scholarly journals Phylogenetic Assessment Of Arthrocnemum Macrostachyum (Chenopodiaceae) Genotypes, Using Ramp Markers

2015 ◽  
Vol 60 (2) ◽  
pp. 293-299
Author(s):  
Basel Saleh
Keyword(s):  
Genetic Diversity ◽  
Cluster Analysis ◽  
Polymorphic Information Content ◽  
Group Method ◽  
Marker Index ◽  
Pair Group ◽  
Genotype 2 ◽  
Upgma Cluster Analysis ◽  
Arthrocnemum Macrostachyum ◽  
Unweighted Pair Group Method

AbstractRandom amplified microsatellite polymorphism (RAMP) marker technique was employed to test its usefulness for assessing phylogenetic relationships in three genotypes of Arthrocnemum macrostachyum (Moric.) Moris. & Delponte from Syria. PCR reactions with 21 RAMP primer combinations (PCs) distinguished 145 loci, 139 of which (95.862%) were polymorphic. The (AG)8TC/OPE18 primer combination generated the highest number of fragments (11 amplicons), and the (AC)8T/OPE04 primer combination the fewest (4 amplicons). Average estimated polymorphic information content (PIC) was 0.431, with an average marker index (MI) of 2.836. Analysis by the unweighted pair group method using arithmetic averages (UPGMA) was performed and a dendrogram was constructed. UPGMA cluster analysis based on RAMP markers distinguished genotype 2, suggested here to be a subspecies, from genotypes 1 and 3. In this study the RAMP marker method proved to be a reliable tool for discriminating and estimating genetic diversity within A. macrostachyum.

Assessment of genetic diversity in 35 Pisum sativum accessions using microsatellite markers

2012 ◽  
Vol 92 (6) ◽  
pp. 1075-1081 ◽  
Author(s):  
Sajjad Ahmad ◽  
Manjit Singh ◽  
Neil Dylan Lamb-Palmer ◽  
Mark Lefsrud ◽  
Jaswinder Singh
Keyword(s):  
Genetic Diversity ◽  
Pisum Sativum ◽  
Microsatellite Markers ◽  
Polymorphic Information Content ◽  
Group Method ◽  
Gene Pools ◽  
Breeding Lines ◽  
High Performing ◽  
Pair Group ◽  
Upgma Cluster Analysis

Ahmad, S., Singh, M., Lamb-Palmer, N. D., Lefsrud, M. and Singh, J. 2012. Assessment of genetic diversity in 35 Pisum sativum accessions using microsatellite markers. Can. J. Plant Sci. 92: 1075–1081. Field pea is an important Canadian pulse crop and therefore developing high-performing cultivars is critical for Canadian pea growers. Information about genetic diversity is a key component for the creation of novel and desirable germplasm to develop elite pea breeding lines. The objective of the present study is to assess genetic diversity in 35 diverse Pisum accessions using 15 polymorphic microsatellites located on different pea chromosomes. Microsatellites were found to be polymorphic, amplifying a total of 41 alleles and were able to differentiate all 35 Pisum genotypes. These markers were scored by their polymorphic information content (PIC), ranging from 0.055 (AA206) to 0.660 (AB72) with an average of 0.460, and by their discriminating power (D), which varied from 0.057 (AA206) to 0.679 (AB 72) with an average of 0.475. Genetic similarity values ranged from 0.074 (between Maple pea NZ and Line 45760) to 0.875 (between Galena and Dakota) with an average of 0.336. Unweighted pair group method with arithmetic averages (UPGMA) cluster analysis grouped the 35 pea accessions into two major clusters and eight sub-clusters. The majority of Canadian and European genotypes were grouped separately, suggesting both these groups are from genetically distinct gene pools. The genetically diverse groups identified in this study can be used to derive parental lines for pea breeding.

Genetic diversity among varieties of the native forage grass Trichloris crinita based on AFLP markers, morphological characters, and quantitative agronomic traits

Genome ◽  
2006 ◽  
Vol 49 (8) ◽  
pp. 906-918 ◽  
Author(s):  
Pablo F Cavagnaro ◽  
Juan B Cavagnaro ◽  
José L Lemes ◽  
Ricardo W Masuelli ◽  
Carlos B Passera
Keyword(s):  
Genetic Diversity ◽  
Cluster Analysis ◽  
Biomass Production ◽  
Agronomic Traits ◽  
Morphological Characters ◽  
Group Method ◽  
Aflp Data ◽  
Basal Diameter ◽  
Pair Group ◽  
Upgma Cluster Analysis

We assessed the genetic diversity in Trichloris crinita (Poaceae) varieties from South America, using AFLPs, morphological characters, and quantitative agronomic traits. Owing to the importance of this species for range grazing, we first characterized the varieties based on forage productivity. Biomass production varied 9 fold among the materials evaluated. Analysis of AFLP fingerprints allowed the discrimination of all varieties with a few selected primer combinations. Pair-wise genetic similarities, using marker data, ranged from 0.31 to 0.92 (Jaccard coefficients). Marker-based unweighted pair group method with arithmetic averaging (UPGMA) cluster analysis did not show geographical clustering, but rather grouped the varieties according to their biomass production. We identified 18 markers associated with biomass production, of which 8 showed complete correlation (r = 1.00) with this trait. These DNA markers can be used to assist selection for high forage productivity in T. crinita. Cluster analysis using morphological and quantitative characters revealed 4 distinct groups of varieties, clearly separated according to their biomass yield. The variables foliage height and basal diameter were strongly correlated with biomass production and these phenotypic markers can be used to select productive plants. The relations among the varieties based on AFLP data were significantly correlated with those based on agronomic and morphological characters, suggesting that the 2 systems give similar estimates of genetic relations among the varieties.Key words: AFLP fingerprinting, genetic diversity, Trichloris crinita, morphology, biomass production.

scholarly journals SSR Markers Reveal the Genetic Diversity of Asian Cercis Taxa at the U.S. National Arboretum

HortScience ◽  
2017 ◽  
Vol 52 (4) ◽  
pp. 498-502 ◽  
Author(s):  
Chandra S. Thammina ◽  
David L. Kidwell-Slak ◽  
Stefan Lura ◽  
Margaret R. Pooler
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
The United States ◽  
Group Method ◽  
Cercis Canadensis ◽  
Landscape Plant ◽  
Pair Group ◽  
Upgma Cluster Analysis ◽  
Eastern Redbud ◽  
The U.S

The redbud (Cercis L. species) is a popular landscape plant grown widely in the United States. There are more than 20 cultivars of eastern redbud (Cercis canadensis L.) and at least three cultivars of Asian taxa (primarily Cercis chinensis Bunge) in the trade. The U.S. National Arboretum (USNA) has a diverse collection of Cercis germplasm collected in North America and Asia. Fourteen genomic simple sequence repeat (genomic-SSR) markers were used to analyze the genetic diversity of 53 accessions of Asian Cercis taxa from our collection, including C. chinensis, Cercis chingii Chun, Cercis gigantea ined., Cercis glabra Pamp., Cercis racemosa Oliv., and Cercis yunnanensis Hu and W. C. Cheng. SSR markers detected an average of 5.7 alleles per locus with a range of two to nine alleles. A dendrogram was generated by unweighted pair group method with arithmetic mean (UPGMA) cluster analysis using the Jaccard similarity coefficient. Four major clusters were identified. Accessions tended to group by taxa or provenance, but with some notable exceptions caused either by misidentification or nomenclatural confusion in the species. This information will be used for collection management and for making decisions in the breeding program to maximize genetic diversity of cultivated Cercis.

Genetic diversity of male sterile and low fertility germplasm of Citrus revealed using SSR markers

2007 ◽  
Vol 4 (2) ◽  
pp. 99-104 ◽  
Author(s):  
Cao Qing-Qin ◽  
Meng Hai-Jun ◽  
Wen Xiao-Peng ◽  
Yi Hua-Lin ◽  
Deng Xiu-Xin
Keyword(s):  
Genetic Diversity ◽  
Cluster Analysis ◽  
Low Fertility ◽  
Group Method ◽  
Male Sterile ◽  
Pair Group ◽  
Male Sterile Cytoplasm ◽  
Group 3 ◽  
Group 2 ◽  
Method Analysis

AbstractThe genetic diversity of 43 male sterile and low fertility Citrus accessions, as well as 13 fertile ones, were assessed using simple sequence repeat markers (SSRs). Thirty-five polymorphic alleles were generated from eight primers (on average 4.4 alleles per primer). Cluster analysis was performed via unweighted pair group method analysis (UPGMA) using the NTSYS-pc version 2.10. The results showed that the accessions could be classified into three groups: cultivars of mandarin were classified into group 1; those of sweet orange, grapefruit, ponkan or tangor into group 2; and Microcitrus with male sterile cytoplasm into group 3. Cluster analysis also revealed that Satsuma mandarin was more closely related to Bendiguangju mandarin than to Zaoju, Mankieh or Huangyan Bendizao tangerine. The present study on genetic diversity of male sterile and low fertility Citrus will provide useful information for further collection, preservation and utilization of this plant.

scholarly journals Assessment of Genetic Diversity in Cultivated Tomato (Solanum Lycopersicum L.) Genotypes Using Rapd Primers

2013 ◽  
Vol 21 (1) ◽  
pp. 83-89 ◽  
Author(s):  
Saida Sharifova ◽  
Sabina Mehdiyeva ◽  
Konstantinos Theodorikas ◽  
Konstantinos Roubos
Keyword(s):  
Genetic Diversity ◽  
Rapd Analysis ◽  
Diversity Index ◽  
Random Amplified Polymorphic Dna ◽  
Arithmetic Mean ◽  
Similarity Coefficient ◽  
Group Method ◽  
Solanum Lycopersicum L ◽  
Pair Group ◽  
Upgma Cluster Analysis

Abstract Random Amplified Polymorphic DNA (RAPD) analysis was carried out on 19 Azerbaijan tomato genotypes, both cultivars and local populations. A total of 26 amplified products were revealed by 6 primers. The genetic similarity among evaluated genotypes ranged from 0.188 to 1.000. The lowest similarity was observed between cultivars ‘Azerbaijan’ and ‘Shakar’ (0.188), while the highest between ‘Elnur’ and ‘Garatag’ (1.000). The Unweighted Pair Group Method with Arithmetic Mean (UPGMA) cluster analysis based on Jaccard’s similarity coefficient divided genotypes into four main groups. The first group was the largest and consisted of 12 genotypes, while the fourth group was the smallest consisted of 1 genotype only. The most polymorphic primer was OPB-18 that presented a genetic diversity index of 0.823, while the least informative was primer OPG-17 with an index of 0.349. The average genetic diversity calculated from RAPD data was 0.665.

scholarly journals Using microsatellite markers to analyze genetic diversity in 14 sheep types in Iran

2017 ◽  
Vol 60 (3) ◽  
pp. 183-189 ◽  
Author(s):  
Mohammad Taghi Vajed Ebrahimi ◽  
Mohammadreza Mohammadabadi ◽  
Ali Esmailizadeh
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Information Content ◽  
Gene Diversity ◽  
Polymorphic Information Content ◽  
Extraction Procedure ◽  
Shannon Index ◽  
Group Method ◽  
Salting Out ◽  
Pair Group

Abstract. Investigation of genetic relationship among populations has been traditionally based on the analysis of allele frequencies at different loci. The prime objective of this research was to measure the genetic polymorphism of five microsatellite markers (McMA2, BM6444, McMA26, HSC, and OarHH35) and study genetic diversity of 14 sheep types in Iran. Genomic DNA was extracted from blood samples of 565 individuals using an optimized salting-out DNA extraction procedure. The polymerase chain reaction (PCR) was successfully performed with the specific primers. Some locus–population combinations were not at Hardy–Weinberg equilibrium (P < 0. 05). The microsatellite analysis revealed high allelic and gene diversity in all 14 breeds. Pakistani and Arabi breeds showed the highest mean number of alleles (11.8 and 11 respectively), while the highest value for polymorphic information content was observed for the Arabi breed (0.88). A UPGMA (unweighted pair group method with arithmetic mean) dendrogram based on the Nei's standard genetic distance among studied breeds showed a separate cluster for Arabi and Pakistani breeds and another cluster for other breeds. The Shannon index (H0) for McMA2, BM6444, McMA26, HSC, and OarHH35 was 2.31, 2.17, 2.27, 2.04 and 2.18, respectively, and polymorphic information content (PIC) values were 0.88, 0.92, 0.87, 0.84, and 0.86 for McMA2, BM6444, McMA26, HSC, and OarHH35, respectively. The high degree of variability demonstrated within the studied sheep types implies that these populations are rich reservoirs of genetic diversity that must be preserved.

scholarly journals Evaluation of Genetic Diversity among Persian Fig Cultivars by Morphological Traits and RAPD Markers

HortScience ◽  
2018 ◽  
Vol 53 (5) ◽  
pp. 613-619 ◽  
Author(s):  
Ghazal Baziar ◽  
Moslem Jafari ◽  
Mansoureh Sadat Sharifi Noori ◽  
Samira Samarfard
Keyword(s):  
Genetic Diversity ◽  
Rapd Markers ◽  
Polymorphic Information Content ◽  
Random Amplified Polymorphic Dna ◽  
Hierarchical Cluster ◽  
Fruit Trees ◽  
Group Method ◽  
Fars Province ◽  
Pair Group

Ficus carica L. is one of the most ancient fruit trees cultivated in Persia (Iran). The conservation and characterization of fig genetic resources is essential for sustainable fig production and food security. Given these considerations, this study characterizes the genetic variability of 21 edible F. carica cultivars in the Fars Province using random amplified polymorphic DNA (RAPD) markers. The collected cultivars were also characterized for their morphological features. A total of 16 RAPD primers produced 229 reproducible bands, of which, 170 loci (74.43%) were polymorphic with an average polymorphic information content (PIC) value of 0.899. Genetic analysis using an unweighted pair-group method with arithmetic averaging (UPGMA) revealed genetic structure and relationships among the local germplasms. The dendrogram resulting from UPGMA hierarchical cluster analysis separated the fig cultivars into five groups. These results demonstrate that analysis of molecular variance allows for the partitioning of genetic variation between fig groups and illustrates greater variation within fig groups and subgroups. RAPD-based classification often corresponded with the morphological similarities and differences of the collected fig cultivars. This study suggests that RAPD markers are suitable for analysis of diversity and cultivars’ fingerprinting. Accordingly, understanding of the genetic diversity and population structure of F. carica in Iran may provide insight into the conservation and management of this species.

scholarly journals Molecular Analysis of Genetic Diversity and Geographic Origin within an Ex Situ Germplasm Collection of Cherimoya by Using SSRs

2007 ◽  
Vol 132 (3) ◽  
pp. 357-367 ◽  
Author(s):  
P. Escribano ◽  
M.A. Viruel ◽  
J.I. Hormaza
Keyword(s):  
Genetic Diversity ◽  
Geographic Origin ◽  
Germplasm Collection ◽  
Ex Situ ◽  
Group Method ◽  
Pair Group ◽  
Ssr Primers ◽  
Upgma Cluster Analysis ◽  
Ssr Loci ◽  
Simple Sequence

Cherimoya (Annona cherimola Mill.) is an underused fruit crop with a clear niche for expansion in subtropical climates. In this study, 16 simple sequence repeat (SSR) loci were used to find molecular polymorphisms among 279 cherimoya accessions from a worldwide ex situ field germplasm collection. A total of 79 amplification fragments were amplified with 16 pairs of SSR primers, with an average of 4.9 bands/SSR. Mean expected and observed heterozygosities averaged 0.53 and 0.44, respectively. The total value for the probability of identity was 4.34 × 10−8. The SSRs studied resulted in 267 different fingerprinting profiles, of which 258 were unique genotypes; the rest were putative cases of synonymies or mislabeling errors. Unweighted pair group method with arithmetic averages (UPGMA) cluster analysis indicated the relationships among the analyzed accessions, showing some specific groups related to their geographical origins. Analysis of molecular variance (AMOVA) was performed to examine the distribution of genetic variation of the 148 accessions collected from putative cherimoya origin areas in Ecuador and Peru, showing that the major variations occurred within valleys in each country. The results confirmed the usefulness of microsatellites for identification of genetic diversity and geographic origin of cherimoya and are discussed in terms of their implications for ex situ conservation of cherimoya genetic resources.

scholarly journals Genetic diversity and relationships in jute (Corchorus spp.) revealed by SSR markers

1970 ◽  
Vol 38 (2) ◽  
pp. 153-161 ◽  
Author(s):  
Saaimatul Huq ◽  
Md Shahidul Islam ◽  
Abu Ashraqur Sajib ◽  
Nadim Ashraf ◽  
Samiul Haque ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Marker ◽  
Group Method ◽  
Individual Plant ◽  
Corchorus Olitorius ◽  
Corchorus Capsularis ◽  
Pair Group ◽  
Ssr Primers ◽  
Upgma Cluster Analysis

Characterization of sixteen jute genotypes, from Corchorus olitorius L. and Corchorus capsularis L. using jute specific SSR marker attained a high polymorphism value of 92.20%. A total of 171 different alleles were amplified by 27 primer pairs with a mean of 6.33 ± 2.04 alleles per locus. The genetic diversity was also relatively high (0.81 ± 0.06). The Un-weighted Pair-group Method with Arithmetic averages (UPGMA) cluster analysis of the 16 jute genotypes produced a dendogram, which was in concordance with known information. The study reinforces the utility of SSR primers for providing useful and high levels of markers for individual plant genotypes even with a narrow genetic base. Key words: Jute; Genetic diversity; SSR; Genotypes; Polymorphism DOI: 10.3329/bjb.v38i2.5140 Bangladesh J. Bot. 38(2): 153-161, 2009 (December)  

Morphological variation in Nereis (Neanthes) virens (Polychaeta: Nereididae) populations

2004 ◽  
Vol 84 (5) ◽  
pp. 983-985 ◽  
Author(s):  
Sophie Breton ◽  
France Dufresne ◽  
Gaston Desrosiers ◽  
Pierre Blier
Keyword(s):  
Cluster Analysis ◽  
Gene Flow ◽  
Phenotypic Plasticity ◽  
Morphological Variation ◽  
Genetic Study ◽  
Group Method ◽  
Restricted Gene Flow ◽  
Pair Group ◽  
Morphological Variants ◽  
Unweighted Pair Group Method

The intraspecific variation in the number and distribution of paragnaths in ten populations of Nereis (Neanthes) virens collected throughout its range was examined. Significant differences among populations are found in the total number of paragnaths and in each paragnath group. The unweighted pair-group method using arithmetic averages cluster analysis revealed three distinct clusters separating Canadian populations, Europe/USA populations and the Japanese population, suggesting the implication of either restricted gene flow, selection on paragnath patterns or phenotypic plasticity. Comparison with a previous genetic study suggests that morphological variants represent ecotypes of the single, widely distributed N. virens species.

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