scholarly journals Use of RAPD Marker Analysis to Assess Changes in the Genetic Diversity of Potato Genebanks

HortScience ◽  
1996 ◽  
Vol 31 (4) ◽  
pp. 595d-595
Author(s):  
A. del Rio ◽  
J.B. Bamberg ◽  
Z. Huaman ◽  
R. Hoekstra ◽  
A. Salas ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Relationships ◽  
Rapd Marker ◽  
Solanum Species ◽  
Breeding Systems ◽  
Common Source ◽  
Wild Potato Species ◽  
Tetraploid Potato ◽  
Potato Germplasm

Effects of genebank seed increases on the genetic integrity and whether germplasm in the genebank still represents the in situ populations from which it was collected are major concerns of the recently formed Association of Potato Intergenebank Collaborators (APIC), a consortium of world potato genebank leaders. This cooperative APIC research used RAPDs and morphological markers 1) to establish genetic relationships between seed increased populations within accessions and (2) to measure genetic differentiation between diploid and tetraploid potato germplasm maintained for many years and current in situ populations from the same collection sites in the wild. Solanum jamesii Torrey (2n = 2x = 24) and S. fendleri A. Gray (2n = 4x = 48), two wild potato species native to North America, were used as plant material. These species represented two major breeding systems found among Solanum species: outcrossing diploids and inbreeding disomic tetraploids, respectively. Comparisons made between populations one generation apart and between sister populations generated from a common source indicated that there has been minimal loss of genetic diversity in captive germplasm using the genebank techniques standard at NRSP-6 and other world potato genebanks. RAPD markers also revealed that significant genetic differences were found between genebank-conserved and re-collected in situ populations for all diploid potato comparisons and for about half of the comparisons within tetraploid potato populations.

scholarly journals Detection of Genetic Variation and Genetic Diversity in Two Indian Mudskipper Species (Boleophthalmus boddarti, B. dussumieri) using RAPD Marker

2013 ◽  
Vol 5 (2) ◽  
pp. 139-143
Author(s):  
Vellaichamy RAMANADEVI ◽  
Muthusamy THANGARAJ ◽  
Anbazhagan SURESHKUMAR ◽  
Jayachandran SUBBURAJ
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Environmental Changes ◽  
Genetic Relationships ◽  
Rapd Marker ◽  
Distinct Species ◽  
Fish Population ◽  
Habitat Destruction ◽  
Arbitrary Primers ◽  
Vellar Estuary

Due to the environmental changes and habitat destruction the mudskipper fish population is decreasing in recent years. To predict the fish population structure, frequent manual survey and molecular methods are widely used. Molecular markers such as RAPD, microsatellite, allozyme, D-loop haplotype are frequently adopted to assess the population structure of an organism. In this study ten- arbitrary primers were screened to estimate the genetic relationships and diversity of two mudskipper species (Boleophthalmus boddarti and B. dussumieri) in Vellar estuary, Tamilnadu, India. By this RAPD marker study, the genetic diversity (H) in B. boddarti was more (0.0116 ± 0.0066) than in B. dussumieri (0.0056 ± 0.0024) in Vellar estuary (India). The genetic distance between B. boddarti and B. dussumieri was 1.7943. By observing the species specific bands and the phylogenetic analysis it is revealed that these two species clearly deviated into separate clusters emphasizing the distinct species status.

scholarly journals Genetic diversity and population structure analyses in the Alpine plum (Prunus brigantina Vill.) confirm its affiliation to the Armeniaca section

2020 ◽  
Author(s):  
Liu Shuo ◽  
Decroocq Stephane ◽  
Harte Elodie ◽  
Tricon David ◽  
Chague Aurelie ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Core Collection ◽  
Genetic Relationships ◽  
Allelic Diversity ◽  
Wild Relatives ◽  
Ex Situ ◽  
Conservation Measures ◽  
Geographical Regions

AbstractIn-depth characterization of the genetic diversity and population structure of wild relatives of crops is of paramount importance for genetic improvement and biodiversity conservation, and is particularly crucial when the wild relatives of crops are endangered. In this study, we therefore sampled the Alpine plum (Briançon apricot) Prunus brigantina Vill. across its natural distribution in the French Alps, where its populations are severely fragmented and its population size strongly impacted by humans. We analysed 71 wild P. brigantina samples with 34 nuclear markers and studied their genetic diversity and population structure, with the aim to inform in situ conservation measures and build a core collection for long-term ex-situ conservation. We also examined the genetic relationships of P. brigantina with other species in the Prunophora subgenus, encompassing the Prunus (Eurasian plums), Prunocerasus (North-American plums) and Armeniaca (apricots) sections, to check its current taxonomy. We detected a moderate genetic diversity in P. brigantina and a Bayesian model-based clustering approach revealed the existence of three genetically differentiated clusters, endemic to three geographical regions in the Alps, which will be important for in situ conservation measures. Based on genetic diversity and population structure analyses, a subset of 36 accessions were selected for ex-situ conservation in a core collection that encompasses the whole detected P. brigantina allelic diversity. Using a dataset of cultivated apricots and wild cherry plums (P. cerasifera) genotyped with the same markers, we detected gene flow neither with European P. armeniaca cultivars nor with diploid plums. In contrast with previous studies, dendrograms and networks placed P. brigantina closer to Armeniaca species than to Prunus species. Our results thus confirm the classification of P. brigantina within the Armeniaca section; it also illustrates the importance of the sampling size and design in phylogenetic studies.

scholarly journals Development and Utilization of a Core Collection in Theobroma cacao based on RAPD Marker-based Estimates of Genetic Distance

HortScience ◽  
1997 ◽  
Vol 32 (3) ◽  
pp. 513C-513
Author(s):  
Jane M. Marita ◽  
José Luis Pires ◽  
W. Martin Aitken ◽  
James Nienhuis
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Random Sampling ◽  
Theobroma Cacao ◽  
Core Collection ◽  
Genetic Relationships ◽  
Rapd Marker ◽  
Sources Of Resistance ◽  
Resistant Varieties ◽  
Broom Disease

An increased need to understand the genetic relationships among cacao (Theobroma cacao) germplasm exists to identify cultivars that possess resistance to witches' broom disease (caused by Crinipellis perniciosa). Loss of production due to witches' broom disease in important cacao-growing areas, such as Bahia, Brazil, has generated a strong demand for disease-resistant varieties. Varieties based on single sources of resistance have been released; however, other genotypes are needed to enlarge the genetic diversity of cultivars in breeding programs. A core collection has been created to represent the range of genetic diversity available among the more than 600 cacao accessions at Centro de Pesquisa do Cacau (CEPEC). The cacao core facilitates access to the collection and is intended to enhance its use. This core collection was created from RAPD marker-based estimates of genetic distance among a subset of 270 accessions from the entire collection. The subset was sampled based on 1) witches' broom disease resistance data, 2) random sampling of the collection, and 3) random sampling of recently acquired accessions. Differences in RAPD marker frequencies were used to identify accessions in a witches' broom disease breeding program that contribute to the genetic diversity of the collection as a whole. In addition, differences in RAPD marker frequency allowed the comparison between accessions in the original collection and those acquired from new geographic regions that may expand the collection's genetic diversity.

Genetic diversity among accessions of an ancient olive variety of Cyprus

Genome ◽  
2003 ◽  
Vol 46 (3) ◽  
pp. 370-376 ◽  
Author(s):  
Georgios Banilas ◽  
John Minas ◽  
Costas Gregoriou ◽  
Cathrine Demoliou ◽  
Anna Kourti ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Relationships ◽  
Rapd Marker ◽  
Fruit Size ◽  
Germplasm Collection ◽  
Group Method ◽  
Dice Similarity Coefficient ◽  
Pair Group ◽  
Electrophoretic Patterns ◽  
Olive Variety

To evaluate germplasm variability and to discriminate between accessions of 'Ladolia', an ancient olive variety of Cyprus, different accessions from a germplasm collection were screened with 11 selected oligonucleotide primers in RAPD-PCRs. A total of 49 polymorphic markers were scored, the combination of which resulted in 70 distinct electrophoretic patterns. Based on either unique or combined patterns, all accessions were identified. Seven genotype-specific markers were detected. One RAPD marker could distinguish accessions according to fruit size. Genetic similarities between accessions, estimated using the Dice similarity coefficient, indicated a high degree of genetic diversity among 'Ladolia' accessions. Genetic relationships were estimated by the unweighted pair-group method with arithmetic averaging (UPGMA) and principal components analysis (PCA). Three main groups of accessions were detected. The first group was generally composed of accessions with small-sized fruits and could be further divided into two subgroups. According to PCA, most accessions with medium- or large-sized fruits were clustered together. Our results support previous observations suggesting that 'Ladolia' is actually a highly variable mixture of genetically distinct landraces.Key words: DNA polymorphism, germplasm variability, RAPD markers, Olea europaea.

461 PB 292 MAPPING RAPD MARKER DIVERSITY IN PHASEOLUS VULGARIS

HortScience ◽  
1994 ◽  
Vol 29 (5) ◽  
pp. 497c-497
Author(s):  
Paul Skroth ◽  
Jim Nienhuis ◽  
Geunhwa Jung ◽  
Dermont Coyne
Keyword(s):  
Genetic Diversity ◽  
Rapd Markers ◽  
Genetic Relationships ◽  
Rapd Marker ◽  
Plant Genetic Resources ◽  
Ex Situ ◽  
Good Tool ◽  
Germplasm Collections ◽  
Efficient Construction ◽  
Two Populations

Knowledge of genetic relationships and genetic diversity among accessions is essential for the efficient construction, maintainance and utilization of large ex-situ germplasm collections. Furthermore, streamlining of large collections into care collections necessitates validation of germplasm sampling techniques. DNA molecular markers provide potentially unbiased estimators of genome diversity end may facilitate organization, maintainance, and sampling of plant genetic resources. Our data suggests that RAPD markers will be o good tool for testing tore collection concepts and organizing genetic diversity in common bean. However, the genomic distribution of markers is unknown. Currently we are using recombinant inbred (RI) populations to place RAPD markers in the context of the bean genetic map. We hove evaluated the the distribution of RAPD markers in three RI populations: Bat93 × Jalo EEP558, PC50 × Xan159, and BAC6 × HT7719. Cultivated P.vulgaris has two primary renters of diversity Mesoamerican and Andean, the RI populations used for mapping RAPD markers ore Meso × Andean, Andean × Andean, and Meso × Meso crosses respectively. In the Bat93 × Jalo EEP558 population 383 markers have been mapped for a map length of 735 cM. However, approximately 150 of these markers ore members of 9 dusters which span only 90 cM. This inter gone pool mop is being integrated with linkage mops constructed in the other two populations to compare within and between gene pool marker distributions and to evaluate clustering of markers on the different mops. Implications for the application of RAPD markers will be discussed.

scholarly journals I-SSR Markers Revealed Inconsistent Phylogeographic Patterns among Populations of Japanese Red Pines in Korea

2007 ◽  
Vol 56 (1-6) ◽  
pp. 22-26 ◽  
Author(s):  
Y.-P. Hong ◽  
H.-Y. Kwon ◽  
I.-S. Kim
Keyword(s):  
Genetic Diversity ◽  
Tree Species ◽  
Population Genetic ◽  
Genetic Relationships ◽  
Natural Process ◽  
Moderate Degree ◽  
Gene Conservation ◽  
Genetic Groups ◽  
Reported Data

Abstract To monitor the level and distribution pattern of genetic diversity in countrywide populations of Japanese red pines in Korea, 80 I-SSR variants were analyzed from 192 individuals in 11 populations. The previously reported data, obtained from the 8 populations of this species, were incorporated into the estimation of the population genetic statistics. Relatively higher level of genetic diversity was observed in 19 populations of Japanese red pines (mean of 0.453) than those in other tree species. From the results of AMOVA, majority of genetic diversity (92%) was allocated within populations, which brought about the moderate degree of population differentiation (ϕST= 0.08). Two genetic groups were observed from the dendrogram reconstructed by UPGMA. Overall correlation between genetic relationships and geographic affinity was inconsistent among the 19 populations. Some probable genetic disturbances, induced by either human interference or the natural process of regeneration for the species after devastation, might be responsible for the discrepancy between genetic relationships and geographical distribution of the populations. These results suggested that simple geographic or ecological grouping might not represent the genetic zone of the Korean populations of Japanese red pines, and that more careful approach should be made for designating in situ gene conservation of this species in Korea.

Genetic diversity of Asian and European common wheat lines assessed by fluorescence in situ hybridization

Genome ◽  
2021 ◽  
Author(s):  
Xiu Yang ◽  
Binwen Tan ◽  
Yulu Yang ◽  
Xiaohui Zhang ◽  
Wei Zhu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
In Situ Hybridization ◽  
Fluorescence In Situ Hybridization ◽  
Common Wheat ◽  
Genetic Relationships ◽  
Structural Variations ◽  
D Genome ◽  
Western Asia ◽  
Wheat Lines

Understanding the genetic diversity of wheat is important for wheat breeding and improvement. However, there have been limited attempts to evaluate wheat diversity using fluorescence in situ hybridization (FISH). In this study, the chromosomal structures of 149 wheat accessions from 13 countries located between the latitudes of 30° and 45°N, the principal growing region for wheat, were characterized using FISH with pTa535 and pSc119.2 probes. The ranges of the numbers of FISH types in the A-, B-, and D-genomes were 2–8, 3–7, and 2–4, respectively, and the average numbers in the A- and B-genomes were greater than in the D-genome. Chromosomal translocations were detected by these probes, and previously undescribed translocations were also observed. Using the FISH, the genetic relationships among the 149 common wheat lines were divided into three groups (G1, G2, and G3). G1 mainly consisted of Southern European lines, G2 consisted of most lines from Japan and some lines from Western Asia, China, and Korea, and G3 consisted of the other lines from Southern Europe and most of the lines from Western Asia, China, and Korea. FISH karyotypes of wheat chromosomes distinguished chromosomal structural variations, revealed the genetic diversity among wheat varieties. Furthermore, these results provide valuable information for the further genetic improvement of wheat in China.

Genetic diversity of the extremely rare Habenaria dentata and the rare Habenaria linearifolia (Orchidaceae) in South Korea: implications for population history and conservation

2018 ◽  
Vol 151 (1) ◽  
pp. 48-60
Author(s):  
Mi Yoon Chung ◽  
Hoa Thi Quynh Le ◽  
Sungwon Son ◽  
Huai Zhen Tian ◽  
Myong Gi Chung
Keyword(s):  
Genetic Diversity ◽  
Southern China ◽  
Geographic Location ◽  
Population History ◽  
Population Variation ◽  
Conservation Strategies ◽  
Ancestral Population ◽  
Allozyme Diversity ◽  
Glacial Origin

Background and aims – Since historical events often leave an indelible mark on levels of genetic diversity of plant populations, one may indirectly infer their evolutionary history with the help of current patterns of genetic diversity. The terrestrial orchid Habenaria dentata, an element of warm-temperate/subtropical vegetation, reaches its northernmost limits in the Korean Peninsula, and thus it is extremely rare there. As H. dentata was absent from the Peninsula during the Last Glacial Maximum (LGM), it is likely to be of post-glacial origin having arrived from either a single refugium or multiple refugia. However, its rare, temperate/boreal congener H. linearifolia might have persisted in situ in either macrorefugia or microrefugia on the Peninsula during the LGM.Methods – To test which hypothesis is most appropriate for each species, we investigated levels of allozyme-based (17 loci) genetic diversity and population genetic structure in the two only known populations of H. dentata and in 12 populations of H. linearifolia.Key results – No allozyme diversity was found in H. dentata (He = 0.000), whereas H. linearifolia exhibited low within-population variation (He = 0.060) and high among-population differentiation (FST = 0.237). We found little association between populations in relation to their geographic location; several populations presented individuals belonging to different clusters.Conclusions – Our results suggest that H. dentata likely originated from a single ancestral population (perhaps from southern Japan or southern China) through post-glacial dispersal, whereas H. linearifolia probably survived the LGM in situ in microrefugia situated at low to mid-elevated regions. We further suggest that separate conservation strategies for each species should be employed, given that the two taxa have different ecological and demographic traits and harbour different levels of genetic diversity.

scholarly journals Molecular Analysis of a Plum pox virus W Isolate in Plum Germplasm Hand Carried into the USA from the Ukraine Shows a Close Relationship to a Latvian Isolate

Plant Disease ◽  
2013 ◽  
Vol 97 (1) ◽  
pp. 44-52 ◽  
Author(s):  
Vessela Mavrodieva ◽  
Delano James ◽  
Karen Williams ◽  
Sarika Negi ◽  
Aniko Varga ◽  
...  
Keyword(s):  
United States ◽  
Genetic Diversity ◽  
The United States ◽  
Common Source ◽  
Plum Pox Virus ◽  
High Genetic Diversity ◽  
Close Relationship ◽  
The Usa ◽  
Sequence Identities ◽  
Germplasm Accessions

Four of 19 Prunus germplasm accessions hand carried from the Ukraine into the United States without authorization were found to be infected with Plum pox virus (PPV). Of the three isolates characterized, isolates UKR 44189 and UKR 44191 were confirmed to be isolates of PPV strain W, and UKR 44188 was confirmed to be an isolate of PPV strain D. UKR 44189 and UKR 44191 are very closely related to the PPV strain W isolate LV-145bt (HQ670748) from Latvia. Nucleotide and amino acid sequence identities between these three isolates were greater than 99%. This indicates that the isolates are very closely related and likely originated from a common source. The high genetic diversity among PPV-W strain isolates allowed the identification of potential recombination events between PPV isolates. It appears also that GF 305 peach and Prunus tomentosa are not hosts for the PPV isolate UKR 44189.

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