The use of random amplified microsatellite polymorphic DNA and coefficients of parentage to determine genetic relationships in barley

Genome ◽  
1998 ◽  
Vol 41 (4) ◽  
pp. 477-486 ◽  
Author(s):  
J A Dávila ◽  
M P Sánchez de la Hoz ◽  
Y Loarce ◽  
E Ferrer
Keyword(s):  
Hordeum Vulgare ◽  
Genetic Similarity ◽  
Genetic Relationships ◽  
Spring Barley ◽  
Genetic Distances ◽  
Mantel Test ◽  
Winter Barley ◽  
Mean Values ◽  
Simple Sequence ◽  
Hordeum Vulgare Ssp

Seventy European barley lines (Hordeum vulgare ssp. vulgare) and 29 Hordeum vulgare ssp. spontaneum accessions were evaluated for random amplified microsatellite polymorphism (RAMP). PCR was performed with 5'-anchored primers complementary to microsatellites in combination with random primers. Of 20 primers assayed in barley, only 9 produced well-resolved fragment patterns in H. vulgare ssp. spontaneum. On the basis of 56 polymorphic fragments, genetic distances between the two subspecies were calculated. Barley samples were subdivided according to growth habit and spike morphology. The smallest genetic distance was found between winter cultivars and accessions of H. vulgare ssp. spontaneum. The 20 primers assayed in the barley lines produced 140 polymorphic fragments that were used to calculate genetic similarity between lines. Mean genetic similarity within groups of lines ranged from 0.693 for 6-rowed winter barley to 0.657 for 6-rowed spring barley. Within these groups, mean values were significantly higher than mean genetic similarity between groups. Principal-coordinate analysis clearly separated the 2-rowed spring and 6-rowed winter types. Cluster analysis of spring and winter types showed subclustering consistent with the available pedigrees. Coefficients of parentage (COPs) were calculated for 29 spring and 20 winter lines. Mean values of 0.0741 for spring barley and 0.0458 for winter barley were obtained. RAMP-based genetic similarity matrices were compared with the corresponding COP-based matrices by the Mantel test. The correlation between them was poor (r = 0.21, P < 0.05), indicating little relationship between these two estimators of genetic similarity. The relative influence of factors involved in the calculation of these two estimators is discussed.Key words: genetic diversity, microsatellites, simple sequence repeats, fingerprinting, barley.

scholarly journals Detection of Genetic Polymorphism in Seven Barley Hordeum vulgare L. Varieties Using SSR

2020 ◽  
Vol 33 (2) ◽  
pp. 115-124
Author(s):  
Maha R. Khalil ◽  
Hussain A. Almahasneh ◽  
Salam Y. Lawand
Keyword(s):  
Genetic Diversity ◽  
Cluster Analysis ◽  
Genetic Polymorphism ◽  
Hordeum Vulgare ◽  
Simple Sequence Repeats ◽  
Genetic Similarity ◽  
Hordeum Vulgare L ◽  
Simple Sequence

Investigation was carried out at the laboratory of Biotechnology, Faculty of Agriculture, Damascus University, during the season 2017-2018. Seven varieties were planted to determine the degree of genetic similarity using SSR-technique (Simple Sequence Repeats), and 14 double primers were used for this purpose. The analysis results revealed that all primers showed polymorphism among the evaluated varieties, except Bmag0385. primers produced a total of 42 alleles with a polymorphic percentage of 88.27%. The number of alleles for each primer varied from 1 allele for the primer (Bmac0067) to 7 alleles for the primer (Bmag0006) in average of 3 alleles per primer. Cluster analysis and Dendrogram showed the highest degree of genetic similarity between variety Arabi asuad  and variety Arabi abiad (0.7619). While it was low between variety Fourat4 and variety Arabi abiad (0.3571), and varieties Fourat4 and Fourat3 (0.3571) which indicated wide genetic diversity among them.

scholarly journals Identity of barley powdery mildew resistances Bw and Ru2

2012 ◽  
Vol 48 (No. 4) ◽  
pp. 185-188 ◽  
Author(s):  
A. Dreiseitl
Keyword(s):  
Hordeum Vulgare ◽  
Powdery Mildew ◽  
Spring Barley ◽  
Blumeria Graminis ◽  
Winter Barley ◽  
Barley Cultivar ◽  
Hordeum Vulgare L ◽  
Barley Line ◽  
Barley Powdery Mildew ◽  
The Difference

A large number of resistances to powdery mildew (Blumeria graminis f.sp. hordei) and their combinations are known in barley (Hordeum vulgare L.). A similarity of resistance spectra between cultivars carrying the resistance Bw, designated for the winter barley cultivar Borwina, and the near-isogenic spring barley line&nbsp;P15, which carries the resistance Ru2, derived from the landrace Rupee, was found. The objective of this study was to test the difference between resistances Bw and Ru2. Six cultivars were tested, four with Bw and two with&nbsp;Ru2. Testing with 40 isolates showed identical reaction spectra between both groups. Testing of the cultivar Kompolti 4 (Bw) and line P15 (Ru2) with 300 isolates confirmed this result. Thus, the resistances currently designated Bw and Ru2 can be regarded as identical, and are determined by the gene Ml(Ru2). Both Bw and Ru2 should be designated by the earlier code, Ru2.

scholarly journals Identifying Blueberry Cultivars and Evaluating Their Genetic Relationships Using Randomly Amplified Polymorphic DNA (RAPD) and Simple Sequence Repeat- (SSR-) anchored Primers

1997 ◽  
Vol 122 (1) ◽  
pp. 74-78 ◽  
Author(s):  
A. Levi ◽  
L.J. Rowland
Keyword(s):  
Genetic Similarity ◽  
Genetic Relationships ◽  
Vaccinium Corymbosum ◽  
Similarity Matrix ◽  
Randomly Amplified Polymorphic Dna ◽  
Pedigree Data ◽  
Chain Reactions ◽  
Polymerase Chain Reactions ◽  
Polymerase Chain ◽  
Simple Sequence

Fifteen highbush (or highbush hybrid) blueberry cultivars (Vaccinium corymbosum Linnaeus), two rabbiteye blueberry cultivars (V. ashei Reade), and one southern lowbush (V. darrowi Camp) selection from the wild were examined using seventeen 10-base RAPD and seven 15- to 18-base SSR-anchored primers (primers comprised of SSR motifs) in polymerase chain reactions (PCRs). Fifteen RAPD and three SSR markers resulting from these reactions were chosen to construct a DNA fingerprinting table to distinguish among the genotypes included in this study. Similarity values were calculated based on 132 RAPD and 51 SSR bands, and a dendrogram was constructed based on the similarity matrix. The V. ashei cultivars and V. darrowi selection grouped out separately from the V. corymbosum cultivars as expected. However, estimates of relative genetic similarity between genotypes within the V. corymbosum group did not agree well with known pedigree data and, thus, indicated that RAPD and SSR data did not accurately assess the genetic relationships of cultivars within this species.

Molecular Markers (RAPD and SSR) Based Characterisation of Genetic Diversity and Population Structure of Moss Hyophila Involuta

2021 ◽  
Vol 63 (1-2) ◽  
pp. 171-193
Author(s):  
S. Pandey ◽  
A. Alam
Keyword(s):  
Genetic Variability ◽  
Polymorphic Information Content ◽  
Genetic Relationships ◽  
Rapd Marker ◽  
Natural Populations ◽  
Reproductive Mode ◽  
Genetic Distances ◽  
Mantel Test ◽  
Resolving Power ◽  
Marker System

Genetic relationships among 24 genotypes of Hyophila involuta collected from five different natural populations of Mount Abu (Rajasthan) is analysed using RAPD and SSR markers. Based on efficiency parameters calculated for each marker system such as polymorphic information content (RAPD = 0.34; SSR = 0.66), marker index (RAPD = 2.78; SSR = 2.62) and resolving power (RAPD = 8.13; SSR = 2.23), the RAPD marker system shows higher values for some indices but microsatellites are more accurately reproducible than RAPD. Moreover, in case of the SSR, the average number of alleles was almost twice compared to RAPD. Mean coefficient of genetic differentiation between populations with RAPD was Gst = 0.269, while with SSR marker was Fst = 0.224. The UPGMA cluster analysis assembled genotypes into two main clusters with diverse levels of sub-clustering within the clusters. Also, the Mantel test showed no significant correlation between geographical and genetic distances. The observed moderately high genetic variability can be explained by efficient spore dispersal. Other factors such as reproductive mode, somatic mutation, continuous propagule recruitment and high degree of intermingling have great impact on the level of genetic variability in moss populations.

GENETIC RELATIONSHIPS AMONG REPRESENTATIVE POPULATIONS OF FIVE CHORISTONEURA SPECIES: C. OCCIDENTALIS, C. RETINIANA, C. BIENNIS, C. LAMBERTIANA, AND C. FUMIFERANA (LEPIDOPTERA: TORTRICIDAE)

1981 ◽  
Vol 113 (9) ◽  
pp. 857-865 ◽  
Author(s):  
M. W. Stock ◽  
P. J. Castrovillo
Keyword(s):  
British Columbia ◽  
Gel Electrophoresis ◽  
Genetic Similarity ◽  
Genetic Relationships ◽  
Interspecific Variation ◽  
Genetic Distances ◽  
Starch Gel Electrophoresis ◽  
Separate Species ◽  
Individual Gene ◽  
Starch Gel

AbstractThe genetic make-up of representative populations of five Choristoneura species was compared using starch gel electrophoresis. Species included C. occidentalis Freeman from Idaho, C. biennis Freeman from British Columbia, C. retiniana (Walsingham) (= C. viridis Freeman) from Oregon, C. lambertiana ponderosana Obraztsov from Colorado, and C. fumiferana (Clemens) from Maine. When variation at individual gene loci was examined, intraspecific variation was often as great, and sometimes greater, than interspecific variation and few significant differences were noted among the species. The highest levels of overall genetic similarity occurred among C. occidentalis, C. biennis, and C. retiniana. Relatively greater genetic distances were found between this group and C. lambertiana and C. fumiferana. C. fumiferana was most distantly related to all other groups. Genetic identity values fell within the range more commonly associated with conspecific populations rather than with separate species.

scholarly journals Assessment of Genetic Relationships between Streptocarpus x hybridus V. Parents and F1 Progenies Using SRAP Markers and FT-IR Spectroscopy

Plants ◽  
2020 ◽  
Vol 9 (2) ◽  
pp. 160
Author(s):  
Monica Hârţa ◽  
Orsolya Borsai ◽  
Cristina M. Muntean ◽  
Nicoleta E. Dina ◽  
Alexandra Fǎlǎmaş ◽  
...  
Keyword(s):  
Ir Spectroscopy ◽  
Genetic Relationships ◽  
Distance Matrix ◽  
Genetic Distances ◽  
Mantel Test ◽  
F1 Hybrids ◽  
Srap Marker ◽  
Ft Ir ◽  
Biochemical Variability ◽  
Ft Ir Spectroscopy

The genetic relationship among three Streptocarpus parents and twelve F1 hybrids was assessed using sequence-related amplified polymorphism (SRAP) molecular markers and Fourier-transform infrared (FT-IR) spectroscopy. Both methods were able to discriminate F1 hybrids and parents as revealed by cluster analysis. For hybrid identification, the type III SRAP marker was the most effective due to the presence of male-specific bands in the hybrids. Different behaviors in the biochemical variability of DNA samples have been observed by FT-IR spectral analysis, which might be attributed to the inherent nature of the genomic DNA from parents and their F1 progenies. Mantel test was also carried out to compare morphological, SRAP, and FT-IR results based on genetic distances. The highest correlation coefficient was found between morphological and SRAP marker distances (R = 0.607; p ≤ 0.022). A lower correlation was observed between the morphological and FT-IR distance matrix (R = 0.231; p ≤0.008). Moreover, a positive correlation was found between the distances generated with SRAP and FT-IR analyses (R = 0.026) but was not statistically significant. These findings show that both SRAP and FT-IR techniques combined with morphological descriptions can be used effectively for nonconventional breeding programs for Streptocarpus to obtain new and valuable varieties.

scholarly journals Molecular characterization and genetic relationships of seven piranha species of the genera Serrasalmus and Pygocentrus (Characiformes: Serrasalmidae) from Paraná-Paraguay, São Francisco and Tocantins River basins in Brazil

2020 ◽  
Vol 80 (4) ◽  
pp. 741-751
Author(s):  
T. S. Bignotto ◽  
V. N. Gomes ◽  
T. C. Maniglia ◽  
T. A. Boni ◽  
C. S. Agostinho ◽  
...  
Keyword(s):  
Species Delimitation ◽  
Genetic Similarity ◽  
Genetic Relationships ◽  
River Basins ◽  
Genetic Distances ◽  
Mitochondrial Genes ◽  
Cytochrome C Oxidase I ◽  
Differentiation Pattern ◽  
Pygocentrus Nattereri ◽  
Tocantins River

Abstract Genetic and phylogenetic relationships among seven piranha species of the genera Serrasalmus and Pygocentrus from the Paraná-Paraguay, São Francisco and Tocantins River basins were evaluated in the present study by partial sequences of two mitochondrial genes, Cytochrome b and Cytochrome c Oxidase I. Phylogenetic analysis of Maximum-Likelihood and Bayesian inference were performed. Results indicated, in general, greater genetic similarity between the two species of Pygocentrus (P. nattereri and P. piraya), between Serrasalmus rhombeus and S. marginatus and between S. maculatus, S. brandtii and S. eigenmanni. Pygocentrus nattereri, S. rhombeus and S. maculatus showed high intraspecific genetic variability. These species have each one, at least two different mitochondrial lineages that, currently, occur in sympatry (S. rhombeus) or in allopatry (P. nattereri and S. maculatus). Species delimitation analysis and the high values of genetic distances observed between populations of S. rhombeus and of S. maculatus indicated that each species may corresponds to a complex of cryptic species. The non-monophyletic condition of S. rhombeus and S. maculatus reinforces the hypothesis. The geographic distribution and the genetic differentiation pattern observed for the piranha species analyzed herein are discussed regarding the geological and hydrological events that occurred in the hydrographic basins.

scholarly journals Simple-sequence Repeat Marker Analysis of Genetic Relationships within Hydrangea paniculata

HortScience ◽  
2009 ◽  
Vol 44 (1) ◽  
pp. 27-31 ◽  
Author(s):  
Sandra M. Reed ◽  
Timothy A. Rinehart
Keyword(s):  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Genetic Similarity ◽  
Genetic Relationships ◽  
Early Flowering ◽  
Sequence Repeat ◽  
Breeding Lines ◽  
Diversity Studies ◽  
Simple Sequence

Genetic diversity studies using 26 simple-sequence repeat (SSR) markers were conducted with 36 cultivars, breeding lines, and wild-collected accessions of Hydrangea paniculata Sieb. The SSR markers were highly variable among the genotypes, producing a mean of 5.8 alleles per marker. Three cultivars (Boskoop, Compact Grandiflora, and Webb) were either identical to or sports of the popular cultivar Grandiflora. The name ‘Pee Wee’ appears to have been applied to two phenotypically different compact forms of H. paniculata, one of which seems to be a sport of ‘Tardiva’, whereas the other is likely derived from ‘Grandiflora’. No close genetic similarity was observed among several cultivars from a long-term Belgium breeding program, although many had one parent in common. Early-flowering genotypes clustered separately from genotypes that flower in midsummer, but close genetic relationships were not observed among early-flowering cultivars. Two genotypes from Taiwan were genetically similar but were distinctly different from the Japanese genotypes. These, along with the early-flowering genotypes and a new collection from Japan, may represent unexploited sources of germplasm for improvement of H. paniculata.

scholarly journals Genetic similarity of Jatropha curcas accessions based on AFLP markers

2010 ◽  
Vol 10 (4) ◽  
pp. 364-369 ◽  
Author(s):  
Carlos Antonio Fernandes Santos ◽  
Marcos Antonio Drumond ◽  
Marciene Amorim Rodrigues ◽  
Marcio Rannieri Viana Evangelista
Keyword(s):  
Genetic Variability ◽  
Jatropha Curcas ◽  
Genetic Similarity ◽  
Aflp Marker ◽  
Genetic Relationships ◽  
Molecular Data ◽  
Genetic Distances ◽  
Similarity Coefficient ◽  
High Variability ◽  
Upgma Dendrogram

The genetic relationships between accessions of Jatropha (Jatropha curcas) were determined based on AFLP marker. A set of 50 plants from 12 accessions of J. curcas was analyzed with molecular data from 164 loci generated from 17 AFLP primer combinations. Molecular variance of data was analyzed by total decomposition between and within accessions. An UPGMA dendrogram was constructed based on genetic distances estimated by Jaccard's similarity coefficient. The well-defined dendrogram showed a cophenetic value of 0.91. Groups of plants were observed in six of the 12 accessions studied with similarity of over 30 %, indicating high genetic variability. The variation among accessions was estimated to be 0.275, also indicating high variability. These results show that the genetic variability of the studied J. curcas accessions is structured according to the origin and that a greater number of populations should be sampled to increase the genetic diversity of the studied genebank.

scholarly journals Dispersal Pattern of Black-Billed Magpies (Pica Hudsonia) Measured by Molecular Genetic (Rapd) Analysis

The Auk ◽  
2001 ◽  
Vol 118 (1) ◽  
pp. 137-146 ◽  
Author(s):  
Xiao-hong Wang ◽  
Charles H. Trost
Keyword(s):  
Genetic Similarity ◽  
Random Amplified Polymorphic Dna ◽  
Molecular Genetic ◽  
Breeding Population ◽  
Genetic Distances ◽  
Mantel Test ◽  
Dispersal Pattern ◽  
Male Population ◽  
Female Population ◽  
Distance Analysis

Abstract Black-billed Magpies (Pica hudsonia) are a relatively sedentary corvid, with greater dispersal of females than males. To genetically confirm that dispersal pattern, 29 reproductively active adults were captured over two years and were scored for primer-specific random amplified polymorphic DNA (RAPD) bands (53 polymorphic bands in 1996 and 104 in 1997). In both years, we captured more previously banded males than females, and individuals recaptured were more often the heaviest nestling in their brood from the previous years. Genetic distances between all possible adult pairs were calculated and degree of genetic similarity between pair-wise comparisons was assessed using the Mantel test. In the pair-wise comparison of genetic distances, data for both years showed that genetic distances between males were significantly less (P < 0.05) than those for other adult combinations (male–female and female–female). Using the same analytical approach, we found that females were no more genetically similar to one another (P > 0.05) than were random pairs of adults. Group-distance analysis using the computer package RAPD also showed higher genetic similarity among males than among females. We suggest that a plausible hypothesis to account for the relatively high genetic homogeneity of the breeding male population compared to the female population is that a long-lasting intraclutch dominance hierarchy exists among siblings. That hierarchy is sufficiently long-lasting to influence the breeding population, resulting in alpha males remaining in the natal area, whereas lower ranking birds, including females, are forced to disperse.

Sign in / Sign up

Export Citation Format

Share Document