scholarly journals Inter simple sequence repeats (ISSRs): Neglected DNA markers for molecular dissection of Plasmodium species in long-tailed Macaque (Macaca fascicularis)

2015 ◽  
Author(s):  
Parastoo Khajeaian ◽  
Soon Guan Tan ◽  
Alireza Valdiani ◽  
Christina Seok Yien Yong ◽  
Mohammad Zareian Jahromi ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Cluster Analysis ◽  
Genetic Variation ◽  
Macaca Fascicularis ◽  
High Efficiency ◽  
Plasmodium Species ◽  
Issr Markers ◽  
Malaria Vectors ◽  
Wide Range ◽  
Simple Sequence

Understanding the genetic variation of the Plasmodium parasites could play an important role in controlling and preventing this lethal infection. Inter simple sequence repeat (ISSR) markers have successfully been tested for investigating the genetic diversity of malaria vectors. It is hypothesized that ISSRs could lead to fruitful results in studying the genetic variation of Plasmodium species, as well. To illustrate the genetic diversity of two infectious Plasmodium species, including Plasmodium knowlesi and Plasmodium cynomolgi, infected and uninfected monkey blood samples were separately collected on filter papers (FTA cards), and used for DNA extraction. A total of 103 and 95 polymorphic ISSR loci were detected in infected and uninfected samples, respectively. Cluster analysis of the Plasmodium and Macaca fascicularis accessions both resulted in the generation of three clusters. However, the most significant result of the cluster analysis was revealing the high efficiency of ISSR markers in the discrimination of the two Plasmodium species from each other. The cluster analysis showed a wide range of genetic diversity among both Plasmodium and the long-tailed Macaque accessions. The principal component analysis (PCA) also confirmed the cluster analysis results.

scholarly journals Inter simple sequence repeats (ISSRs): Neglected DNA markers for molecular dissection of Plasmodium species in long-tailed Macaque (Macaca fascicularis)

2015 ◽  
Author(s):  
Parastoo Khajeaian ◽  
Soon Guan Tan ◽  
Alireza Valdiani ◽  
Christina Seok Yien Yong ◽  
Mohammad Zareian Jahromi ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Cluster Analysis ◽  
Genetic Variation ◽  
Macaca Fascicularis ◽  
High Efficiency ◽  
Plasmodium Species ◽  
Issr Markers ◽  
Malaria Vectors ◽  
Wide Range ◽  
Simple Sequence

Understanding the genetic variation of the Plasmodium parasites could play an important role in controlling and preventing this lethal infection. Inter simple sequence repeat (ISSR) markers have successfully been tested for investigating the genetic diversity of malaria vectors. It is hypothesized that ISSRs could lead to fruitful results in studying the genetic variation of Plasmodium species, as well. To illustrate the genetic diversity of two infectious Plasmodium species, including Plasmodium knowlesi and Plasmodium cynomolgi, infected and uninfected monkey blood samples were separately collected on filter papers (FTA cards), and used for DNA extraction. A total of 103 and 95 polymorphic ISSR loci were detected in infected and uninfected samples, respectively. Cluster analysis of the Plasmodium and Macaca fascicularis accessions both resulted in the generation of three clusters. However, the most significant result of the cluster analysis was revealing the high efficiency of ISSR markers in the discrimination of the two Plasmodium species from each other. The cluster analysis showed a wide range of genetic diversity among both Plasmodium and the long-tailed Macaque accessions. The principal component analysis (PCA) also confirmed the cluster analysis results.

Genetic variability of Orobanche aegyptiaca infesting tobacco in Iran by Bayesian analysis

Biologia ◽  
2014 ◽  
Vol 69 (12) ◽  
Author(s):  
Samaneh Abedi ◽  
Reza Darvishzadeh ◽  
Iraj Bernousi ◽  
Babak Abdollahi Mandoulakani ◽  
Hamid Hatami Maleki ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Inter Simple Sequence Repeat ◽  
Issr Markers ◽  
Similarity Coefficients ◽  
Genetic Groups ◽  
Wide Range ◽  
Orobanche Aegyptiaca ◽  
Simple Sequence ◽  
Issr Primers

AbstractBroomrapes (Orobanche L.) are holoparasitic plants, parasitizing roots of a wide range of host plants. In this study, genetic polymorphism among 44 Orobanche aegyptiaca Pers. individuals collected from different regions of northwest Iran was investigated using inter-simple sequence repeat (ISSR) markers. Two hundred-sixty one discernible bands were amplified using 20 ISSR primers which 245 (94%) was polymorphic, indicating considerable genetic variation among the examined individuals. The number of polymorphic bands per primer ranged from 4 to 17, averaging 12.25. UPGMA clustering using Jaccard’s similarity coefficients revealed six main groups. Genetic similarity coefficients varied from 0.71 (between individuals 23 and 27) to 0.34 (between 13 and 30). A model-based Bayesian approach subdivided 38 out of 44 broomrape genotypes into 2 genetic groups and the remaining ones were categorized as mixed genotypes based on Q values. According to an analysis of molecular variance, 99% of the total variation was partitioned within genetic groups. The results demonstrated the potential usefulness of ISSR markers for determination of genetic variation in O. aegyptiaca. Understanding the variability in broomrape is important when attempting to develop resistant host crops against this parasite.

scholarly journals Genetic diversity and phenetic relationships of five Trifolium L. species (Fabaceae) by inter simple sequence repeats markers

2016 ◽  
Vol 23 (2) ◽  
pp. 167-173
Author(s):  
Yourang Hwang ◽  
Man Kyu Huh
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Gene Flow ◽  
Simple Sequence Repeats ◽  
Issr Markers ◽  
Phenetic Relationships ◽  
Inter Simple Sequence Repeats ◽  
Total Genetic Diversity ◽  
Plant Taxon ◽  
Simple Sequence

Five species of Trifolium L. (T. repens L., T. pretense L., T. hybridum L., T. campestre Schreb., and T. dubium Sibth.) were analyzed used to evaluate the genetic diversity and their phenetic relationships using inter-simple sequence repeats (ISSR) markers. Overall, T. pratense exhibited higher variation than other species. 114 amplicons were produced by ISSR markers, of which 77 (67.5%) bands were polymorphic. T. dubium showed the low genetic variation. Total genetic diversity values (HT) varied between 0.333 and 0.487, for an average over all polymorphic loci of 0.282. On a perlocus basis, the proportion of total genetic variation due to differences among species (GST) was 0.380. This indicated that about 38.0% of the total variation was among species. The estimate of gene flow, based on GST, was very low among species of genus Trifolium (Nm = 0.816). An assessment of the proportion of diversity present within species, HPOP/HSP, indicated that about 95.8% the total genetic diversity was within species. T. pratense and T. hybridum were grouped together and this clade was sister with T. repens. Two remainder species with yellow flowers were grouped together. Information on genetic diversity for Trifolium is valued for the management of germplasm and for evolving conservation strategies.Bangladesh J. Plant Taxon. 23(2): 167-173, 2016 (December)

scholarly journals KEANEKARAGAMAN GENETIK KAPULASAN [NEPHELIUM RAMBOUTAN-AKE (LABILL.) LEENH.] DI JAWA BERDASARKAN MARKA SSR DAN ISSR

Floribunda ◽  
2020 ◽  
Vol 6 (4) ◽  
Author(s):  
Nina Ratna Djuita ◽  
Alex Hartana ◽  
Tatik Chikmawati ◽  
Dorly
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Genomic Dna ◽  
Inter Simple Sequence Repeat ◽  
Issr Markers ◽  
Sequence Repeat ◽  
Polymorphic Bands ◽  
Simple Sequence

Nina Ratna Djuita, Alex Hartana, Tatik Chikmawati, Dorly. 2020. Genetic Diversity of Pulasan [Nephelium ramboutan-ake (Labill.) Leenh.] of Java Based on SSR and ISSR Markers. Floribunda 6(4): 117–126. —  Pulasan is one of the potential local fruits to be developed. This study aimed to analyze the genetic diversity of pulasan of Java using Simple Sequence Repeat (SSR) and Inter Simple Sequence Repeat (ISSR) markers and to obtain information whether primers of the markers could be used to distinguish male and her-maphrodite plants. The results showed that two primers in the SSR markers and seven primers in the ISSR markers produced polymorphic bands. The genomic DNA of the pulasan amplified with SSR markers produced bands 140–500 bp, while those from the ISSR markers were 150–1500 bp. The population of pulasan in Babakan Madang has the highest genetic diversity, while that of Patean is the lowest. Genetic variation of pulasan based on SSR and ISSR markers in the population and among populations have different compositions. Variation in the population is 72% while among the population is 28%. Primers of LML Y6 and LML Y12 from SSR markers and primers of ISSR 2, 3, 4, 5, 6, 8, 9 cannot be used to distinguish male and hermaphrodite pulasan plants. Nina Ratna Djuita, Alex Hartana, Tatik Chikmawati, Dorly. 2020. Keanekaragaman Genetik Kapulasan [Nephelium ramboutan-ake (Labill.) Leenh.] di Jawa Berdasarkan Marka SSR dan ISSR. Floribunda 6(4): 117–126. —  Kapulasan merupakan salah satu buah lokal yang potensial untuk dikembangkan. Penelitian ini bertujuan untuk menganalisis keanekaragaman genetik kapulasan di Jawa dengan menggunakan marka Simple Sequence Repeat (SSR) dan Inter Simple Sequence Repeat (ISSR) serta untuk mendapatkan informasi apakah primer dari marka tersebut dapat dipakai untuk membedakan tumbuhan jantan dan hermafrodit.  Hasil penelitian menunjukkan bahwa dua primer pada marka SSR dan tujuh primer pada marka ISSR menghasilkan pita polimorfik. DNA genom kapulasan yang diamplifikasi dengan  marka SSR menghasilkan pita-pita dengan ukuran 110–500 bp, sedangkan dari marka ISSR berukuran 150–1500 bp. Populasi kapulasan di Babakan Madang mempunyai keanekaragaman genetik paling tinggi, sedangkan populasi di Patean paling rendah. Variasi genetik kapulasan berdasarkan  marka SSR dan ISSR di dalam populasi dan di antara populasi mempunyai komposisi yang berbeda. Variasi di dalam populasi sebesar 72 % sedangkan di antara populasi sebesar 28%. Primer LML Y6 dan LML Y12 dari marka SSR dan primer ISSR 2, 3, 4, 5, 6, 8, 9  tidak dapat digunakan untuk membedakan tumbuhan kapulasan jantan dan hermafrodit.   

ISSR Marker Based Genetic Diversity in Morinda Spp. For Its Enhanced Collection, Conservation and Utilization

2021 ◽  
Author(s):  
Lalit Arya ◽  
Ramya Kossery Narayanan ◽  
Anjali Kak ◽  
Chitra Devi Pandey ◽  
Manjusha Verma ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Gene Diversity ◽  
Inter Simple Sequence Repeat ◽  
Issr Markers ◽  
Morinda Citrifolia ◽  
Species Differentiation ◽  
Information Index ◽  
Upgma Cluster Analysis ◽  
Simple Sequence

Abstract Morinda (Rubiaceae) is considerably recognized for its multiple uses viz. food, medicine, dyes, firewood, tools, oil, bio-sorbent etc. The molecular characterization of such an important plant would be very useful for its multifarious enhanced utilization. In the present study, 31 Morinda genotypes belonging to two different species Morinda citrifolia and Morinda tomentosa collected from different regions of India were investigated using Inter Simple Sequence Repeat (ISSR) markers. Fifteen ISSR primers generated 176 bands with an average of 11.7 bands per primer, of which (90.34%) were polymorphic. The percentage of polymorphic bands, mean Nei’s gene diversity, mean Shannon’s information index in Morinda tomentosa and Morinda citrifolia was [(69.89%, 30.68%); (0.21 ± 0.19, 0.12 ± 0.20); (0.32 ± 0.27 0.17 ± 0.28)] respectively, revealing higher polymorphism and genetic diversity in Morinda tomentosa compared to Morinda citrifolia. Structure, and UPGMA cluster analysis placed the genotypes into well-defined separate clusters belonging to two species Morinda tomentosa and Morinda citrifolia revealing the utility of ISSR markers in species differentiation. Distinct ecotypes within a particular species could also be inferred emphasizing the collection and conservation of Morinda genotypes from different regions, in order to capture the overall diversity of respective species. Further higher diversity of M. tomentosa must be advanced for its utilization in nutraceutical, nutritional and other nonfood purposes.

scholarly journals Measurement of Genetic Diversity of Chinese Seashore Paspalum Resources through Morphological and Sequence-related Amplified Polymorphism Analysis

2019 ◽  
Vol 144 (6) ◽  
pp. 379-386
Author(s):  
Yan Liu ◽  
Hailin Guo ◽  
Yi Wang ◽  
Jingang Shi ◽  
Dandan Li ◽  
...  
Keyword(s):  
United States ◽  
Genetic Diversity ◽  
Cluster Analysis ◽  
Genetic Variation ◽  
Genetic Distance ◽  
Morphological Characteristics ◽  
The United States ◽  
Germplasm Resources ◽  
Seashore Paspalum ◽  
Chinese Germplasm

Seashore paspalum (Paspalum vaginatum) is a notable warm-season turfgrass. Certain germplasm resources are distributed in the southern regions of China. The objectives of this study were to investigate the genetic diversity and genetic variation of Chinese seashore paspalum resources. Morphological characteristics and sequence-related amplified polymorphism (SRAP) markers were used to assess genetic relationships and genetic variation among 36 germplasm resources from China and six cultivars from the United States. The results showed significant variation for 13 morphological characteristics among 42 tested seashore paspalum accessions, and that the phenotypic cv was, in turn, turf height > turf density > internode length > inflorescence density > leaf width > reproductive branch height > spikelet width > leaf length > spikelet number > inflorescence length > internode diameter > inflorescence width > spikelet length. According to the morphological characteristics and cluster analysis, 42 seashore paspalum accessions were divided into six morphological types. In total, 374 clear bands were amplified using 30 SRAP primer combinations; among these bands, 321 were polymorphic with 85.83% polymorphism. SRAP marker cluster analysis showed that 42 seashore paspalum accessions were grouped into seven major groups, with a genetic similarity coefficient ranging from 0.4385 to 0.9893 and genetic distance values ranging from 0.0108 to 0.8244. The high level of genetic diversity occurred among Chinese germplasm, and the genetic distance was relatively high between Chinese germplasm and cultivars introduced from the United States. The patterns in morphological trait variations and genetic diversity will be useful for the further exploitation and use of Chinese seashore paspalum resources.

scholarly journals Genetic diversity in potato (Solanum tuberosum L.)

1970 ◽  
Vol 36 (2) ◽  
pp. 121-125 ◽  
Author(s):  
MAA Mondal ◽  
MM Hossain ◽  
MG Rasul ◽  
M Shalim Uddin
Keyword(s):  
Genetic Diversity ◽  
Cluster Analysis ◽  
Multivariate Analysis ◽  
Solanum Tuberosum ◽  
Key Words ◽  
Diversity Pattern ◽  
Wide Range ◽  
Cluster Distance ◽  
Range Of Variation

Genetic diversity in 31 potato genotypes (parents and their hybrid progenies) was determined using multivariate analysis. Cluster analysis revealed that the parents and their hybrid progenies could be grouped into five different clusters. The maximum number of genotypes were included in clusters II and V. Cluster V had maximum and cluster I had minimum intra-cluster distance. Cluster mean showed wide range of variation for several characters among single as well as multi-genotypic clusters. Considering diversity pattern, parents should be selected from clusters I, III and V for the improvement of potato.   Key words: Genetic diversity, Cluster analysis, Potato DOI = 10.3329/bjb.v36i2.1499 Bangladesh J. Bot. 36(2): 121-125, 2007 (December)

scholarly journals Genetic diversity and interspecific relationships of some Allium species using inter simple sequence repeat markers

2015 ◽  
Vol 22 (2) ◽  
pp. 67-75 ◽  
Author(s):  
Leila Samiei ◽  
Mahnaz Kiani ◽  
Homa Zarghami ◽  
Farshid Memariani ◽  
Mohammad Reza Joharchi
Keyword(s):  
Genetic Diversity ◽  
Simple Sequence Repeat ◽  
Gene Diversity ◽  
Inter Simple Sequence Repeat ◽  
Issr Markers ◽  
Group Method ◽  
Sequence Repeat ◽  
Allium Species ◽  
Interspecific Relationships ◽  
Simple Sequence

In this study genetic diversity and interspecific relationships of 11 Allium L. species from Khorassan province of Iran including 32 accessions were investigated by inter simple sequence repeat (ISSR) markers. Nine ISSR primers produced a total of 80 polymorphic markers and revealed high polymorphism among the studied species. The average gene diversity, effective number of alleles and Shannon’s information index were 0.2, 1.28 and 0.3, respectively. Allium kuhsorkhense exhibited the greatest level of variation (He: 0.18), whereas A. stipitatum demonstrated the lowest level of variability (He: 0.05). UPGMA (Unweighted Pair Group Method with Arithmetic mean) analysis showed that Allium accessions have a similarity range of 0.60 to 0.95. Allium scapriscapum composed the most distant group in the dendrogram. The clustered groups of Allium species clearly reflect the recent taxonomic concept of the genus at the subgenus and section levels. The present study showed that the ISSR technique is an effective molecular approach for analyzing genetic diversity and relationship in Allium species.Bangladesh J. Plant Taxon. 22(2): 67-75, 2015 (December)

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