded samples. Though various SNP loci are used for analysis of degraded samples, it is unclear which ones are more appropriate. To identify SNPs that were resistant to degradation, we artificially degraded DNA obtained from the buccal swabs of six volunteers and the K562 cell line by heat treatment. Subsequently, the amplified fragment length polymorphism (AFLP) technique was used for SNP screening. We focused on the AFLP bands detected in both the heat-treated and untreated samples, and DNA extracted from these bands was directly sequenced. DNA degradation increased as the duration of heat treatment increased, and no STR profiles could be generated after 6h of heat treatment. When the AFLP band patterns were compared between 6h heat-treated and untreated samples, eight common bands were detected. The sequences of the DNA fragments of these common bands had higher adenine-thymine (A-T) content and included 17 SNPs. The SNPs detected in the heat-treated and untreated samples were considered to be resistant to degradation. Although there was a little information available in databases regarding the nine SNPs identified in this study, this study shows that some of these SNPs might be useful for human identification of extremely degraded DNA.

Analysis of drought tolerance and genetic and epigenetic variations in a somatic hybrid between Ipomoea batatas (L.) Lam. and I. triloba L.

The somatic hybrid KT1 was previously obtained from protoplast fusion between sweetpotato (Ipomoea batatas (L.) Lam.) cv. Kokei No. 14 and its wild relative I. triloba L. However, its genetic and epigenetic variations have not been investigated. This study showed that KT1 exhibited significantly higher drought tolerance compared to the cultivated parent Kokei No. 14. The content of proline and activities of superoxide dismutase (SOD) and photosynthesis were significantly increased, while malonaldehyde (MDA) content was significantly decreased compared to Kokei No. 14 under drought stress. KT1 also showed higher expression level of well-known drought stress-responsive genes compared to Kokei No. 14 under drought stress. Amplified fragment length polymorphism (AFLP) and methylation-sensitive amplified polymorphism (MSAP) analyses indicated that KT1 had AFLP and MSAP band patterns consisting of both parent specific bands and changed bands. Further analysis demonstrated that in KT1 the proportions of Kokei No. 14 specific genome components and methylation sites were much greater than those of I. triloba. KT1 had the same chloroplast and mitochondrial genomes as Kokei No. 14. These results will aid in developing the useful genes of I. triloba and understanding the evolution and phylogeny of the cultivated sweetpotato.

Molecular genetic analysis of heterosis in interspecific hybrids of Argopecten purpuratus x A. irradians irradians.

Argopecten purpuratus and Argopecten irradians irradians hybridization was successfully performed and the hybrid offspring displayed apparent heterosis in growth traits. To better understand the genetic basis of heterosis, the genomic composition and genetic variation of the hybrids were analyzed with amplified fragment length polymorphism (AFLP) and simple sequence repeat (SSR) markers. Seven of eight universal SSR primers displayed polymorphism in the hybrids and their parental groups, and hybrids inherited both parental geno-types at each locus. Using five primer combinations in AFLP analysis, 433 loci were amplified in the hybrids and their parental groups. The frequency of polymorphisms was 88.22%. F1 hybrids inherited 88.11 and 92.88% of AFLP bands from their parents. Some loci did not follow Mendelian Law, including 48 loci in parents that were lost, and 11 new loci that were amplified in the hybrids. The parameters of Nei's gene diversity, Shannon's Information index, genetic distance, and molecular variance between groups were calculated. The genetic differentiation between two hybrid groups (0.253) was smaller than that between hybrids and their parents (0.554 to 0.645), and was especially smaller than that between two parental groups (0.769). The high genetic similarity (0.9347) and low genetic differentiation (0.2531) between two hybrid groups suggests that these hybrid groups were genetically very close. Heterozygosities of hybrid groups were higher than those of parental groups, indicating that the hybrids had increased genetic diversity.

POPULATION STRUCTURE OF THE POTATO TUBER MOTH ,PHTHORIMAEA OPERCULELLA (ZELLER) , LEPIDOPTERA: GELECHIIDAE) IN DELTA EGYPT USING RAPD ANALYSIS

Little is known about the nature and extent of genetic diversity in potato tuber moth Phthorimaea operculella (Zeller),Lepidoptera: Gelechiidae). Analysis of amplified fragment length polymorphism (AFLP) has the potential to become a powerfulnew DNA fingerprinting technique for studying genetic relationships and genetic diversity in insects. Random amplifiedpolymorphic DNA polymerase chain reaction (RAPD-PCR)was used to examine variation in three governorates in the Deltaof Egypt. The objective of this study was to provide baseline information on the population structure of potato tuber worm inEgypt. The applicability of CTAB -based DNA extraction protocol provided suitable for AFLP analysis. Potato tuber wormadults were collected from potato fields in the major production regions in the Egypt . We used 20 random 10-oligomer primerindividuals and 179 polymorphic AFLP bands were used to infer the geographic population structure of potato tuber worm.This study provides baseline data for the molecular characterization of potato tuber worm populations, which will aid in trackingthe origin of future invasions within Egypt.

Development of SCAR Markers for Korean Wheat Cultivars Identification

Son Jae-Han, Kyeong-Hoon Kim, Sanghyun Shin, Induk Choi, Hag-Sin Kim, Young-Keun Cheong, Choon-Ki Lee, Sung-Il Lee, Ji-Yeong Choi, Kwang-Geun Park, and Chon-Sik Kang. Plant Breeding and Biotechnology 2014;2:224-30. https://doi.org/10.9787/PBB.2014.2.3.224

A study of the genetic variation of the aquatic fern Marsilea quadrifolia L. preserved in botanical collections in Poland and originated from natural populations in Europe

Aim of the present study was to evaluate the genetic diversity of selected European populations of Marsilea quadrifolia L. and to assess the applicability of those genetic resources of Marsilea quadrifolia L. that have been preserved in Polish botanical gardens, for the reintroduction of this species into its historical range in Poland. Three Polish populations that originated from botanical collections (Zabrze, Żarów and Puławy) and four natural populations (two from Slovakia (Slovakia I and Slovakia II), one from France and one from Germany) were analyzed using Amplified Fragment Length Polymorphism (AFLP) markers. A very low level of genetic variation was found both within and between the populations in the study, which likely resulted from a genetic bottleneck probably caused by human activities. Plants with the same AFLP fingerprint were found across several populations; however, singleton samples with a unique AFLP band pattern were also present within all of the populations. The presence of singletons led to relatively high values of Simpson's diversity index, which may suggest a considerable effect of mutations and some possibility of sexual reproduction as sources of the observed variation. The partitioning of molecular variance was calculated using hierarchical AMOVA, which showed that a negligible value of only 0.81% of the variation was explained by the category of population, i.e. plants originating from the botanical collections or from the natural habitats. This result indicates that M. quadrifolia populations from botanical collections resemble natural populations in terms of the level of their genetic variation and that the populations that were obtained from the Polish collections could be used for the successful reintroduction of this species into its historical range in Poland, and a similar situation may be given also in other areas of occurrence of this plant that is under threat throughout its area of occurrence in Europe.

Citrus somatic hybrid: an alternative system to study rapid structural and epigenetic reorganization in allotetraploid genomes

Citrus somatic hybrids produced in the past years provide a novel opportunity to study the immediate effects of allopolyploidization on genome structure and methylation. Here, we present a first attempt to investigate the alterations in genome structure and methylation in three sets of citrus somatic allotetraploids and their diploid parents using amplified fragment length polymorphism (AFLP) and methylation-sensitive amplified polymorphism (MSAP) techniques. Our results indicate that all the allotetraploids mainly have the AFLP and MSAP banding patterns containing specific bands from both parents plus some alterations. The incidences of the AFLP polymorphic bands in allotetraploids show a range from 4.61 to 7.88 %, while from 12.50 to 15.67 % of the sites are methylated. In addition, the proportions of callus-parent-specific DNA structure and methylation alterations are much greater than those of leaf-parent-specific alterations in the somatic hybrids. Furthermore, we find that the somatic hybrids take on a greater divergence from the callus parent and a closer relationship to leaf parent in all groups of plants by dendrogram analysis based on AFLP or MSAP data. Taken together, our results suggest that somatic hybrids are very useful in elucidating the immediate changes that occur in newly synthesized allotetraploid.

Genetic diversity in African yam bean accessions based on AFLP markers: towards a platform for germplasm improvement and utilization

Accurate knowledge of intra-specific diversity of underutilized crop species is a prerequisite for their genetic improvement and utilization. The diversity of 77 accessions of African yam bean (AYB, Sphenostylis stenocarpa) was assessed by amplified fragment length polymorphism (AFLP) markers. A total of EcoRI/MseI primer pairs were selected and 227 AFLP bands were generated, of which 59(26%) were found to be polymorphic in the 77 accessions of AYB. The most efficient primer combination for polymorphic detection was E-ACT/M-CAG with a polymorphic efficiency of 85.5%, while the least efficient was E-AGC/M-CAG with a polymorphic efficiency of 80.6%. The Jaccard genetic distance among the accessions of AYB ranged between 0.048 and 0.842 with a mean of 0.444. TSs98 and TSs104B were found to be the most similar accessions with a genetic similarity of 0.952. The neighbour-joining dendrogram grouped the 77 accessions of AYB into four distinct clusters comprising 8, 20, 21 and 28 accessions. The major clustering of the accessions was not related to their geographical origin. Cluster I was found to be the most diverse. The mean fixation index (0.203) and the mean expected heterozygosity (0.284) revealed a broad genetic base of the AYB accessions. The same germplasm set was previously evaluated for several agro-morphological traits. As the collection of additional AYB germplasm continues, the phenotypic profile, the clustering of the accessions and the AFLP primer combinations from this study can be used to augment breeding programmes.

Ecological Adaptation of the EndemicShepherdia rotundifoliato Conditions in Its Colorado Plateau Range

Due to limited water supplies, use of drought-tolerant species to conserve water in irrigated urban landscapes is increasingly important in the Intermountain West. The Colorado Plateau endemic shrub Shepherdia rotundifolia Parry is a potential candidate for use in sustainable urban low-water landscapes (LWLs) for its aesthetic and drought-tolerant qualities. However, the species is difficult to establish in urban landscapes of different fertility and water availability than found in regional native habitats. A better understanding of environmental and genetic constraints, as well as morphological adaptation in native habitats, may facilitate greater use of S. rotundifolia in LWLs. The goal of this study was to investigate variability in environmental conditions, morphology, and genetics among 6 populations of S. rotundifolia along an elevation gradient (range 1200–2500 m) in the species' native range. Aboveground environmental conditions were characterized from 30-year proximal weather station data, intra-annual weather collected on-site, and site relative light intensity (RLI) from hemispherical canopy images. Belowground, we analyzed site-specific soils for texture, pH, salinity, organic matter (OM), and macronutrients. We characterized plant morphology and genetics from leaf area and specific leaf area (SLA), scanning electron microscopic imaging of tri chôme structure and leaf thickness, and amplified fragment length polymorphism (AFLP) genetic variation among populations. Precipitation, air temperature, RLI, and soil properties varied widely among populations. Differences among leaf area, SLA, and leaf trichome structure suggest population-level adaptations consistent with environmental differences, particularly between high- and low-elevation populations. Similarly, distinct AFLP banding patterns among high- and low-elevation populations suggest differences due to isolation by distance. SLA was correlated with RLI, OM, and potassium (K). Relatively high native levels and positive correlation with SLA suggest that K may be a limiting factor in urban landscape soils. Selection of plants adapted to environmental conditions similar to those present in urban landscapes may enhance successful use of S. rotundifolia. Genetic variation also suggests potential for cultivar selection.

English

The genetic diversity of 40 African yam bean (AYB) accessions was assessed using amplified fragment length polymorphism (AFLP) markers. Seeds of 40 accessions of AYB obtained from the International Institute of Tropical Agriculture (IITA) and Institute of Agricultural Research and Training (IAR&T) Ibadan, Nigeria, were grown in a greenhouse and young leaves from two weeks old plants collected for DNA extraction. The four primer combinations used generated a total of 1730 amplification fragments across the AYB accessions used in this study of which 1647 were polymorphic (95.20%). The number of amplified polymorphic AFLP bands per primer pair varied from 360 to 520 with an average percentage polymorphism of 95.6%. E-AGC/M-CAG produced the highest number of polymorphic bands (520). Polymorphic information content (PIC) values ranged from 0.9447 to 0.9626. The highest level of polymorphism (100%) was recorded for two primer combinations (E-AAC/M-CAG and E-ACT/M-CAG). The results of cluster analysis using UPGMA tree, grouped the 40 accessions of AYB into two major clusters with an overall similarity of 67.5%. The level of similarity between the accessions spanned 0.66 to 0.91. TSs 138 and TSs 139 were the most closely related accessions with high level of similarity index (0.91). Comparable results were obtained using Factorial Coordinate Analysis (FCO).  The results from the present study confirm the robustness and the suitability of the AFLP as a molecular tool for the assessment of genetic diversity in AYB accessions.   Key words: Amplified fragment length polymorphism (AFLP), cluster analysis, genetic diversity, Sphenostylis stenocarpa, polymorphism.

Genetic Diversity of Musa balbisiana Colla in Indonesia Based on AFLP Marker

Musa balbisiana Colla, known as Pisang Klutuk/Pisang Batu, is important for banana breeding program due to its B genome and often considered to be resistant to pest, disease and drought. Banana is a big and tall herb up to 7-9 m in height.The study was conducted to assess genetic diversity of 21 accessions of M. balbisiana cultivars/varieties from Indonesia based on Amplified Fragment Length Polymorphism (AFLP) markers in order to provide basic information to support banana breeding program. Analyses of similarity index of Nei and Li and clustering based on UPGMA was conducted using NTSYS program. Principal Component Analysis (PCA) was conducted by MINITAB 14. Twenty two primer pairs of AFLP markers produced 485 AFLP bands varying from 51-3206 bp in size and 46.18% of the AFLP bands were polymorphic. Genetic diversity among the 21 accessions of M. balbisiana was 13.8%. The genetic diversity of wild M. balbisiana was 12.9%, higher than the genetic diversity of cultivated M. balbisiana which was 11.5%. Cluster analysis based on UPGMA suggested that wild M. balbisiana and cultivated M. balbisiana could not be separated into different clusters. Both cluster analysis and PCA produced the same three groups of the accessions. The PCA analyses showed that 17 AFLP bands were responsible for the grouping.

Ploidy level and molecular phylogenic relationship among novel Ipomoea interspecific hybrids

Interspecific hybridization can be used to broaden the genetic base, generate novel species, postulate genetic relationships, and to introgress elite alien genes. However, interspecific hybridizations using wild parents outside the Ipomoea section Batatas are very difficult and have not been much studied. We used an improved hybridization technology to generate three novel interspecific hybrids by crossing Ipomoea batatas (L.) Lam. × I. hederacea Jacq., I. batatas (L.) Lam. × I. muricata (L.) Jacq., and I. batatas (L.) Lam. × I. lonchophylla J.M. Black. The ploidy level of the interspecific hybrids was determined by flow cytometry. The cross, I. batatas × I. hederacea, yielded the first artificial pentaploid Ipomoea hybrid ever. The other two hybrids, I. batatas × I. hederacea and I. batatas × I. muricata were tetraploid. The first two hybrids showed normal storage roots, a significant improvement in the storage roots of currently existing interspecific Ipomoea hybrids. AFLP (Amplified Fragment Length Polymorphism) molecular markers were used to explore the genetic relationship of these three novel interspecific hybrids with three other natural diploid, tetraploid, and hexaploid species of the Ipomoea section Batatas. Cluster analysis of AFLP bands showed that these three new interspecific hybrids were closely related to cultivated sweet potato (I. batatas/L./Lam.), which indicated that these novel hybrids can be used as an interspecific bridge to transfer alien genes from wild to cultivated species.

Genetic variation in Danish and Norwegian germplasm collections of hops

The germplasm collections of hops (Humulus lupulus L.) in Denmark and Norway are maintained in clonal archives funded by the national authorities. The plants have been collected over the last decades as part of a strategy to conserve plant genetic resources for future generations. The major part of the various collections consist of plants collected in villages and gardens. About 20% are plants used for breeding, mainly kept in a collection at Carlsberg, Denmark. In order to identify any duplicates and with a view to learning more about the various collections, a DNA fingerprinting study was initiated, analysing 62 Danish and 34 Norwegian clones with a set of five amplified fragment length polymorphism (AFLP) markers. The AFLP analyses resulted in 41 polymorphic bands and were able to separate the majority of the Danish and the Norwegian accessions. UPGMA dendrograms showed 21 accession groups, and potential duplicates were found within 13 of these groups. Principal coordinates analysis revealed that plants were differentiated according to country of origin. In addition, regional separation of the plants within each country was also detected, and similar levels of diversity were found in the Danish and the Norwegian collections. Compared to the rest of the plants, there was less diversity within the Carlsberg material. For the Norwegian as well as a part of the Danish collection, morphological characterisation and chemical analysis was carried out, allowing a comparison of these to the AFLP data. A correlation with AFLP bands and both morphological and chemical characteristics was detected. The most promising results for further breeding was an association of AFLP bands with the content of colupulon in the cones, measured by relative values compared to the total alpha acid content. Further studies are needed to verify such an association with the potential to develop a PCR-based marker for hop breeding carried out in the clones now analysed with AFLP markers, making it possible to search for any association between AFLP data and phenotypic data.