Molecular genetic diversity of the French-American grapevine hybrids cultivated in North America

Genome ◽  
2003 ◽  
Vol 46 (6) ◽  
pp. 1037-1048 ◽  
Author(s):  
Patrick Pollefeys ◽  
Jean Bousquet
Keyword(s):  
Genetic Diversity ◽  
North America ◽  
Genetic Background ◽  
Molecular Genetic ◽  
Group Method ◽  
Dna Profile ◽  
Vitis Riparia ◽  
The North ◽  
Pair Group ◽  
Molecular Genetic Diversity

French-American hybrid grapevines are most popular in eastern and mid-western North America: they are hardy cultivars derived from crosses between the European Vitis vinifera and American wild vines. The aim of this study was to characterize their genetic background using 6 microsatellite (SSR) markers and a set of 33 diagnostic RAPD markers. The latter were reproducible with different PCR thermal cyclers. Two SSR loci were found to be synonymous, VrZAG47 and VVMD27. The DNA profile frequencies estimated for each cultivar were much lower with multi-locus SSR data than that obtained from multi-fragment RAPD data. There was no significant correlation between the multi-locus DNA profile frequencies derived from SSRs and those from RAPDs. Estimates of genetic diversity derived from SSRs were generally higher and the average similarity between cultivars was generally lower than values reported for subgroups of V. vinifera, in accordance with expectations for hybrid cultivars. The phenetic relationships depicted by UPGMA (unweighted pair-group method with arithmetic averaging) and neighbor-joining analyses of microsatellite data were congruent and, to a large extent, in agreement with the known pedigree or history of each cultivar. A major dichotomy was observed between one group where the known genetic background was dominated by the North American Vitis riparia and Vitis labrusca, and another one where the genetic background was dominated by the European V. vinifera. Two Kulhmann varieties thought to be synonymous were found to be different, though closely related.Key words: French-American hybrids, genetic diversity, RAPD, SSR, Vitis.

Molecular Diversity Analysis of Lentil (Lens culinaris Medik.) through RAPD Markers

2012 ◽  
Vol 22 (1) ◽  
pp. 51-58 ◽  
Author(s):  
M.E. Hoque ◽  
M.M. Hasan
Keyword(s):  
Genetic Distance ◽  
Rapd Markers ◽  
Gene Diversity ◽  
Random Amplified Polymorphic Dna ◽  
Molecular Genetic ◽  
Group Method ◽  
Diversity Analysis ◽  
Pair Group ◽  
Molecular Genetic Diversity

Random Amplified Polymorphic DNA (RAPD) markers were used to study the molecular genetic diversity analysis among six BARI released lentil varieties viz. BARI masur-1, BARI masur-2, BARI masur-3, BARI masur-4, BARI masur-5 and BARI masur-6. PCR amplified products were visualized on 1.0% agarose gel and the band for each primer were scored. Ten RAPD markers were used in this study. Out of them 7 primers showed amplification of 53 DNA fragments with 60.37% of them being polymorphic. The highest number of polymorphic loci was noticed in the variety BARI masur-3. The same variety also showed maximum Nei’s gene diversity value (0.0552). The highest Nei’s genetic distance (0.5002) was observed in BARI masur-1 vs. BARI masur-5 whereas, the lowest genetic distance (0.0692) was found in BARI masur-1 vs. BARI masur-2. The unweighted pair group method of arithmetic mean (UPGMA) dendrogram based on Nei’s genetic distance grouped the six cultivars into two main clusters. BARI masur-1, BARI masur-2 and BARI masur-3 were in cluster I and BARI masur-4, BARI masur-5 and BARI masur-6 were in cluster II. The cultivar BARI masur-4 was closest to the cultivar BARI masur-6 with the lowest genetic distance (0.0972) and the highest genetic distance (0.5002) was found between BARI masur-1 and BARI masur-5. The RAPD markers were found to be useful in molecular characterization of lentil varieties which could be utilized by the breeders for the improvement of lentil cultivars. DOI: http://dx.doi.org/10.3329/ptcb.v22i1.11260 Plant Tissue Cult. & Biotech. 22(1): 51-58, 2012 (June)

Molecular genetic diversity and population structure in Eucalyptus pauciflora subsp. pauciflora (Myrtaceae) on the island of Tasmania

2014 ◽  
Vol 62 (3) ◽  
pp. 175 ◽  
Author(s):  
Archana Gauli ◽  
Dorothy A. Steane ◽  
René E. Vaillancourt ◽  
Brad M. Potts
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Molecular Genetic ◽  
Glacial Refugia ◽  
Altitudinal Distribution ◽  
The North ◽  
Chloroplast Haplotype ◽  
Molecular Genetic Diversity ◽  
Nuclear Microsatellite ◽  
Chloroplast Dna Markers

Genetic diversity and population structure of Tasmanian populations of Eucalyptus pauciflora were assessed using chloroplast and nuclear microsatellite markers. Maternal trees and open-pollinated progeny from 37 populations were sampled across the species’ geographic and altitudinal distribution in Tasmania. The distribution of chloroplast haplotype richness showed a clear geographic structure with suggestion of three major refugia (Storm Bay, Tamar Valley and St Pauls River Valley), two of which are consistent with previously reported glacial refugia. Chloroplast haplotype affinities provided evidence of migration of populations from the north and east towards the south and west of Tasmania. High nuclear microsatellite diversity was observed across the species’ range. Most of this variation was distributed within populations with low but significant FST, suggesting high gene flow among populations that is more pronounced in mature stands. Higher nuclear genetic diversity in newly colonised areas compared with lowland putative refugial regions, and the converse in chloroplast DNA markers, suggest limited seed dispersal into newly colonised regions combined with high pollen flow between different source populations in newly colonised areas. Our results do not support the suggestion that highland populations of E. pauciflora originate from in situ high-altitude refugia, but instead argue they originate from lowland refugia.

First identification of core accessions of Jatropha curcas from India based on molecular genetic diversity

2015 ◽  
Vol 14 (1) ◽  
pp. 77-80 ◽  
Author(s):  
Pratima Sinha ◽  
Md Aminul Islam ◽  
Madan Singh Negi ◽  
Shashi Bhushan Tripathi
Keyword(s):  
Tamil Nadu ◽  
Fragment Length Polymorphism ◽  
Molecular Genetic ◽  
Allelic Diversity ◽  
Group Method ◽  
Indian States ◽  
The Core ◽  
Pair Group ◽  
Molecular Genetic Diversity ◽  
Entire Collection

We report on identification of core collection from 192 accessions collected from 12 Indian states and five other countries based on 109 polymorphic amplified fragment length polymorphism (AFLP) markers. Pairwise Jaccard's similarity coefficient for accessions varied from 0.25 to 1 with a maximum genetic distance of 0.75 obtained between accessions Jc428 (from Mexico) and J204 (from Madurai, Tamil Nadu). Both UPGMA (Unweighted Pair Group Method of Arithmetic Averages) clustering and principal coordinate analyses showed similar grouping of accessions in three major clusters in which Mexican accessions clustered separately from Indian, Chinese and African accessions. Results obtained from analysis of molecular variance indicated that 59% of the genetic variation was distributed among the populations, while 41% of variation was within the populations. A total of 16 (8.3% of the entire collection) core accessions were identified, which contained the entire allelic diversity of 192 accessions with respect to the sampled AFLP loci. The core accessions would be highly useful for future genetic improvement of Jatropha. To the best of our knowledge, this is the first report on identification of core accessions in Jatropha.

scholarly journals Population Differentiation Within Anisogramma anomala in North America

2019 ◽  
Vol 109 (6) ◽  
pp. 1074-1082 ◽  
Author(s):  
Megan F. Muehlbauer ◽  
Janine Tobia ◽  
Joshua A. Honig ◽  
Ning Zhang ◽  
Bradley I. Hillman ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
North America ◽  
Group Method ◽  
Summary Statistics ◽  
Upgma Dendrogram ◽  
Pair Group ◽  
Anisogramma Anomala ◽  
High Degree ◽  
Degree Of Similarity ◽  
Simple Sequence

Anisogramma anomala, a biotrophic ascomycete in the order Diaporthales, causes eastern filbert blight (EFB) of hazelnuts (Corylus spp.). Until recently, little has been documented on its genetic diversity and population structure. In this study, 18 simple sequence repeat markers were used to fingerprint 182 accessions of the fungus originating from across North America. Our results, based on summary statistics of the allelic data, a discriminant analysis of principal components (DAPC) scatterplot, an unweighted pair group method with arithmetic mean (UPGMA) dendrogram, and analysis of multilocus genotypes, show that A. anomala exhibits considerable genetic diversity across multiple populations. Eleven clusters were resolved from the DAPC scatterplot, five of which were validated by statistically supported clusters in the UPGMA dendrogram. The 11 DAPC clusters were statistically significant via an analysis of molecular variance. Dendrogram topology and DAPC scatterplot groups showed some correlation with collection origin; samples collected in proximity tended to cluster together and be genetically similar. However, some locations held populations that were diverse and some populations with a high degree of similarity had disparate origins, suggesting movement by humans. Overall, the results demonstrate the presence of multiple, genetically distinct populations of A. anomala in North America and serve as a reference to assist in understanding and managing EFB.

Genetic variation among Stipa grandis P. Smirn populations with different durations of fencing in the Inner Mongolian Steppe

2010 ◽  
Vol 32 (4) ◽  
pp. 427 ◽  
Author(s):  
Jian-bo Wu ◽  
Yu-bao Gao ◽  
Xiao-ying Bao ◽  
Hui Gao ◽  
Mei-qing Jia ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Genetic Structure ◽  
Molecular Genetic ◽  
Critical Role ◽  
Morphological Characteristics ◽  
Group Method ◽  
Scaling Analysis ◽  
Pair Group ◽  
Inner Mongolian Steppe

The genetic structure of a population should be carefully considered in ecological restoration because it may play a critical role in maintaining the persistence of a restored ecosystem. In the present study, we examined genetic diversity and genetic structure of Stipa grandis P. Smirn populations from fenced and grazed plots using amplified fragment length polymorphism markers. Molecular genetic variation showed that the genetic diversity of the fenced populations was greater compared with the overgrazed population. There was a significant variation among the populations (Fst = 0.3689, P < 0.001) by AMOVA analysis, and the gene flow was 0.4039 among the populations. The results from a comparison of limited morphological characteristics and from an unweighted pair group method with arithmetic mean cluster analysis and non-metric multi-dimensional scaling analysis suggested that genetic differentiation had occurred between the fenced populations and the grazed populations. The largest genetic diversity was in the moderately grazed population, which might be related to higher population density and greater sexual reproduction due to less disturbances in the plots. The genetic diversity of the long-term (24 years) fenced population was similar to that of a short-term fenced population (fenced for 11 years). These results suggested that the genetic diversity in the overgrazed population might be increased to some extent through fencing, but this effect did not occur beyond 11 years.

scholarly journals Genetic Diversity Among Some Walnut (Juglans regia L.) Genotypes by SSR Markers

2021 ◽  
Vol 13 (12) ◽  
pp. 6830
Author(s):  
Murat Guney ◽  
Salih Kafkas ◽  
Hakan Keles ◽  
Mozhgan Zarifikhosroshahi ◽  
Muhammet Ali Gundesli ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Plant Genetic Resources ◽  
Juglans Regia ◽  
Genetic Distances ◽  
Mean Value ◽  
Central Anatolia ◽  
Group Method ◽  
Arithmetic Average ◽  
Pair Group ◽  
Principal Coordinates

The food needs for increasing population, climatic changes, urbanization and industrialization, along with the destruction of forests, are the main challenges of modern life. Therefore, it is very important to evaluate plant genetic resources in order to cope with these problems. Therefore, in this study, a set of ninety-one walnut (Juglans regia L.) accessions from Central Anatolia region, composed of seventy-four accessions and eight commercial cultivars from Turkey, and nine international reference cultivars, was analyzed using 45 SSR (Simple Sequence Repeats) markers to reveal the genetic diversity. SSR analysis identified 390 alleles for 91 accessions. The number of alleles per locus ranged from 3 to 19 alleles with a mean value of 9 alleles per locus. Genetic dissimilarity coefficients ranged from 0.03 to 0.68. The highest number of alleles was obtained from CUJRA212 locus (Na = 19). The values of polymorphism information content (PIC) ranged from 0.42 (JRHR222528) to 0.86 (CUJRA212) with a mean PIC value of 0.68. Genetic distances were estimated according to the UPGMA (Unweighted Pair Group Method with Arithmetic Average), Principal Coordinates (PCoA), and the Structure-based clustering. The UPGMA and Structure clustering of the accessions depicted five major clusters supporting the PCoA results. The dendrogram revealed the similarities and dissimilarities among the accessions by identifying five major clusters. Based on this study, SSR analyses indicate that Yozgat province has an important genetic diversity pool and rich genetic variance of walnuts.

scholarly journals Genetic diversity in table grapes based on RAPD and microsatellite markers

2011 ◽  
Vol 46 (9) ◽  
pp. 1035-1044 ◽  
Author(s):  
Patrícia Coelho de Souza Leão ◽  
Sérgio Yoshimitsu Motoike
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Genetic Relationships ◽  
Similarity Index ◽  
Genetic Distances ◽  
Table Grape ◽  
Group Method ◽  
Molecular Characteristics ◽  
Table Grapes ◽  
Pair Group

The objective of this work was to analyze the genetic diversity of 47 table grape accessions, from the grapevine germplasm bank of Embrapa Semiárido, using 20 RAPD and seven microsatellite markers. Genetic distances between pairs of accessions were obtained based on Jaccard's similarity index for RAPD data and on the arithmetic complement of the weighted index for microsatellite data. The groups were formed according to the Tocher's cluster analysis and to the unweighted pair‑group method with arithmetic mean (UPGMA). The microsatellite markers were more efficient than the RAPD ones in the identification of genetic relationships. Information on the genetic distance, based on molecular characteristics and coupled with the cultivar agronomic performance, allowed for the recommendation of parents for crossings, in order to obtain superior hybrids in segregating populations for the table grape breeding program of Embrapa Semiárido.

Study on molecular genetic diversity of native duck breeds in China

2006 ◽  
Vol 62 (04) ◽  
pp. 603-611
Author(s):  
H. LI ◽  
N. YANG ◽  
K. CHEN ◽  
G. CHEN ◽  
Q. TANG ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Molecular Genetic ◽  
Molecular Genetic Diversity

AFLP-based assessment of genetic diversity among nine alfalfa germplasms using bulk DNA templates

Genome ◽  
2003 ◽  
Vol 46 (1) ◽  
pp. 51-58 ◽  
Author(s):  
A Segovia-Lerma ◽  
R G Cantrell ◽  
J M Conway ◽  
I M Ray
Keyword(s):  
Genetic Diversity ◽  
Medicago Sativa ◽  
High Throughput ◽  
Genetic Distances ◽  
Group Method ◽  
Aflp Analysis ◽  
Dna Templates ◽  
Arithmetic Average ◽  
Pair Group ◽  
Large Numbers

Improving commercial utilization of perennial Medicago collections requires developing approaches that can rapidly and accurately characterize genetic diversity among large numbers of populations. This study evaluated the potential of using amplified fragment length polymorphism (AFLP) DNA markers, in combination with DNA bulking over multiple genotypes, as a strategy for high-throughput characterization of genetic distances (D) among alfalfa (Medicago sativa L.) accessions. Bulked DNA templates from 30 genotypes within each of nine well-recognized germplasms (African, Chilean, Flemish, Indian, Ladak, Medicago sativa subsp. falcata, Medicago sativa subsp. varia, Peruvian, and Turkistan) were evaluated using 34 primer combinations. A total of 3754 fragments were identified, of which 1541 were polymorphic. The number of polymorphic fragments detected per primer combination ranged from 20 to 85. Pairwise D estimates among the nine germplasms ranged from 0.52 to 1.46 with M. sativa subsp. falcata being the most genetically dissimilar. Unweighted pair-group method arithmetic average (UPGMA) analysis of the marker data produced two main clusters, (i) M. sativa subsp. sativa and M. sativa subsp. varia, and (ii) M. sativa subsp. falcata. Cluster-analysis results and D estimates among the Chilean, Peruvian, Flemish, and M. sativa subsp. varia germplasms supported the hypothesis that Peruvian was more similar to original Spanish introductions into Central and South America than Chilean. Hierarchical arrangement of the nine germplasms was supported by their respective geographic, subspecific, and intersubspecific hybrid origins. Subsets of as few as seven highly informative primer pairs were identified that produced comparable D estimates and similar heirarchical arrangements compared with the complete dataset. The results indicate that use of primer-pair subsets for AFLP analysis of bulk DNA templates could serve as a high-throughput system for accurately characterizing genetic diversity among large numbers of alfalfa populations.Key words: Medicago sativa, DNA bulking, genetic distance.

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