scholarly journals 467 PB 330 RAPD ASSAY TO IMPROVE BRASSICA GENETIC RESOURCES COLLECTION MANAGEMENT

HortScience ◽  
1994 ◽  
Vol 29 (5) ◽  
pp. 498b-498
Author(s):  
Winthrop B. Phippen ◽  
James R. McFerson ◽  
Stephen Kresovich
Keyword(s):  
Genetic Resources ◽  
Rapd Markers ◽  
Genetic Relationships ◽  
Molecular Genetic ◽  
Cost Effective ◽  
Genetic Distances ◽  
Gene Bank ◽  
Collection Management ◽  
Specific Level ◽  
Bank Management

Genetic variation and relationships in genetic resources collections can be assessed using molecular genetic markers. We examined the applicability of the RAPD assay for quick, cost-effective, and reliable use in improving collection management. Fourteen accessions of Brassica oleracea spp. capitata `Golden Acre' (cabbage) were screened using nine decamer oligonucleotide primers. We obtained 110 reproducible fragments, of which 80 were polymorphic, ranging in size from 370-1730 bp. Individual accessions were readily distinguished. A cluster analysis of genetic distances generated by bootstrapping reflected all known genetic relationships, except one. Bulking strategies were also investigated. RAPD markers can be applied to gene bank management to measure variation, identify accessions, and establish genetic similarity at the intra-specific level addressing the needs of both curators and users.

scholarly journals Use RAPD Technique for Characterization of Genotypical Variability of Maize Germplasm from SCDA Turda

2010 ◽  
Vol 67 (1) ◽  
Author(s):  
Rodica POP ◽  
Doru PAMFIL ◽  
Monica HÂRŢA ◽  
Ioan HAŞ ◽  
Iulia POP
Keyword(s):  
Rapd Markers ◽  
Rapd Analysis ◽  
Genetic Relationships ◽  
Germplasm Collection ◽  
Genetic Distances ◽  
Maize Germplasm ◽  
Upgma Dendrogram ◽  
Maize Genotypes ◽  
Polymorphic Bands

Genetic analysis with RAPD markers has been extensively used to determine diversity among maize genotypes. The aim of the present study was to estimate genetic relationships among 70 genotypes, provided from SCDA Turda Cluj germplasm collection. RAPD analysis was performed with 14 decamer primers. These primers generated, among the studied genotypes, a number of polymorphic bands comprised between 13 bands (OPA 04) and 7 bands (OPAL 20). The highest numbers of polymorphic bands were obtained with primer OPA 04, respectively 13 bands, following by OPO 12 (12 polymorphic bands), OPAB 11 and OPA 17 (11 polymorphic bands). Lowest number was obtained with primer OPAL 20, respectively 7 polymorphic bands. Genetic distances were established using Nei-Li coefficient and UPGMA dendrogram was constructed with RAPDistance 1.04 software. The built dendrogram shows phylogenetic relationships between genotypes analyzed.

scholarly journals Genetic variation and molecular relationships taxa of Conringia heist. ex Fabr. (Brassicaceae) based on RAPD markers in Turkey

Genetika ◽  
2020 ◽  
Vol 52 (1) ◽  
pp. 107-114
Author(s):  
Emre Sevġndġk ◽  
Yavuz Paksoy ◽  
Melike Aydoğan ◽  
Feyzanur Topseçer
Keyword(s):  
Genetic Variation ◽  
Phylogenetic Tree ◽  
Rapd Markers ◽  
Uv Light ◽  
Genetic Relationships ◽  
Genetic Distances ◽  
Genomic Dna Isolation ◽  
Pcr Products ◽  
Polymerase Chain ◽  
Molecular Relationships

In this study, genetic variation and phylogenetic analysis of 13 populations of 6 species belonging to Conringia genus spreading in Turkey were performed using RAPD markers. Genomic DNA isolation from the leaves of the Conringia plant samples was performed via using a commercial kit. Seven RAPD primers were used to identify the genetic diversity between the populations. Polymerase Chain Reaction (PCR) was performed using DNA samples and primers. PCR products were resolved using agarose gel electrophoresis and visualized under UV light. All gel images were analyzed, and the absence and presence of polymorphic bands were scored. The total of 34 DNA bands were detected by seven RAPD primers. PAUP 4.0b10 analysis program was used to calculate phylogenetic tree and genetic distances between the species. The phylogenetic tree was obtained using the UPGMA algorithm and it was composed of two clades. According to the PAUP analysis, the species having the closest distance between each other are C. planisiliqua (Ankara-Aya?) and C. planisiliqua (Ankara-Nall?han) with the value of 0.000 and those having the longest distance are C. grandiflora (Akseki ?ukurk?y) and C. orientalis (Elaz??-Baskil) with the value of 0.6000. The results suggest that the RAPD markers are useful tools to demonstrate the genetic relationships between populations of the Conringia species.

Managing genetic resources in selected and conserved populations

2004 ◽  
Vol 30 ◽  
pp. 113-132 ◽  
Author(s):  
B. Villanueva ◽  
R. Pong-Wong ◽  
J.A. Woolliams ◽  
S. Avendaño
Keyword(s):  
Genetic Resources ◽  
Genetic Relationships ◽  
Molecular Genetic ◽  
Selection Response ◽  
Pedigree Information ◽  
Genetic Progress ◽  
Breeding Populations ◽  
Expected Gain ◽  
Best Linear Unbiased ◽  
Estimated Breeding Values

AbstractManaging the rate of inbreeding (ΔF) provides a general framework for managing genetic resources in farmed breeding populations. Methods for managing ΔF have been developed over the last five years and they allow the attainment of the greatest expected genetic progress while restricting at the same time the increase in inbreeding. This is achieved by optimising the contribution that each candidate for selection must have to produce the next generation. The methods take into account all available performance and pedigree information and use Best Linear Unbiased Prediction (BLUP) estimates as a predictor of merit. Importantly, these tools give at least equal, but more often more gain than traditional selection based on truncation of BLUP estimated breeding values when compared at the same ΔF. Deterministic predictions for the expected gain obtained with optimised selection with ΔF restricted are now available. The optimisation tool can be also applied in a conservation context to minimise ΔF with restrictions to avoid loss in performance in valuable traits. Information on known quantitative trait loci or on markers linked to them can be incorporated into the optimisation process to further increase selection response. Molecular genetic information can also be incorporated into these tools to increase the precision of genetic relationships between individuals and to manage ΔF at specific positions or genome regions.

The management of rice genetic resources

Genome ◽  
1989 ◽  
Vol 31 (2) ◽  
pp. 825-831 ◽  
Author(s):  
T. T. Chang
Keyword(s):  
Genetic Resources ◽  
Management System ◽  
Germ Plasm ◽  
In Situ Conservation ◽  
Public Information ◽  
Genetic Erosion ◽  
Gene Bank ◽  
Database Management System ◽  
Gene Pools ◽  
Bank Management

Rice growers and researchers are endowed with an enormously rich germ plasm of pantropical distribution, mostly conserved before serious genetic erosion sets in. Efficient management of the conserved resources and effective use of the diverse gene pools justify arduous and costly investments in conservation. A sound conservation system requires adequate field space for seed increase and rejuvenation, cost-efficient and secure storage facilities, a database management system, availability of conserved materials and related information to users, and vigilant monitoring of seed viability. Linkage with evaluators, breeders, and biotechnologists is essential for full use of the conserved materials. Periodic consultation with specialists will extend a collection's usefulness, through further collection or re-collection of germ plasm and in situ conservation, compatibility of documentation systems, and enhanced interinstitutional and international collaboration. Training of germ-plasm workers should be part of the management system. The continuity in human resources will provide security, their dedication will ensure service, interdisciplinary communication will promote use. Improving the capability of national genebanks augments the security of collections preserved at duplicate sites. Gene-bank management must be sustained by adequate administrative and financial support. An effective public information program will further ensure support and security.Key words: rice, Oryza sativa, genetic resources, genetic conservation, gene-bank management.

Genetic variation and relationship of alfalfa populations and their progenies based on RAPD markers

2014 ◽  
Vol 9 (8) ◽  
pp. 768-776 ◽  
Author(s):  
Ksenija Taški-Ajduković ◽  
Nevena Nagl ◽  
Dragan Milić ◽  
Slobodan Katić ◽  
Miroslav Zorić
Keyword(s):  
Genetic Variation ◽  
Rapd Markers ◽  
Genetic Relatedness ◽  
Genetic Relationships ◽  
Cost Effective ◽  
Model Based Clustering ◽  
Information Index ◽  
Bulked Dna ◽  
Clustering Approach ◽  
Relationship Of

AbstractThe aim of investigation was to evaluate genetic variation and relationship among alfalfa populations and their offspring, with minimal cost, by using DNA marker analysis. RAPD analysis was performed on bulked DNA samples of five alfalfa parental populations and their progenies: 20 F1 populations from reciprocal diallel crosses and five S1 populations from self-pollination. Twenty primers generated 217 bands, ranging in size from 300 to 6000 bp, with the average number of bands per primer of 10.85 and polymorphism information content of 0.246. Percentage of polymorphic loci, effective number of alleles, expected heterozygosity and Shannon’s information index were used to estimate genetic variation. Higher diversity was observed in F1 progeny populations, while genetic variation in parental populations and S1 progenies remained similar. The genetic relatedness of alfalfa populations was analysed by UPGMA and Bayesian model-based clustering approach. In both types of analysis selfpollinated progenies were grouped. Furthermore, the hybrid offspring where Zuzana, and RSI 20 were maternal parents were placed in separate groups. The results indicate that use of RAPD markers on bulked DNA samples can be fast and cost-effective way for differentiation of alfalfa parental populations and their offspring, as well as for evaluation of their genetic relationships.

scholarly journals Molecular Characterization of Vitex agnus-castus L. (Verbenaceae) Populations Grown in Aydin, Turkey

2019 ◽  
Vol 11 (2) ◽  
pp. 218-221
Author(s):  
Emre SEVİNDİK ◽  
Serkan CANER ◽  
Mahmut COŞKUN
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
Genomic Dna ◽  
Rapd Markers ◽  
Genetic Relationships ◽  
Genetic Distances ◽  
Purple Flower ◽  
A Value ◽  
Pink Flower ◽  
Agnus Castus

In this study, we performed a genetic diversity analysis using RAPD markers for some Vitex agnus-castus populations grown in Aydin, Turkey. Total genomic DNA isolation from the leaves of Vitex agnus-castus was performed using a commercial kit. Seven RAPD primers (OPA-02, OPA-05, OPA-13, OPA-15, OPA-16, OPA-18, OPA-20) were used to determine genetic diversity among populations. Polymerase Chain Reaction (PCR) was performed with all genomic DNA samples and primers. PCR products were run in agarose gel electrophoresis and visualized under UV light. The amplified products were scored as bands (1) and no bands (0) for all gel images and their matrix files were generated. A total of 36 characters were obtained from the primers. Phylogenetic relationships and genetic distances between the cultivars were calculated by using the PAUP* (Phylogenetic Analysis Using Parsimony and other methods) program. According to PAUP analysis, the closest genetic distances were between Çine pink flower and Çakmar purple flower, and Çakmar pink flower and Çakmar purple flower populations with a value of 0.05556; and the greatest genetic distance was between Çakmar pink flower and Köşk purple flower populations with a value of 0.36111. In the phylogenetic analysis obtained using UPGMA algorithms, the phylogenetic tree consisted of four groups. The results suggest that RAPD markers are useful tools for determining genetic relationships among Vitex agnus-castus genotypes.

scholarly journals EVALUATION OF GENETIC VARIABILITY WITHIN SWEET CHERRY (Prunus avium L.) GENETIC RESOURCES BY MOLECULAR SSR MARKERS

2019 ◽  
Vol 18 (3) ◽  
Author(s):  
Josef Patzak ◽  
Alena Henychová ◽  
František Paprštein ◽  
Jiří Sedlák
Keyword(s):  
Genetic Variability ◽  
Genetic Resources ◽  
Sweet Cherry ◽  
Prunus Avium ◽  
Genetic Relationships ◽  
Molecular Genetic ◽  
Hierarchical Cluster ◽  
Fruit Production ◽  
Perennial Plant ◽  
Breeding History

Sweet cherry is a vegetatively propagated, perennial plant with high level of heterozygosity and ancient breeding history. Therefore, it is necessary to keep, conserve and evaluate known genetic resources for fu- ture breeding programs and fruit production stability. In present, the utilization of DNA molecular genetic analyses is the best suitable method for evaluation of individual accessions, thus we eliminated duplications and characterized the genetic relationships. In our work, we used PCR primer combinations for 19 SSR and 2 EST-SSR loci for analyses of 123 current, old and local sweet cherry cultivars from Czech genetic resources of Research and Breeding Institute of Pomology in Holovousy. In total, 115 polymorphic fragments were amplified, which we used for hierarchical cluster analysis of genetic variability. The result dendrograms were divided into three main clusters and ten subgroups. Clustering corresponded to genealogical and geobotanical characteristics of individual accessions as breeding history of several known accessions.

scholarly journals Genetic Relationships and Reproductive Traits of Romanian Populations of Silver Fir (Abies alba): Implications for the Sustainable Management of Local Populations

2020 ◽  
Vol 12 (10) ◽  
pp. 4199
Author(s):  
Irina Maria Todea Morar ◽  
Stephanie Rensen ◽  
Santiago Vilanova ◽  
Monica Boscaiu ◽  
Liviu Holonec ◽  
...  
Keyword(s):  
Seed Germination ◽  
Genetic Resources ◽  
Genetic Relationships ◽  
Abies Alba ◽  
Reproductive Traits ◽  
Genetic Distances ◽  
Silver Fir ◽  
Positive Trend ◽  
Molecular Variance ◽  
Storage Methods

Assessment of the diversity of reproductive traits and genetic variation is of great relevance to the conservation of genetic resources and management of silver fir (Abies alba) populations. We have evaluated reproductive characteristics associated with female cones and seed morphology, as well as seed germination after subjecting seeds to five storage methods, in nine Romanian populations of A. alba. The genetic diversity of the populations was assessed with 12 polymorphic simple sequence repeat (SSR) markers. We detected significant differences between populations for all reproductive traits and considerable differences in seed germination and storage methods; seed storage in wet sand was the method resulting in the highest germination in all populations. Genomic SSRs (gSSRs) were more informative on average than expressed sequence tag SSRs (EST-SSRs) in the populations studied. The nine populations were genetically diverse, with an average number of alleles (N) per SSR locus between 3.50 and 4.83. The observed heterozygosity (Ho) in the nine populations was always lower than the expected heterozygosity (He), which resulted in values of the inbreeding coefficient (Fis) between 0.261 and 0.709. Genetic distances between populations ranged between 0.077 and 0.410. The cluster analysis based on genetic distances did not group accessions according to their geographical proximity, and despite a positive trend, the correlation between geographic and genetic distances was non-significant. The results of an analysis of molecular variance (AMOVA) revealed that only 9.1% of the total molecular variance is attributable to differences between populations. This low degree of genetic differentiation between populations is confirmed by the intermingling of individuals of different populations in a principal coordinate analysis (PCoA). We found evidence of a positive relationship between He and germination, as well as a negative one between Fis and germination, suggesting that populations with low diversity and high consanguinity may have a reduced fitness and long-term viability. The results are relevant for the conservation and management of local genetic resources and populations, as well as for reforestation programmes of silver fir.

scholarly journals Comparison of morphological and molecular genetic distances of maize inbreds

Genetika ◽  
2012 ◽  
Vol 44 (1) ◽  
pp. 119-128 ◽  
Author(s):  
Milosav Babic ◽  
Vojka Babic ◽  
Slaven Prodanovic ◽  
Milomir Filipovic ◽  
Violeta Andjelkovic
Keyword(s):  
Environmental Effects ◽  
Genetic Relationships ◽  
Molecular Genetic ◽  
Morphological Characterization ◽  
Genetic Distances ◽  
Measurement Scale ◽  
Morphological Markers ◽  
Pedigree Data ◽  
Similarity Coefficients ◽  
Maize Inbreds

Due to an unknown mechanism of genetic control and great environmental effects in the process of trait expression, morphological markers are often considered unreliable indicators of genetic relationships. Morphological characterization of 19 maize inbreds was done according to the UPOV descriptor, while molecular characterization was performed with RAPD markers. Based on the estimation of phenotypes according to the UPOV descriptor, the squared Euclidean distance was calculated and then, on the basis of this distance, a morphological similarity matrix was formed. Jaccard similarity coefficients were calculated on the basis of presence absence of bands on gels in the RAPD analysis. When data were standardized, the comparison between morphological and genetic similarity of observed maize inbreds was done. The correlations varied from 0.47 (inbred L 217) to 0.76 (inbred L 86). The average value of correlations for all studied inbreds amounted to 0.64. Furthermore, the results of the cluster analysis for both markers, molecular and morphological, had high concordance with pedigree data. Environmental effects were decreased in morphological markers (according to the UPOV descriptor) by rescaling a measurement scale from a scale to an ordinal level of measurement and in such a way results of morphological markers approached results of molecular markers in the estimation of the genetic distance (GD) of maize inbred lines.

scholarly journals Identification of Pecan Cultivars and Their Genetic Relatedness as Determined by Randomly Amplified Polymorphic DNA Analysis

2001 ◽  
Vol 126 (4) ◽  
pp. 474-480 ◽  
Author(s):  
Patrick J. Conner ◽  
Bruce W. Wood
Keyword(s):  
Genetic Similarity ◽  
Rapd Markers ◽  
Dna Analysis ◽  
Genetic Relatedness ◽  
Genetic Relationships ◽  
Genetic Distances ◽  
Similarity Coefficient ◽  
Carya Illinoinensis ◽  
Randomly Amplified Polymorphic Dna ◽  
Average Value

Genetic variation among pecan [Carya illinoinensis (Wangenh.) C. Koch] cultivars was studied using randomly amplified polymorphic DNA (RAPD) markers. Using a combination of primers, a unique fingerprint is presented for each of the pecan genotypes studied. The genetic relatedness between 43 cultivars was estimated using 100 RAPD markers. Genetic distances, based on the similarity coefficient of Nei & Li, varied from 0.91 to 0.46, with an average value of 0.66 among all cultivars. The phenetic dendrogram developed from cluster analysis showed relatively weak grouping association. However, cultivars with known pedigrees usually grouped with at least one of the parents and genetic similarity estimates appear to agree with known genetic relationships.

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