Isolation, identification, and study of the genetic diversity between three entomopathogenic nematodes belonging to Heterorhabditis sp. using ISSR technique

Abstract Background Entomopathogenic nematodes (EPNs) are widely used in biological control for soil-dwelling stages of many insect pests that are characterized by their safety to most non-target organisms and to the environment. Results The objectives of the present study were isolation of EPNs from agricultural soil in Egypt for further use in biological control programs and study the genetic variation among them using the molecular marker inter-simple sequence repeats (ISSR). Three out of 25 soil samples collected from fields cultivated with strawberry, tangerine, and pumpkin were positive for the presence of EPNs, using the Galleria baiting technique. Sequencing of the internal transcribed spacer (ITS) region indicated that the isolates obtained belong to Heterorhabditis sp. The ITS sequences were submitted to the National Center for Biotechnology Information (NCBI) and registered under accession nos. MH553165, MH553168, and MH553169. Six ISSR primers were used. The numbers of polymorphic bands were 42 out of 56, and the polymorphism percentage was 75%. The highest number of bands was 12 bands generated by primer ISSR8 followed by UBC-809 (11 bands) while recorded the lowest band number (4 bands), the percentage of polymorphism ranged from 40% (ISSR1) to 100% (ISSR6). Conclusion ISSR marker can be considered a good marker to study genetic diversity and detecting the genetic polymorphism among the nematodes species.

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Genetic diversity and relationships among Egyptian Galium (Rubiaceae) and related species using ISSR and RAPD markers

Biologia ◽

10.2478/s11756-013-0314-z ◽

2014 ◽

Vol 69 (3) ◽

Cited By ~ 2

Author(s):

Kadry Abdel Khalik ◽

Magdy Abd El-Twab ◽

Rasha Galal

Keyword(s):

Genetic Diversity ◽

Genetic Variation ◽

Rapd Markers ◽

Phylogenetic Analyses ◽

Randomly Amplified Polymorphic Dna ◽

Inter Simple Sequence Repeats ◽

Close Relationship ◽

Rapd And Issr ◽

Simple Sequence ◽

Issr Primers

AbstractGenetic diversity and phylogenetic analyses of 24 species, representing nine sections of the genus Galium (Rubiaceae), have been made using the Inter Simple Sequence Repeats (ISSR), Randomly Amplified Polymorphic DNA (RAPD), and combined ISSR and RAPD markers. Four ISSR primers and three RAPD primers generated 250 polymorphic amplified fragments. The results of this study showed that the level of genetic variation in Galium is relatively high. RAPD markers revealed a higher level of polymorphism (158 bands) than ISSR (92 bands). Clustering of genotypes within groups was not similar when RAPD and ISSR derived dendrograms were compared. Six clades can be recognized within Galium, which mostly corroborate, but also partly contradict, traditional groupings. UPGMA-based dendrogram showed a close relationship between members of section Leiogalium with G. verum and G. humifusum (sect. Galium), and G. angustifolium (sect. Lophogalium). Principal coordinated analysis, however, showed some minor differences with UPGMA-based dendrograms. The more apomorphic groups of Galium form the section Leiogalium clade including the perennial sections Galium, Lophogalium, Jubogalium, Hylaea and Leptogalium as well as the annual section Kolgyda. The remaining taxa of Galium are monophyletic.

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Analysis of genetic diversity and association of seed and mucilage yields with inter simple sequence repeats (ISSR) polymorphism in a collection of Plantgao species

10.1101/2020.07.06.189266 ◽

2020 ◽

Author(s):

Bagheri Motahareh ◽

Bahram Heidrai ◽

Zolfaghar Shahriari ◽

Ali Dadkhodaie ◽

Zahra Heidari ◽

...

Keyword(s):

Genetic Diversity ◽

Simple Sequence Repeats ◽

Phylogenetic Network ◽

Germplasm Conservation ◽

Inter Simple Sequence Repeats ◽

Geographical Regions ◽

The Mean ◽

Polymorphic Bands ◽

Simple Sequence ◽

Issr Primers

AbstractAnalysis of genetic diversity in medicinal plants assists germplasm conservation and selection for use in breeding schemes. The aims of the present study were to assess genetic diversity and differentiation of several Plantago species using Inter Simple Sequence Repeats (ISSR) markers and identify marker-trait associations (MTAs). Thirty-one Plantago accessions belonging to eight species with various mating system and chromosome number were collected from geographical regions of Iran environments. Polymorphism in the DNA of Plantago accessions were analyzed using polymerase chain reaction (PCR) of 25 ISSR primers. The data for number of polymorphic bands were analyzed on the basis of several genetic diversity parameters. The results of gel analysis indicated that the ISSR primers amplified 5 to 21 polymorphic bands with 100 to 3000 bp size. The mean polymorphism was 83.83% and five primers showed 100% polymorphism among Plantago accessions. The Polymorphism Information Content (PIC) for ISSR as a dominant marker ranged from 0.1103 to 0.3829 with the mean 0.2727 in the species tested. Accessions in P. amplexicaulis and P. pysillum species represented the highest Nei’s and Shannon’s genetic diversity whilst the lowest obtained for P. lagopus. Analysis of phylogenetic network generated by the Neighbor-Net Algorithm showed moderate split of the eight species tested and the network depicted moderate conflict. The principal coordinate analysis (PCoA) results showed lower conflict in separation of accessions of the eight species. Fifty-six significant MTAs were detected for the traits tested in Plantago accessions, of which six were shared between three seed and mucilage traits and 24 were common between two traits. The coefficient of determination (R2) for the identified MTAs varied between 32 and 73%. In conclusion, the results of genetic diversity analysis suggested that ISSR marker could efficiently differentiate Plantago species and the information of genetic diversity might assist Plantago improvement and conservation.

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Phylogenetic relationships between Leymus and related diploid Triticeae species revealed by ISSR markers

Biologia ◽

10.2478/s11756-014-0395-3 ◽

2014 ◽

Vol 69 (8) ◽

Author(s):

Guo-Ye Guo ◽

Rui-Wu Yang ◽

Chun-Bang Ding ◽

Li Zhang ◽

Yong-Hong Zhou ◽

...

Keyword(s):

Genetic Diversity ◽

Phylogenetic Relationships ◽

Diploid Species ◽

Issr Markers ◽

Similarity Coefficients ◽

Triticeae Species ◽

Inter Simple Sequence Repeats ◽

Great Genetic Diversity ◽

Simple Sequence ◽

Issr Primers

AbstractTo investigate the genetic diversity and phylogenetic relationships between polyploid Leymus and related diploid species of the Triticeae tribe, inter-simple sequence repeats (ISSR) markers was used to analyze 41 Leymus accessions representing 22 species and 2 subspecies, together with Pseudoroegneria stipifolia (St), Psathyrostachys fragilis (Ns), Australopyrum retrofractum (W), Hordeum bogdanii, H. chilense (H) and Lophopyrum elongatum (Ee). A total of 376 clear and reproducible DNA fragments were amplified by 29 ISSR primers, among which 368 (97.87%) fragments were found to be polymorphic. 8–18 polymorphic bands were amplified by each polymorphic primer, with an average of 12.69 bands. The data of 376 ISSR bands were used to generate Nei’s similarity coefficients and to construct a dendrogram by means of UPGMA. The similarity coefficients data suggested great genetic diversity in genus Leymus and related diploid Triticeae species, the genetic diversity among the different species more abundant than that of the different accessions. The dendrogram and principal coordinate analysis showed explicit interspecific relationships and demonstrated close phylogenetic relationships between Leymus species and Psathyrostachys.

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Genetic variability among three Egyptian isolates of Heterorhabditis indica using a new marker technique (SCoT)

Egyptian Journal of Biological Pest Control ◽

10.1186/s41938-021-00419-0 ◽

2021 ◽

Vol 31 (1) ◽

Author(s):

Amany M. Abd El Azim ◽

Etr H. K. Khashaba

Keyword(s):

Biological Control ◽

Agricultural Soils ◽

Insect Pests ◽

Genetic Relationships ◽

Its Region ◽

Start Codon ◽

Heterorhabditis Indica ◽

Control Programs ◽

Scot Marker ◽

First Time

Abstract Background Entomopathogenic nematodes (EPNs) are a group of nematode families, have the ability to search for their hosts, and are considered as promising biological control candidates for insect pests, providing protection to non-target organisms and the environment. Results This study was conducted to isolate indigenous EPN isolates from Egyptian agricultural soils for further use in biological control programs and study their genetic polymorphism among the previously isolated isolates under accession no. MH553167 and MK300683 and the new isolate (MH496627), using the start codon targeted (SCoT) marker. One out of 15 soil samples obtained from a banana cultivated field was positive for the presence of EPNs, using the Galleria baiting method. Morphological analysis and sequencing of the internal transcribed spacer (ITS) region suggested that the isolate obtained belongs to Heterorhabditis indica. The sequence of the ITS was submitted to the National Center for Biotechnology Information (NCBI) and registered under accession no. MH496627. Ten SCoT primers were used in the study; the polymorphic bands were 68 out of 76 with 89% as polymorphism percentage. The highest numbers of bands were 10 bands generated by SCoT 1 and SCoT 18 while SCoT 48 and SCoT 60 recorded the lowest band number (5 bands). Conclusions The present study is considered as a preliminary study to demonstrate the effectiveness of the SCoT marker for the first time in assessing genetic relationships in EPNs.

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Morphological and Molecular Characterization of Iranian Wild Blackberry Species Using Multivariate Statistical Analysis and Inter-Simple Sequence Repeats (ISSR) Markers

10.21203/rs.3.rs-136174/v1 ◽

2021 ◽

Author(s):

Ali Gharaghani ◽

Mehdi Garazhian ◽

Saeid Eshghi ◽

Ahmad Tahmasebi

Keyword(s):

Genetic Diversity ◽

Simple Sequence Repeats ◽

Morphological Traits ◽

Diversity Index ◽

Issr Markers ◽

Multivariate Statistical ◽

Principal Coordinates ◽

Inter Simple Sequence Repeats ◽

Simple Sequence ◽

Issr Primers

Abstract This study was carried out to estimate the genetic diversity and relationships of 74 Iranian blackberry genotypes assigned to 5 different species using inter-simple sequence repeats (ISSR) marker analysis and morphological trait characterization. Sixteen traits including phenological, vegetative and reproductive attributes were recorded, and 10 ISSR primers were screened. Results showed that yield and leaf width have the highest and lowest genetic diversity, (diversity index = 62.57 and 13.74), respectively. Flowering and ripening date recorded as traits having the strongest correlations (r = 0.98). The selected 10 ISSR primers produced a total of 161 amplified fragments (200 to 3500 bp) of which 113 were polymorphic. The highest, lowest and average PIC values were 0.53, 0.38 and 0.44, respectively. Principle component analysis (PCA) based on morphological traits showed that the first six components explained 84.9% of the variations of traits studied, whilst the principal coordinate analysis (PCoA) based on ISSR data implied the first eight principal coordinates explained 67.06% of the total variation. Cluster analysis based on morphological traits and ISSR data classified all genotypes into two and three major groups, respectively, and the distribution pattern of genotypes was mainly based on species and the geographic origins.

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Genetic diversity and relationships among salvia species by ISSR markers

Genetika ◽

10.2298/gensr2102559y ◽

2021 ◽

Vol 53 (2) ◽

pp. 559-574

Author(s):

Zhao Yanpeng ◽

Wang Hongmei ◽

Liang Wei ◽

Majid Khayatnezhad ◽

F Faisal

Keyword(s):

Genetic Diversity ◽

Conservation Biology ◽

Issr Markers ◽

High Genetic Diversity ◽

Marker Index ◽

Relationship Analysis ◽

Inter Simple Sequence Repeats ◽

Issr Molecular Markers ◽

Simple Sequence ◽

Issr Primers

Species identification is fundamentally important within the fields of conservation, biology, biogeography and ecology. Salvia species are herbaceous, biennial or annual, strongly aromatic. Inter-Simple sequence repeats (ISSR) molecular markers were used for evaluate genetic diversity and relationship analysis of 30 Salvia species. Ten selected ISSR primers amplified 116 loci, respectively, of which all were polymorphic. The obtained average polymorphism information content 0.39, average band informativeness 10.5 and the marker index 3.1 revealed high genetic diversity prevailing among Salvia accessions. The dendrogram was constructed based on ISSR separated the individuals into sub-clusters in accordance with their species. Our results indicated that ISSR markers can be used as a reliable and informative technique for evaluation of genetic diversity and relationships among Salvia species. The objectives of present study are: 1) can ISSR markers identify Salvia species, 2) what is the genetic of these taxa in Iran, and 3) to investigate the species inter-relationship?

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Genetic diversity and population structure among strains of the entomopathogenic fungus, Beauveria bassiana, as revealed by inter-simple sequence repeats (ISSR)

Mycological Research ◽

10.1017/s0953756205003709 ◽

2005 ◽

Vol 109 (12) ◽

pp. 1364-1372 ◽

Cited By ~ 51

Author(s):

Sibao Wang ◽

Xuexia Miao ◽

Weiguo Zhao ◽

Bo Huang ◽

Meizhen Fan ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Beauveria Bassiana ◽

Simple Sequence Repeats ◽

Entomopathogenic Fungus ◽

Inter Simple Sequence Repeats ◽

Fungus Beauveria Bassiana ◽

Simple Sequence

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Assessment of Genetic Diversity of Rheum species (Endangered Medicinal Herb of Indian Himalayan Region) using Molecular Markers

Research Journal of Biotechnology ◽

10.25303/1611rjbt147154 ◽

2021 ◽

Vol 16 (11) ◽

pp. 147-154

Author(s):

Anjali Uniyal ◽

Akhilesh Kumar ◽

Sweta Upadhyay ◽

Vijay Kumar ◽

Sanjay Gupta

Keyword(s):

Genetic Diversity ◽

Molecular Markers ◽

Fragment Length Polymorphism ◽

Dna Polymorphisms ◽

Inter Simple Sequence Repeats ◽

Pharmaceutical Industries ◽

Endangered Medicinal Herb ◽

Identification And Characterization ◽

Simple Sequence

The Rheum species are important medicinal plants that are facing extinction due to their unplanned development and overexploitation by pharmaceutical industries. DNA polymorphisms are not prone to environmental modifications, thus they are widely used for the identification and characterization of plants. The use of different molecular markers has enabled the researchers for the valuation of genetic variability and diversity in its natural zone of distribution. The conventional approach may take several years to yield this information. For the estimation of molecular and genetic variations in geographical zone of distribution, various molecular markers technique are available like RAPD (Randomly Amplified Polymorphic DNA), RFLP (Restriction fragment length polymorphism), ISSR (Inter-Simple Sequence Repeats), SSR and AFLP. The uses of different molecular markers for the study of genetic diversity have been discussed in the review.

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Entomopathogenic nematodes: can we use the current knowledge on belowground multitrophic interactions in future plant protection programmes? – Review

Plant Protection Science ◽

10.17221/24/2019-pps ◽

2019 ◽

Vol 55 (No. 4) ◽

pp. 242-253 ◽

Cited By ~ 2

Author(s):

Anamarija Jagodič ◽

Stanislav Trdan ◽

Žiga Laznik

Keyword(s):

Biological Control ◽

Entomopathogenic Nematodes ◽

Insect Pests ◽

Current Knowledge ◽

Plant Protection ◽

Multitrophic Interactions ◽

Herbivore Attack ◽

Below Ground ◽

Chemical Stimuli

Plants under herbivore attack emit mixtures of volatiles that can attract the natural enemies of the herbivores. Entomopathogenic nematodes (EPNs) are organisms that can be used in the biological control of insect pests. Recent studies have shown that the movement of EPNs is associated with the detection of chemical stimuli from the environment. To date, several compounds that are responsible for the mediation in below ground multitrophic interactions have been identified. In the review, we discuss the use of EPNs in agriculture, the role of belowground volatiles and their use in plant protection programmes.

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