scholarly journals Genetic variability of Colletotrichum sublineolum through ISSR markers

2021 ◽  
Vol 10 (2) ◽  
pp. e20210212223
Author(s):  
Thallita Santos Guimarães ◽  
Marco Antonio Aparecido Barelli ◽  
Carla Lima Corrêa ◽  
Valvenarg Pereira da Silva ◽  
Alex Junior Sandol Floriano ◽  
...  
Keyword(s):  
Genetic Variability ◽  
Information Content ◽  
Polymorphic Information Content ◽  
Descriptive Analysis ◽  
Geographic Origin ◽  
Issr Markers ◽  
Allelic Frequency ◽  
Limiting Factor ◽  
Colletotrichum Sublineolum ◽  
Sorghum Production

The occurrence of diseases is a limiting factor in the development of sorghum crop. Among the diseases that causes losses in sorghum production, anthracnose is the main and most severe, mainly by the genetic variability of the pathogen. In this context, the aim of this study was to evaluate the genetic variability of Colletotrichum sublineolum isolates. DNA were extracted from 56 monosporic isolates of C. sublineolum using a DNA extraction kit, and to perform the analysis of genetic diversity of the isolates were used ISSR primers. After amplification, it was determined the polymorphic information content (PIC), allelic frequency, UPGMA and Tocher clustering analyzes and, using software Structure, the genetic structure. According to the descriptive analysis of the genetic variability of C. Sublineolum isolates, primer AP1 presented the higher value of polymorphic information content (PIC). The higher allelic frequency was observed in loci 06, 09, 10, and 24, and the lowest in locus 02. As for the clustering method, it was observed a tendency of grouping C. sublineolum isolates according the geographic origin and, in addition to demonstrating the genetic variability between the C. sublineolum isolates, it was observed the occurrence of introgression among the isolates.

scholarly journals Application of the ISSR method to estimate the genetic similarity of Dasypyrum villosum (L.) P. Candargy Greek populations to Triticum and Secale species

2011 ◽  
Vol 21 (1) ◽  
pp. 7-12
Author(s):  
Agnieszka Grądzielewska
Keyword(s):  
Information Content ◽  
Genetic Similarity ◽  
Polymorphic Information Content ◽  
Similarity Index ◽  
Issr Markers ◽  
Mean Value ◽  
Dasypyrum Villosum ◽  
Reproducible Method ◽  
The Mean ◽  
High Diversity

Application of the ISSR method to estimate the genetic similarity of Dasypyrum villosum (L.) P. Candargy Greek populations to Triticum and Secale species In the study, the genetic similarity between Dasypyrum villosum L. (P.) Candargy and Triticum L. and Secale L. species was studied on the basis of ISSR markers. As a very polymorphic, effective and reproducible method, ISSR can be successfully employed to evaluate polymorphism between and inside different species. The polymorphic information content values (PIC) of ISSR method ranged from 0.57 to 0.87, with the mean value of 0.7. The genetic similarity of the forms analyzed ranged from 0.27 to 0.97, with the mean value of 0.47, indicating their high diversity. A higher similarity of Dasypyrum villosum to Triticum species, in comparison with Secale was found - the mean Dice genetic similarity index between genera was calculated at 0.40 for Dasypyrum and Triticum, and at 0.31 for Dasypyrum and Secale.

scholarly journals Genetic structure and diversity among individuals of Copaifera langsdorffii Desf. from Mato Grosso, Brazilian Amazon, using ISSR markers

2021 ◽  
Vol 10 (16) ◽  
pp. e187101623025
Author(s):  
Daniele Paula Maltezo ◽  
Julliane Dutra Medeiros ◽  
Ana Aparecida Bandini Rossi
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Genetic Variability ◽  
Polymorphic Information Content ◽  
Issr Markers ◽  
Group Method ◽  
Mato Grosso ◽  
Copaifera Langsdorffii ◽  
Genetic Structure And Diversity ◽  
Issr Primers

The Amazon is the largest tropical forest in the world and is home to around 20% of all the biodiversity on the planet, among the species present in the Amazon is Copaifera langsdorffii, exploited mainly for the extraction of oil-resin and wood, often in ways incorrect, which can cause the loss of genetic variability. The aim of this study was to evaluate the genetic structure and diversity among individuals of C. langsdorffii located in Mato Grosso, Brazil, using ISSR markers. We sampled leaves from 27 adult individuals of C. langsdorffii, whose total genomic DNA was extracted. A total of 12 ISSR primers were used for the molecular characterization of the individuals. A grouping analysis was performed using the unweighted pair group method, Bayesian analysis and characterized by the genetic diversity. The genetic diversity among and within the groups was demonstrated by the AMOVA. As a result, 106 fragments were amplified and 98.11% were polymorphic. The polymorphic information content of each primer ranged from 0.45 to 0.81.  The dendrogram showed the formation of 4 distinct groups. The greatest genetic variability is found within the groups and not between them. The percentage of polymorphism, genetic dissimilarity values and genetic diversity indexes indicate that there is high genetic variability among Copaifera langsdorffii individuals, suggesting that ISSR primers were efficient in detecting polymorphism in this species and that the individuals have potential for compose programs aimed at the preservation of the species and the ability to integrate germplasm banks.

scholarly journals Assessment of genetic diversity in Moroccan sesame (Sesamum indicum) using ISSR molecular markers

OCL ◽  
2021 ◽  
Vol 28 ◽  
pp. 3
Author(s):  
Meriem El Harfi ◽  
Jamal Charafi ◽  
Karim Houmanat ◽  
Hafida Hanine ◽  
Abdelghani Nabloussi
Keyword(s):  
Genetic Diversity ◽  
Genetic Variability ◽  
Polymorphic Information Content ◽  
Issr Markers ◽  
Sesamum Indicum ◽  
Simple Method ◽  
Low Genetic Diversity ◽  
Simple Repeats ◽  
New Germplasm ◽  
Issr Primers

There is a need for sesame (Sesamum indicum L.) breeding in Morocco to release performant and adapted varieties, which requires a large genetic variability in the germplasm to be used. In this context, genetic diversity of sesame populations from different locations in Tadla area was investigated using ISSR (Inter Sequence Simple Repeats) markers as a simple method to reveal polymorphism among them. A total of 130 individuals representing 31 populations were sampled. Twenty-four ISSR primers were used for analysis of individuals representing the 31 different sesame populations grown in different agroclimatic zones of Tadla, accounting for 90% of sesame cultivation area in Morocco. Indeed, seven primers showed legible and reproducible genomic profiles with an interesting number of bands. A total of 57 bands were obtained with ISSR primers, of which 47 were polymorphic. PIC (Polymorphic Information Content) ranged from 0.002 to 0.350, showing that ISSR markers are informative and relevant for discriminating the populations evaluated. The similarity coefficient of ISSR data ranged from 0.509 to 1, with an average of 0.870. The results obtained showed that Moroccan sesame populations are characterized by a low genetic diversity, suggesting a genetic proximity among them. Therefore, new germplasm should be either introduced from diverse geographical origins or created through mutagenesis breeding in order to broaden the existing genetic variability.

scholarly journals Genetic Diversity Analysis in Chickpea (Cicer arietinum L) Genotypes Grown in Northwestern Algeria using Microsatellite Markers (SSR)

2019 ◽  
Author(s):  
Bouri Amina ◽  
Mediouni Mohammed Rida ◽  
Ameur Ameur Abdelkader ◽  
Udupa Sripada ◽  
Gaouar Souheil Bechir Semir
Keyword(s):  
Genetic Diversity ◽  
Information Content ◽  
Cicer Arietinum ◽  
Gene Diversity ◽  
Polymorphic Information Content ◽  
Geographic Origin ◽  
Diversity Analysis ◽  
Factorial Correspondence Analysis ◽  
Genetic Diversity Analysis ◽  
Cicer Arietinum L

The present study aimed to characterize a subset of 10 selected chickpea accessions (Cicer arietinum L.) using SSR. The result indicated a presence of a total of 59 alleles. The genetic diversity at the 15 microsatellites loci was varied from 0, 32 for TA22 to 0.78 for TA72 and TA117 with an average of 0.66. Polymorphic information content (PIC) values ranged from 0.27 to 0.74. This study also detected a high significant (P less than 0.01) positive correlation between alleles per locus, gene diversity (H) and polymorphism information content (PIC). In the dendrogram and on the PCoA bi-plots, chickpea genotypes were adjoined according to their geographic origin, type of chickpea (Kabuli/ Desi). Nevertheless, the distribution of the different grouping through the factorial correspondence analysis (AFC) is due to the genetic variability.

Inter Simple Sequence Repeat markers for analysis of molecular diversity and genetic structure of eighteen Dendrobium cultivars in Sri Lanka

2018 ◽  
Vol 6 (3) ◽  
pp. 91-102
Author(s):  
Thanuja Dilrukshi Dharmarathna ◽  
H.M.D.A.K. Herath ◽  
P.A. Weerasinghe ◽  
H.M.V.G. Herath
Keyword(s):  
Information Content ◽  
Simple Sequence Repeat ◽  
Polymorphic Information Content ◽  
Morphological Characters ◽  
Inter Simple Sequence Repeat ◽  
Issr Markers ◽  
Sequence Repeat ◽  
Information Index ◽  
Expected Heterozygosity ◽  
Simple Sequence

The genus Dendrobium is one of the largest genera in the family Orchidaceae having more than thousand species over the world with diverse morphological characters. Dendrobium is a popular ornamental plant with complex genetic background which emphasize on the species identification at molecular level. The present study was aimed to identify Inter-Simple Sequence Repeat (ISSR) markers capable of detecting genetic polymorphism to characterize 18 hybrid, commercially available Dendrobium cultivars. Genomic DNA of each cultivar was extracted using CTAB method. A total of 17 different ISSR primers were evaluated. Only the reproducible bands were scored and number of different alleles (Na), number of effective alleles (Ne), Shannon’s Information Index (I), Expected heterozygosity (He), Unbiased expected heterozygosity (UHe), polymorphic percentage and polymorphic information content (PIC) of each primer were calculated. The highest Shannon’s Information Index (0.537±0.08) was recorded by the primer UBC 826 while the highest polymorphic information content (PIC) was generated by primer UBC 807. The PIC values of the primers were ranged from 0.0068 to 0.451, indicating that primers are moderately informative. In total, 631 bands representing 120 loci were amplified showing 85.71% - 100% polymorphism. The genetic similarities between individuals were compiled in the Nei’s genetic identity matrix in order to construct the UPGMA dendrogram. Principle component analysis (PCA) and clustering analysis were done to divide different cultivars into groups. The analysis revealed the presence of four major clusters and two minor clusters among the cultivars. The study suggested that the ISSR markers originated from eight primers 12, 155, UBC 807, UBC 812, UBC 826, UBC 835, UBC 841 and UBC 842 can be used in the detection of molecular variation among cultivars in the genus Dendrobium.

scholarly journals Validation of 10 Microsatellite Loci for Their use in Parentage Verification and Individual Identification in the Yugoslavian Shepherd Dog Sharplanina / Walidacja 10 Loci Mikrosatelitarnych Do Kontroli Pochodzenia Oraz Identyfikacji Osobniczej Jugosłowiańskiego Psa Pasterskiego Z Szar Płaniny

2013 ◽  
Vol 13 (4) ◽  
pp. 715-722 ◽  
Author(s):  
Vladimir Dimitrijevic ◽  
Jevrosima Stevanovic ◽  
Mila Savic ◽  
Branko Petrujkic ◽  
Predrag Simeunovic ◽  
...  
Keyword(s):  
Genetic Variability ◽  
Microsatellite Markers ◽  
Information Content ◽  
Microsatellite Loci ◽  
Gene Pool ◽  
Polymorphic Information Content ◽  
Diversity Indices ◽  
Individual Identification ◽  
Variable Gene ◽  
Primary Focus

Abstract The aim of the study was to assess a commercially available microsatellite panel for use in paternity and identification analyses in the Yugoslavian Shepherd Dog Sharplanina, an ancient livestock guarding breed. Allele frequencies for 10 microsatellite loci (PEZ01, FHC2054, FHC2010, PEZ05, PEZ20, PEZ12, PEZ03, PEZ06, PEZ08 and FHC2079) were determined in 103 unrelated Yugoslavian Shepherd Dog individuals. The loci revealed varied levels of polymorphism (five to 12 alleles), with an average of 7.83 per locus. Average values of observed heterozygosity and polymorphic information content (PIC) were 0.64 and 0.66, respectively. Nine out of 10 microsatellite markers were highly informative with PIC values higher than 0.5. The obtained value of combined power of exclusion (0.9989) confirms usefulness of this panel of microsatellites for parentage verification, while the value of combined power of discrimination of 0.9999 clearly shows that the panel can conclusively identify individual dogs. In conclusion, the results obtained suggest that the selected set of commercially available microsatellite markers may be used as a routine tool for parentage verification and individual identification in the Yugoslavian Shepherd Dog. Although analysis of genetic variability of the Yugoslavian Shepherd Dog was not the primary focus of the study, the established values of major diversity indices disclose a highly variable gene pool in the breed.

scholarly journals Genetic variability of cultivated plum (Prunus domestica L. & Prunus salicina Lindl.) in Morocco assessed by ISSR markers

2021 ◽  
pp. 948-954
Author(s):  
Youssef Ait bella ◽  
Said Bouda ◽  
Youssef Khachtib ◽  
Abdelmajid Haddioui
Keyword(s):  
Genetic Variability ◽  
Geographic Origin ◽  
Inter Simple Sequence Repeat ◽  
Issr Markers ◽  
Gene Pools ◽  
Mean Values ◽  
Model Based Clustering ◽  
Prunus Salicina ◽  
Clustering Approach ◽  
The Mean

Moroccan plum cultivars were genetically characterized for assessing diversity and relatedness. In this study, a total of 23 plum cultivars were analyzed using 14 Inter-Simple Sequence Repeat (ISSR) primers. A total of 100 bands were obtained, of which 84 were polymorphic (84%). The mean values of PIC, Rp, I and Ht were 0.45; 3.03; 0.42 and 0.27, respectively, implying the important genetic variability between the plum cultivars. Furthermore, the coefficient of genetic differentiation (GST) between all groups was 0.21 indicating that 21 % of total genetic variability was between groups and 79 % was within groups. The UPGMA dendrogram and Bayesian model-based clustering approach identified four gene pools of cultivars independently of their geographic origin and denomination. These results showed that the ISSRs markers can be a useful tool for detecting molecular polymorphism and to survey the genetic diversity in this fruit crop.

scholarly journals Genetic Diversity of Groundnut (Arachis hypogaea L.) Accessions using Inter Simple Sequence Repeats (ISSRs) Marker

2020 ◽  
Author(s):  
Mohammed Abdela ◽  
Mulugeta Kebede ◽  
Tiliye Feyissa
Keyword(s):  
Genetic Diversity ◽  
Genetic Variability ◽  
Arachis Hypogaea ◽  
Gene Diversity ◽  
Polymorphic Information Content ◽  
Issr Markers ◽  
Similarity Coefficients ◽  
Average Value ◽  
Band Size ◽  
Arachis Hypogaea L

Abstract Background: Groundnut (Arachis hypogaea L.) belongs to the family Leguminoseae. It is the world’s most important source of edible oil and vegetable protein. To our knowledge, little is known about the genetic variability of cultivated Ethiopian A. hypogaea at a molecular level. It is important to understand the genetic diversity of the crop to collect, conserve and use the germplasm for variety development. In the present study, ISSR markers were used to determine the genetic variability and diversity of 43 accessions of A. hypogaea collected from different regions of Ethiopia.Results: Four ISSR primers were used to generate 56 reproducible bands of which 29 (51.8%) were polymorphic. The band size ranges from 120 bp to 1100 bp. The number of amplified bands varied from 12 in primer UBC841 to 18 in primer UBC 881. The polymorphic bands percentage ranges from 27.8 % of Primer UBC 881 to 84.6 % of primer UBC 857. The polymorphic information content (PIC) value ranges from 0.29 to 0.76 with the average value 0.49. The mean Nei’s gene diversity and Shannon’s information index were 0.25 and 0.33, respectively. Genetic relationship between A. hypogaea accessions based on Jaccard’s pair wise similarity coefficients varies from 44% to 83% with an average value of 63.5%. The UPGMA dendrogram based on cluster analysis grouped A. hypogaea accessions into five distinct clusters at 63.5% similarity coefficient, and the principal coordinate analysis revealed similar grouping. Conclusions: Even though in both UPGMA and PCoA most of the accessions were grouped in separate clusters irrespective of their geographic origins, the ISSR marker-based analysis shows the presence of genetic variability among the accessions. Moreover, the current study demonstrated the potential informativeness of ISSR markers in estimating the extent of genetic variation in A. hypogaea accessions.

scholarly journals Genetic divergence in basil cultivars and hybrids

2019 ◽  
Vol 37 (2) ◽  
pp. 180-187
Author(s):  
Rodrigo P Alves ◽  
Ana Veruska C Silva ◽  
Camila S Almeida-Pereira ◽  
Tatiana S Costa ◽  
Sheila V Alvares-Carvalho ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Molecular Markers ◽  
Genetic Variability ◽  
Polymorphic Information Content ◽  
Dna Amplification ◽  
Issr Markers ◽  
Economic Importance ◽  
Dissimilarity Index ◽  
The World ◽  
Issr Molecular Markers

ABSTRACT Basil is an aromatic herb that stands out for its economic importance. It is consumed in natura and used to obtain essential oil. The cultivation of this species in several regions of the world has allowed variations by natural crosses and euploidy, leading to the wide genetic variability found nowadays. Considering the importance of this species, we aimed to analyze the genetic diversity of 27 basil genotypes using ISSR molecular markers. Fourteen primers were employed for DNA amplification, resulting in 86% polymorphism. Based on the Jaccard’s dissimilarity index, the highest index (0.80) was observed between the individuals BAS001 and BAS012, while the lowest index (0.18) was detected between the genotypes BAS014 and BAS015. The genetic similarity among individuals was calculated, forming four distinct clusters. Most individuals (40.7%) were allocated in cluster I. The polymorphic information content (PIC) (0.89) indicated considerable levels of genetic diversity among genotypes. In this sense, the ISSR markers were efficient in the detection of polymorphisms between the accessions, suggesting the genetic variability of the collection. This result demonstrates the importance of the use of molecular markers and the advantages that this information provides to the breeding of the species.

Assessment of genetic variability amongst cultivated populations of Khasi mandarin (Citrus reticulata Blanco) detected by ISSR

2021 ◽  
pp. 1-11
Author(s):  
Karishma Kashyap ◽  
Rasika M. Bhagwat ◽  
Sofia Banu
Keyword(s):  
Genetic Diversity ◽  
Genetic Variability ◽  
Inter Simple Sequence Repeat ◽  
Northeast India ◽  
Issr Markers ◽  
Citrus Reticulata ◽  
Brahmaputra Valley ◽  
Indian Food ◽  
Cultivated Populations ◽  
High Level

Abstract Khasi mandarin (Citrus reticulata Blanco) is a commercial mandarin variety grown in northeast India and one of the 175 Indian food items included in the global first food atlas. The cultivated plantations of Khasi mandarin grown prominently in the lower Brahmaputra valley of Assam, northeast India, have been genetically eroded. The lack in the efforts for conservation of genetic variability in this mandarin variety prompted diversity analysis of Khasi mandarin germplasm across the region. Thus, the study aimed to investigate genetic diversity and partitioning of the genetic variations within and among 92 populations of Khasi mandarin collected from 10 cultivated sites in Kamrup and Kamrup (M) districts of Assam, India, using Inter-Simple Sequence Repeat (ISSR) markers. The amplification of genomic DNA with 17 ISSR primers yielded 216 scorable DNA amplicons of which 177 (81.94%) were polymorphic. The average polymorphism information content was 0.39 per primer. The total genetic diversity (HT = 0.28 ± 0.03) was close to the diversity within the population (HS = 0.20 ± 0.01). A high mean coefficient of gene differentiation (GST = 0.29) reflected a high level of gene flow (Nm = 1.22), indicating high genetic differentiation among the populations. Analysis of Molecular Variance (AMOVA) showed 78% of intra-population differentiation, 21% among the population and 1% among the districts. The obtained results indicate the existence of a high level of genetic diversity in the cultivated Khasi mandarin populations, indicating the need for preservation of each existing population to revive the dying out orchards in northeast India.

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