Microsatellite Fingerprinting Research Articles

Authentication of a food product based on DNA analysis of an added natural biological tracer: Testing the application to dry cured hams

Food authenticity is crucial for all value chains, including many meat products. Various methods have been developed to authenticate meat products based on the intrinsic DNA information of the animals from which the products originated. In this study, we propose an alternative method of authentication based on DNA analysis of a biological tracer added to the product. To demonstrate its effectiveness, we conducted a pilot study focused on dry-cured hams that were authenticated using genetically characterised wheat flours, obtained from different accessions. The study consisted of three main steps: first, we analysed 23 wheat accessions using random amplified polymorphic DNA assays and seven wheat microsatellites to assess the accession homogeneity/homozygosity and establish accession specific microsatellite fingerprinting; next, we tested, as a proof-of-concept, the feasibility of using genetically characterised wheat flours as natural tracers when mixed with lard (used to cover the skin-free part of the legs) and ink (used to label the legs), which are routinely applied in ham production; finally, we tested the possibility of authenticating hams by retrieving DNA information from the applied matrices (lard and ink mixed with flour) on the legs that were cured and ripened for 16 months. The DNA fingerprinting was consistent throughout all evaluation stages enabling the authentication of the marked hams. One advantage of this system is that the tracer (and its DNA profile) is known only to the authentication system managers. This approach can be adapted to authenticate many other food products.

Multiannual patterns of genetic structure and mating type ratios highlight the complex bloom dynamics of a marine planktonic diatom

Understanding the genetic structure of populations and the processes responsible for its spatial and temporal dynamics is vital for assessing species’ adaptability and survival in changing environments. We investigate the genetic fingerprinting of blooming populations of the marine diatom Pseudo-nitzschia multistriata in the Gulf of Naples (Mediterranean Sea) from 2008 to 2020. Strains were genotyped using microsatellite fingerprinting and natural samples were also analysed with Microsatellite Pool-seq Barcoding based on Illumina sequencing of microsatellite loci. Both approaches revealed a clonal expansion event in 2013 and a more stable genetic structure during 2017–2020 compared to previous years. The identification of a mating type (MT) determination gene allowed to assign MT to strains isolated over the years. MTs were generally at equilibrium with two notable exceptions, including the clonal bloom of 2013. The populations exhibited linkage equilibrium in most blooms, indicating that sexual reproduction leads to genetic homogenization. Our findings show that P. multistriata blooms exhibit a dynamic genetic and demographic composition over time, most probably determined by deeper-layer cell inocula. Occasional clonal expansions and MT imbalances can potentially affect the persistence and ecological success of planktonic diatoms.

Evaluation of microsatellite allelic patterns to DNA fingerprinting in rubber tree clones

The rubber tree (Hevea brasiliensis) is native to the Amazon region, and it is widely exploited due to natural rubber produced from latex. There are many clonal varieties, without certification tests. In order to determine a genetic certification, 15 clones were genotyped to identify their genetic pattern. Ten microsatellites were used to determine a subset of alleles exclusive for each genetic profile. The genetic estimates obtained were: number of alleles per locus (N), expected (HE) and observed (HO) heterozygosity, Polymorphic Information Content (PIC) and Discriminatory Power (DP). The number of alleles (N) ranged from five to 14, with an average of 9.2. The HE mean (0.80) was higher than HO (0.60), indicating a selection for homozygotes. The locus informativeness was verified with PIC (0.77) and DP (0.90) means showing high polymorphism. The dendrogram represented the formation of three groups related to geographical origin. Clone MDF 180 presented the highest genetic divergence. Two genic pools represented the genetic composition of genotypes. Based on allelic profiles, a set of two microsatellites (A2365 and A2368) was able to distinguish all examined clones. The genetic certification using microsatellite fingerprinting proved to be an alternative to morphological traits.

Genetic Diversity and Genome Size Variability in the Russian Genebank Collection of Tea Plant [Camellia sinensis (L). O. Kuntze

The tea collection of the FRC SSC RAS (Sochi, Maykop in Russia) represents one of the northernmost germplasm comprising a number of locally derived cultivars and ɣ-irradiation mutants. The latter are often characterized by larger genome size, which may lead to better adaptation to biotic and abiotic stress. Such genotypes may be a valuable genetic resource for better adaptability to extreme environmental conditions, which could enable tea cultivation outside global growing regions. Microsatellite markers are often the best choice for genetic diversity analysis in genebank collections. However, their use in polyploid species is questionable because simple sequence repeat (SSR) allele dosage cannot be readily determined. Therefore, the efficiency of SSR and start codon targeted (SCoT) markers was investigated using 43 selected cultivars from the Russian genebank collection derived from mutant breeding and clonal selection. Previously, the increase in genome size was confirmed in 18 mutants within this collection. Despite the presence of polyploid tea genotypes, our study revealed higher efficiency of SSR markers than SCoT markers. Subsequent SSR analysis of the 106 genotypes in the Russian genebank collection revealed three distinct genetic clusters after STRUCTURE analysis. Greater genetic variation was observed within genetic clusters than between clusters, indicating low genetic variation between collections. Nevertheless, the northernmost tea collection exhibited a greater genetic distance from the other two clusters than they did from each other. Close genetic relationships were found between many cultivars with particularly large leaves and mutant forms. Pearson’s correlation analysis revealed a significant, moderate correlation between genome size and leaf area size. Our study shows that microsatellite fingerprinting is useful to estimate the genetic diversity and genetic background of tea germplasm in Russia despite polyploid tea accessions. Thus, the results of our study contribute to the development of future tea germplasm conservation strategies and modern tea breeding programs.

Microsatellite fingerprinting and metabolite profiling for the geographical authentication of commercial green teas

The authentication of geographical provenance is an important issue with respect to commercial tea products. Here, simple sequence repeat (SSR) fingerprinting and metabolite profiling were implemented to differentiate between 37 commercial green teas, produced in China, Japan and Korea. A set of 21 SSR assays detected 175 alleles, and a multiplex of three of these assays was sufficient to distinguish each of the samples. Metabolite profiling based on ultra-high performance liquid chromatography coupled with high resolution mass spectrometry detected features which proved to be correlated with a specific provenance. There was only a moderate level of correlation between the SSR and metabolite profiles. Such a level of correlation suggests that genotype, environment and post-harvest processing are all determinants of end-use quality. The two analytical approaches are complementary to one another, and are recommended to be used in conjunction.

Dear old peonies\u2013for gene banks and gardeners; microsatellite fingerprinting of herbaceous peonies in Fennoscandia

The genetic diversity of 334 herbaceous peonies from Fennoscandia was analysed using 18 microsatellites (simple sequence repeats, SSRs). The samples included peonies mostly from Finnish home gardens (284) and nurseries (5) as well as from Norwegian (20) and Swedish (25) peony collections. The study focused on the following species and hybrids: Paeonia anomala L., P. × hybrida Pall., P. officinalis ‘Nordic Paradox’ (Marstein 2015), P. tenuifolia L., and P. × festiva Tausch. The 18 microsatellites amplified a total of 249 alleles and were used to calculate genetic distances between samples and to build a dendrogram. In the dendrogram, samples formed clear groups according to their species. The outcome from the genetic analysis was mainly confirmed by preliminary morphological observations of the Finnish home garden samples performed within the project and the previous morphological study of peonies in Norwegian clone archives. The results of the study will be used to create a Finnish genetic resources collection of the most diverse and vigorous peonies, and to update the Norwegian and Swedish collections.

Improved strategies to efficiently isolate thermophilic, thermotolerant, and heat-resistant fungi from compost and soil

Thermophilic, thermotolerant and heat-resistant fungi developed different physiological traits, enabling them to sustain or even flourish under elevated temperatures, which are life-hostile for most other eukaryotes. With the growing demand of heat-stable molecules in biotechnology and industry, the awareness of heat-adapted fungi as a promising source of respective enzymes and biomolecules is still increasing. The aim of this study was to test two different strategies for the efficient isolation and identification of distinctly heat-adapted fungi from easily accessible substrates and locations. Eight compost piles and ten soil sites were sampled in combination with different culture-dependent approaches to describe suitable strategies for the isolation and selection of thermophilous fungi. Additionally, an approach with a heat-shock treatment, but without elevated temperature incubation led to the isolation of heat-resistant mesophilic species. The cultures were identified based on morphology, DNA barcodes, and microsatellite fingerprinting. In total, 191 obtained isolates were assigned to 31 fungal species, from which half are truly thermophilic or thermotolerant, while the other half are heat-resistant fungi. A numerous amount of heat-adapted fungi was isolated from both compost and soil samples, indicating the suitability of the used approaches and that the richness and availability of those organisms in such environments are substantially high.

Microsatellite fingerprinting and analysis of intra-population divergence in morphotaxonomic traits in a large Musa (AAB genome) germplasm.

Plantain (Musa spp. AAB genome) is a major staple with an incredibly enormous potential for domestic and global trade that can serve as a vital source of income for many developing countries. The fruits are extraordinarily significant, providing an important and cheap source of dietary energy, vitamins, and several essential minerals to millions of consumers within the humid and sub-humid tropics. As molecular characterization is important for sustainable exploitation of crops, the extent of genetic and agro-morphological differentiation in a large Musa population of 109 accessions was evaluated using 10 microsatellite (SSR) markers and 14 morphotaxonomic descriptors, as a basis for selection of high yielding varieties. Measurement of DNA diversity delineated the plantains into 2 major groups and 8 distinct clusters, each with several sub-clusters. There was equally a very wide diversity detected in morphotaxonomic traits including pseudostem girth, number of bunches per plant, number of hands per bunch, number of fruits per bunch, number of fruits per hand, bunch weight, length of plant cycle, and flowering to harvest interval, which varied significantly (p < 0.05) amongst the accessions. Selection based on cluster analysis using standard morphological data also delineated the cultivars into 8 distinct clusters, with one of these containing samples that were most distant to all others and exhibited a 'double bunching' phenotype at fruiting; tacitly implying the presence of significant variability that symbolizes an excellent opportunity to bring about genetic improvement through selection of improved varieties. Principal component analysis based on morphotaxonomic traits revealed 7 attributes which contributed to 79.95% of total variation that was quite similar to the 71.87% detected using microsatellite fingerprinting. Correlation analysis between selected agronomic traits demonstrated that pseudostem girth was positively associated with bunch weight, number of hands per bunch, number of fruits per bunch, number of fruits per hand, and flowering to harvest interval across all accessions. Collectively, the data in this study suggest that plantain accessions with very unique traits expressing paramount horticultural significance are available within the diverse germplasm evaluated and are currently being collected for future breeding purposes to broaden the genetic base of this important crop.

Validating Blackberry Seedling Pedigrees and Developing an Improved Multiplexed Microsatellite Fingerprinting Set

Confirming parentage and clonal identity is an important aspect of breeding and managing germplasm collections of clonally propagated, outcrossing crops, like blackberry (Rubus subgenus Rubus). DNA fingerprinting sets are used to identify off-cross progeny and confirm clonal identity. Previously, a six-simple sequence repeat (6-SSR) fingerprinting set was developed for blackberry using a small number of samples. The usefulness of the 6-SSR fingerprinting set for pedigree confirmation had not been evaluated. Therefore, it was used in this study to validate parentage for 6 and 12 biparental populations from the University of Arkansas (UA) and US Department of Agriculture Agricultural Research Service (USDA-ARS), Horticultural Crops Research Unit (HCRU) breeding programs, respectively. Twenty-seven of the 489 individuals in these breeding populations were identified as off-cross. The 6-SSR fingerprinting set was sufficient for parentage confirmation; however, a total of 61 plants distributed across 28 sets of genotypes could not be distinguished from each other. An 8-SSR fingerprinting set with improved resolution was subsequently developed and used to evaluate 177 Rubus accessions from the USDA-ARS National Clonal Germplasm Repository, UA, and USDA-ARS HCRU programs. The 8-SSR fingerprinting set distinguished all samples expected to have unique genotypes and identified differing DNA fingerprints for two sets of accessions suspected to have identical fingerprints. Cluster analysis grouped the accessions from the eastern and western US breeding programs based on geography and descent. Future work will focus on establishing a database of DNA fingerprints for germplasm identification and for determining pedigree relationships between blackberry accessions.

Nuclear populations of the multinucleate fungus of leafcutter ants can be dekaryotized and recombined to manipulate growth of nutritive hyphal nodules harvested by the ants

ABSTRACTWe dekaryotized the multinucleate fungus Leucocoprinus gongylophorus, a symbiotic fungus cultivated vegetatively by leafcutter ants as their food. To track genetic changes resulting from dekaryotization (elimination of some nuclei from the multinuclear population), we developed two multiplex microsatellite fingerprinting panels (15 loci total), then characterized the allele profiles of 129 accessions generated by dekaryotization treatment. Genotype profiles of the 129 accessions confirmed allele loss expected by dekaryotization of the multinucleate fungus. We found no evidence for haploid and single-nucleus strains among the 129 accessions. Microscopy of fluorescently stained dekaryotized accessions revealed great variation in nuclei number between cells of the same vegetative mycelium, with cells containing typically between 3 and 15 nuclei/cell (average = 9.4 nuclei/cell; mode = 8). We distinguish four mycelial morphotypes among the dekaryotized accessions; some of these morphotypes had lost the full competence to produce gongylidia (nutritive hyphal-tip swellings consumed by leafcutter ants as food). In mycelial growth confrontations between different gongylidia-incompetent accessions, allele profiles suggest exchange of nuclei between dekaryotized accessions, restoring full gongylidia competence in some of these strains. The restoration of gongylidia competence after genetic exchange between dekaryotized strains suggests the hypothesis that complementary nuclei interact, or nuclear and cytoplasmic factors interact, to promote or enable gongylidia competence.

Changing Ploidy as a Strategy: The Irish Potato Famine Pathogen Shifts Ploidy in Relation to Its Sexuality.

The oomycete Phytophthora infestans was the causal agent of the Irish Great Famine and is a recurring threat to global food security. The pathogen can reproduce both sexually and asexually, with high potential to adapt to various environments and great risk to break disease resistance genes in potato. As are other oomycetes, P. infestans is regarded to be diploid during the vegetative phase of its life cycle, although some studies reported trisomy and polyploidy. Using microsatellite fingerprinting, genome-wide assessment of single nucleotide polymorphisms, nuclear DNA quantification, and microscopic counting of chromosome numbers, we assessed the ploidy level of a comprehensive selection of isolates. All progenies from sexual populations of P. infestans in nature were found to be diploid, in contrast nearly all dominant asexual lineages, including the most important pandemic clonal lineages US-1 and 13_A2 were triploid. Such triploids possess significantly more allelic variation than diploids. We observed that triploid genotype can change to a diploid genome constitution when exposed to artificial stress conditions. This study reveals that fluctuations in the ploidy level may be a key factor in the adaptation process of this notorious plant destroyer and imposes an extra challenge to control this disease.

PCR based DNA fingerprinting of mercury resistant and nitrogen fixing Pseudomonas spp.

Mercury resistant Pseudomonas strains were isolated from polluted water, rhizospheric soil and root nodules of different plant species. Selected bacterial isolates showed potential to produce florescence under UV light and to tolerate heavy metal stress of 10-20 µg/ml HgCl2. Biochemical characterization revealed all selected bacterial isolates belong to genus Pseudomonas. A total of 27 bacterial isolates were evaluated for bioremediation of mercury due to their ability to produce H2S and fix nitrogen. Genomic DNA of 12 Pseudomonas strains was isolated and their genetic diversity was evaluated using SSR (GACA)4 microsatellite finger printing. On the basis of banding pattern of PCR amplified products, a phylogenetic tree was constructed using Minitab 13 software which showed 71%, 46% and 44% homology of SZ-30, SZ-6 and SZ-8 with strains of cluster 1 and SZ-16 respectively. Results exhibited significant diversity among selected Pseudomonas strains.

Characterization of in vitro haploid and doubled haploid Chrysanthemum morifolium plants via unfertilized ovule culture for phenotypical traits and DNA methylation pattern.

Chrysanthemum is one of important ornamental species in the world. Its highly heterozygous state complicates molecular analysis, so it is of interest to derive haploid forms. A total of 2579 non-fertilized chrysanthemum ovules pollinated by Argyranthemum frutescens were cultured in vitro to isolate haploid progeny. One single regenerant emerged from each of three of the 105 calli produced. Chromosome counts and microsatellite fingerprinting showed that only one of the regenerants was a true haploid. Nine doubled haploid derivatives were subsequently generated by colchicine treatment of 80 in vitro cultured haploid nodal segments. Morphological screening showed that the haploid plant was shorter than the doubled haploids, and developed smaller leaves, flowers, and stomata. An in vitro pollen germination test showed that few of the haploid's pollen were able to germinate and those which did so were abnormal. Both the haploid and the doubled haploids produced yellow flowers, whereas those of the maternal parental cultivar were mauve. Methylation-sensitive amplification polymorphism (MSAP) profiling was further used to detect alterations in cytosine methylation caused by the haploidization and/or the chromosome doubling processes. While 52.2% of the resulting amplified fragments were cytosine methylated in the maternal parent's genome, the corresponding proportions for the haploid's and doubled haploids' genomes were, respectively, 47.0 and 51.7%, demonstrating a reduction in global cytosine methylation caused by haploidization and a partial recovery following chromosome doubling.

Temperate origin and diversification via southward colonization in Fatsia (Araliaceae), an insular endemic genus of the West Pacific Rim

Islands isolated by oceans that act as a geographical barrier for plant migration often possess high species endemism and have been deemed as a natural laboratory for studying species divergence. Fatsia Decne. & Planch. (Araliaceae), with three species, is one of the few plant genera absent in continents while exclusively spanning continental and oceanic islands. The nuclear ribosomal internal transcribed spacer (nrITS) phylogeny uncovered a pattern with reciprocal monophyly of Fatsia oligocarpella Koidz. (Bonin) and Fatsia polycarpa Hayata (Taiwan) vs. paraphyly of Fatsia japonica (Thunb.) Decne. & Planch. (Japan and Ryukyus), suggesting ancestry of the species in Japan and a likely temperate origin; whereas, lack of monophyly of all three allopatrically distributed species at chloroplast DNA (cpDNA) trnL–trnF spacer likely resulted from lineage sorting. In spite of the limited habitats for F. oligocarpella, unexpectedly high genetic variations in this species of oceanic islands were likely attributable to multiple colonizations and recurrent gene introgression. Biogeographical analyses suggested that Fatsia likely diverged via southward colonization in Bonin Islands and Taiwan during the late Pliocene to Pleistocene. Besides, Fatsia species with an allopatric distribution provide a perfect model for testing speciation modes of insular endemics. Nonzero gene flow between species was detected based on MIGRATE and STRUCTURE analyses of DNA sequences and microsatellite fingerprints, suggesting that allopatric speciation is less likely.

The Puzzle of Italian Rice Origin and Evolution: Determining Genetic Divergence and Affinity of Rice Germplasm from Italy and Asia

The characterization of genetic divergence and relationships of a set of germplasm is essential for its efficient applications in crop breeding and understanding of the origin/evolution of crop varieties from a given geographical region. As the largest rice producing country in Europe, Italy holds rice germplasm with abundant genetic diversity. Although Italian rice varieties and the traditional ones in particular have played important roles in rice production and breeding, knowledge concerning the origin and evolution of Italian traditional varieties is still limited. To solve the puzzle of Italian rice origin, we characterized genetic divergence and relationships of 348 rice varieties from Italy and Asia based on the polymorphisms of microsatellite fingerprints. We also included common wild rice O. rufipogon as a reference in the characterization. Results indicated relatively rich genetic diversity (H e = 0.63-0.65) in Italian rice varieties. Further analyses revealed a close genetic relationship of the Italian traditional varieties with those from northern China, which provides strong genetic evidence for tracing the possible origin of early established rice varieties in Italy. These findings have significant implications for the rice breeding programs, in which appropriate germplasm can be selected from a given region and utilized for transferring unique genetic traits based on its genetic diversity and evolutionary relationships.

Characterization of 42 Microsatellite Markers from Poison Ivy, Toxicodendron radicans (Anacardiaceae)

Poison ivy, Toxicodendron radicans, and poison oaks, T. diversilobum and T. pubescens, are perennial woody species of the Anacardiaceae and are poisonous, containing strong allergens named urushiols that cause allergic contact dermatitis. Poison ivy is a species distributed from North America to East Asia, while T. diversilobum and T. pubescens are distributed in western and eastern North America, respectively. Phylogreography and population structure of these species remain unclear. Here, we developed microsatellite markers, via constructing a magnetic enriched microsatellite library, from poison ivy. We designed 51 primer pairs, 42 of which successfully yielded products that were subsequently tested for polymorphism in poison oak, and three subspecies of poison ivy. Among the 42 loci, 38 are polymorphic, while 4 are monomorphic. The number of alleles and the expected heterozygosity ranged from 1 to 12 and from 0.10 to 0.87, respectively, in poison ivy, while varied from 2 to 8 and, from 0.26 to 0.83, respectively in poison oak. Genetic analysis revealed distinct differentiation between poison ivy and poison oak, whereas slight genetic differentiation was detected among three subspecies of poison ivy. These highly polymorphic microsatellite fingerprints enable biologists to explore the population genetics, phylogeography, and speciation in Toxicodendron.

Variation Among Phytophthora cinnamomi Isolates from Oak Forest Soils in the Eastern United States.

Phytophthora cinnamomi isolates from geographically diverse oak forest soils in the Mid-Atlantic regions were studied to determine the extent of genotypic, phenotypic, and pathogenic variation. Four microsatellite loci were targeted for genetic analysis. Phenotypic characteristics measured included sexual and asexual spore dimensions and colony growth rate and morphology. Red oak (Quercus rubra) logs were inoculated with selected isolates to determine relative pathogenicity. Microsatellite analysis showed that the genetic variability of P. cinnamomi isolates was low, with two predominant microsatellite fingerprint groups (MFG). Isolates in MFG1 (48% of the total isolates examined) were characterized by DNA fragment lengths of 120 and 122 bp at locus d39, 169 and 170 bp at locus e16, and 254 and 255 bp at locus g13. MFG2 isolates were characterized by marker sizes of 122 and 124 bp at locus d39, 161 and 163 bp at locus e16, and 247 and 248 bp at locus g13. Asexual and sexual spore dimensions varied greatly among isolates but were similar to previously published descriptions. Phenotypic differences were most pronounced when data were grouped by MFG; the most significant were colony morphology and growth rate. Neither characteristic was a reliable predictor of isolate genotype. Differences in growth rates of MFGs were observed, with MFG1 being less tolerant at higher incubation temperatures. No variation in pathogenicity was observed on red oak logs. The low level of phenotypic and genotypic variation of P. cinnamomi suggest that other factors such as climate might play a more important role in its northern distribution and the diseases it causes.

Inferring Multiple Refugia and Phylogeographical Patterns in Pinus massoniana Based on Nucleotide Sequence Variation and DNA Fingerprinting

Background Pinus massoniana, an ecologically and economically important conifer, is widespread across central and southern mainland China and Taiwan. In this study, we tested the central–marginal paradigm that predicts that the marginal populations tend to be less polymorphic than the central ones in their genetic composition, and examined a founders' effect in the island population.Methodology/Principal FindingsWe examined the phylogeography and population structuring of the P. massoniana based on nucleotide sequences of cpDNA atpB-rbcL intergenic spacer, intron regions of the AdhC2 locus, and microsatellite fingerprints. SAMOVA analysis of nucleotide sequences indicated that most genetic variants resided among geographical regions. High levels of genetic diversity in the marginal populations in the south region, a pattern seemingly contradicting the central–marginal paradigm, and the fixation of private haplotypes in most populations indicate that multiple refugia may have existed over the glacial maxima. STRUCTURE analyses on microsatellites revealed that genetic structure of mainland populations was mediated with recent genetic exchanges mostly via pollen flow, and that the genetic composition in east region was intermixed between south and west regions, a pattern likely shaped by gene introgression and maintenance of ancestral polymorphisms. As expected, the small island population in Taiwan was genetically differentiated from mainland populations.Conclusions/SignificanceThe marginal populations in south region possessed divergent gene pools, suggesting that the past glaciations might have low impacts on these populations at low latitudes. Estimates of ancestral population sizes interestingly reflect a recent expansion in mainland from a rather smaller population, a pattern that seemingly agrees with the pollen record.

Sidik Jari DNA 88 Plasma Nutfah Ubi Jalar di Indonesia Berdasarkan Delapan Penanda SSR

&lt;p&gt;DNA Fingerprinting of Indonesian 88 Sweet Potato&lt;br /&gt;Germplasm Based on Eight SSR Markers. Nurul&lt;br /&gt;Hidayatun, Chaerani, and Dwinita W. Utami. Indonesia&lt;br /&gt;possesses a great number of sweet potato varieties.&lt;br /&gt;Understanding the diversity and distribution of this genetic&lt;br /&gt;resource is essential for its management and future use. The&lt;br /&gt;objective of this study was to elaborate the molecular&lt;br /&gt;character as DNA finger print of Indonesian sweet potato&lt;br /&gt;germplasm. Eight fluorescent labeled SSR primers were&lt;br /&gt;used to amplify DNA of 88 sweet potato accessions&lt;br /&gt;consisting of improved varieties and landraces collected&lt;br /&gt;from 7 islands in Indonesia. The amplified products were&lt;br /&gt;detected using capillary electrophoresis method in CEQ&lt;br /&gt;Genetic Analysis System machine. A total of 135 alleles&lt;br /&gt;ranging from 8 to 36 alleles per locus with an average of 17&lt;br /&gt;alleles were generated. Each accession had a unique&lt;br /&gt;microsatellite finger print marked by specific combination of&lt;br /&gt;11 to 22 alleles in 8 SSR loci. Dendrogram generated by&lt;br /&gt;UPGMA based on simple matching coefficients produced 4&lt;br /&gt;nonspecific groups at 80% similarity. The groups revealed&lt;br /&gt;the possibilities that the accessions were distributed from&lt;br /&gt;similar genetic resources.&lt;/p&gt;

Keragaman Genetik 50 Aksesi Plasma Nutfah Kedelai Berdasarkan Sepuluh Penanda Mikrosatelit

&lt;p&gt;Genetic Diversity of 50 Soybean Accessions Based on Ten&lt;br /&gt;Microsatellite Markers. Chaerani, Nurul Hidayatun, and&lt;br /&gt;Dwinita W. Utami. Soybean accessions in germplasm&lt;br /&gt;collection have increased in number as a result of&lt;br /&gt;exploration, introduction as well as development or release&lt;br /&gt;of new commercial varieties. This complicates accurate and&lt;br /&gt;reliable evaluation of an accession for purposes of utilization&lt;br /&gt;in breeding program and discrimination of a new&lt;br /&gt;commercial variety for purposes of plant variety protection.&lt;br /&gt;The aims of this study were to identify the genetic diversity&lt;br /&gt;of soybean germplasm to complement the existing&lt;br /&gt;phenotypic database as the basis for efficient management&lt;br /&gt;and accurate discrimination of commercial varieties, and to&lt;br /&gt;identify potential parents for hybridizations. Fifty soybean&lt;br /&gt;accessions consisting of 12 released varieties, 32 local&lt;br /&gt;varieties, and 6 introductions were analyzed using&lt;br /&gt;microsatellite DNA markers based on semi-automatic sizing&lt;br /&gt;system. A total of 86 alleles were detected with the number&lt;br /&gt;of alleles per locus ranged from 4 to 16. Rare alleles were&lt;br /&gt;detected at a rate of 53% which was shown by 68% of the&lt;br /&gt;genotypes. Informativeness of the microsatellite markers as&lt;br /&gt;measured by the average gene diversity (D) or&lt;br /&gt;polymorphism information content (PIC) was 0.60 and 0.58,&lt;br /&gt;respectively. A heterozygosity level of 0.09 as detected by&lt;br /&gt;seven loci was observed among 64% of the genotypes. The&lt;br /&gt;average genetic distance among the genotypes was 0.56,&lt;br /&gt;which indicated the relatively low polymorphism among the&lt;br /&gt;analyzed soybean germplasm. Four microsatellites that&lt;br /&gt;showed a high D or PIC value (over 0.75) were able to&lt;br /&gt;discriminate between accession reliably. Each soybean&lt;br /&gt;accession had different DNA microsatellite fingerprint which&lt;br /&gt;can be used for accurate discrimination to complement the&lt;br /&gt;previous conventional characterizations. UPGMA clustering&lt;br /&gt;separated the 50 accessions into 10 major clusters, which&lt;br /&gt;showed no clear pattern of clustering according to varietal&lt;br /&gt;group or geographical origin. Genetic similarity data&lt;br /&gt;identified five clusters and 15 genotypes with highest intercluster&lt;br /&gt;or inter-genotype genetic distances which are&lt;br /&gt;potential candidates to be exploited as parents in&lt;br /&gt;hybridizations for development of new commercial varieties.&lt;/p&gt;