Evaluation of genetic diversity of Rubus hyrcanus using Inter Simple Sequence Repeat (ISSR) and morphological markers

Biologia ◽  
2015 ◽  
Vol 70 (3) ◽  
Author(s):  
Ehsan Sedighi ◽  
Mehdi Rahimmalek
Keyword(s):  
Genetic Diversity ◽  
Caspian Sea ◽  
Gene Diversity ◽  
Inter Simple Sequence Repeat ◽  
Morphological Markers ◽  
The Caspian Sea ◽  
Geographical Regions ◽  
North Eastern ◽  
North Western ◽  
Simple Sequence

AbstractRubus hyrcanus is considered as an important wild blackberry species scattered around the Caspian Sea. In this research, ISSR and morphological markers were used to assess genetic diversity in several populations of R. hyrcanus from various geographical regions of Caspian Sea in Iran. Twenty-five populations of R. hyrcanus from three regions (North- Western (NW), North- Eastern (NE) and Central (C)) and one population from R. discolor were applied in this research. Ten primers were used to amplify bands out of which 157 (77.13%) were polymorphic. Cluster and Principle coordinate analyses (PCoA) showed the higher similarity of NE and NW populations. Analysis of molecular variance (AMOVA) revealed that the differences among three collection regions only accounted for 28.09% of the total variation, whereas differences among populations within groups were 66.03%. Analyses among three regions showed that the minimum gene diversity over loci was observed in NW (0.16) and NE (0.17), while the highest one was found in C (0.238) region. Furthermore, narrow genetic base and relatively high genetic differentiation obtained for studied R. hyrcanus genotypes. The results of morphological analysis in most cases corresponded to those obtained through molecular analyses.

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 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)

Genetic diversity in local barley accessions collected from different geographical regions of Tunisia

2009 ◽  
Vol 7 (02) ◽  
pp. 169-176 ◽  
Author(s):  
M. A. Ould Med Mahmoud ◽  
S. Hamza
Keyword(s):  
Genetic Diversity ◽  
Geographical Origin ◽  
Expressed Sequence Tag ◽  
Gene Diversity ◽  
North West ◽  
The North ◽  
Geographical Regions ◽  
The Impact ◽  
Expressed Sequence ◽  
Simple Sequence

To assess the genetic diversity among Tunisian local barley, a set of 120 barley accessions representing five distinct geographical regions (North-West, Littoral, South, Jerba and Kerkennah Islands) was characterized with 20 simple sequence repeats (SSR) and 8 expressed sequence tag (EST)-SSR markers. The 28 loci revealed a total of 98 alleles, with an average of 3.76 alleles per locus (range 2–10). Gene diversity averaged 0.50 (range 0.09–0.84). Partitioning analysis of genetic diversity showed that about 95% of the total variation was within regions and no geographical differentiation could be found except for the North-West population. Similarly, neighbour joining clustering of the genotypes did not indicate any clear pattern of division among the barley accessions based on geographical origin. These results may reflect the impact of seed exchange between farmers which is likely to limit highlighting favourable alleles due to local adaptation.

scholarly journals Assessment of genetic diversity in Fusarium wilt tolerant and susceptible oil palm (Elaeis guineensis Jacq) progenies in Nigeria using inter- simple sequence repeat (ISSR) molecular markers

2019 ◽  
Author(s):  
Nnamdi Ifechukwude Chidi ◽  
Adedotun Adeyinka Adekunle ◽  
Temitope Oluwaseun Samuel ◽  
Emmanuel Ifechukwude Eziashi ◽  
David Okeh Igwe
Keyword(s):  
Genetic Diversity ◽  
Molecular Markers ◽  
Oil Palm ◽  
Simple Sequence Repeat ◽  
Elaeis Guineensis ◽  
Gene Diversity ◽  
Inter Simple Sequence Repeat ◽  
Mean Value ◽  
Sequence Repeat ◽  
Simple Sequence

Abstract Background Improving oil palm in Nigeria for food security and subsequent export requires a better understanding of the genetic diversity among oil palm progenies tolerant and susceptible to Fusarium wilt disease. In view of the limitations of the orthodox method used in screening this disease, and the advantages of molecular markers, fourteen (14) Inter-simple sequence repeat (ISSR) DNA markers were applied to evaluate the genetic diversity, population structure and cluster resolutions of alleles responsible for tolerance of 560 Elaeis guineensis Jacq palms representing 8 different progenies distributed across NigeriaResults The amplification product revealed a moderately high level of genetic diversity with a total of 46 alleles identified, resulting in an average of 4.9091 alleles per locus detected between the oil palm progenies. Polymorphic information content (PIC) values varied between 0.3706-0.7861, with a mean value of 0.6829. The genetic diversity values ranged from 0.4063-0.8125 with a mean of 0.7216, while the major allele frequency ranged from 0.2500- 0.7500 with a mean value of 0.3750. Shannon's information index (I), Nei's gene diversity (H), and the effective number of alleles (Ne) had values of 0.6931, 0.5000, and 2.000, respectively. The genetic diversity was highest in progeny 3023, and lowest in progeny 4189. Mean values of the total gene diversity (Ht), gene diversity within the population (Hs) of the progenies, coefficient of gene differentiation among the progenies (Gst) and level of gene flow (Nm) were 0.4899, 0.3520, 0.2815 and 1.2764, respectively. The dendrogram clustered the progenies into six major clusters, while Principal Component Analysis (PCA) grouped the progenies into five clusters. PCA further identified the coordinate positions of tolerant and susceptible alleles of oil palm progeniesConclusion This study confirmed the identification of the coordinate positions of tolerant alleles in the gene loci, which could be exploited by breeders to developing tolerant oil palm seedlings.

scholarly journals Evaluation of Genetic Diversity Among Kongpo Monkshood (Aconitum kongboense L.) Germplasm Accessions Revealed by Inter Simple Sequence Repeat Markers

HortScience ◽  
2015 ◽  
Vol 50 (7) ◽  
pp. 940-943 ◽  
Author(s):  
Fanjuan Meng ◽  
Ruoding Wang ◽  
Mu Peng ◽  
Chao Wang ◽  
Zhongkui Wang ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Simple Sequence Repeat ◽  
Gene Diversity ◽  
Molecular Data ◽  
Inter Simple Sequence Repeat ◽  
Tibet Plateau ◽  
Polymorphism Analysis ◽  
Sequence Repeat ◽  
The Mean ◽  
Simple Sequence

Inter simple sequence repeat (ISSR) were used to evaluate the genetic diversity of Kongpo Monkshood (Aconitum kongboense L.) in Motuo, Tibet Plateau. From 70 accessions of three populations, 10 out of 100 informative ISSR primers were chosen for polymorphism analysis. Percentage of polymorphic bands was 50% to 66.67% with a mean of 58.42%. The effective number of alleles (Ne) was between 1.545 (population 3) and 1.586 (population 2), and the mean value was 1.564; the Nei’s gene diversity (h) ranged from 0.315 to 0.327 with the average value of 0.320; the value of Shannon’s information index (I) ranged from 0.459 to 0.478, with the mean of 0.469. Based on molecular data, cluster analysis classified the 70 cultivars into three groups. Most accessions were related to the geographical origin and their genetic backgrounds. Bayesian structure and PCoA analysis were consistent with the dendrogram result. Based on the analysis, it will provide a reference for Kongpo Monkshood breeding purposes and contribute to identification, rational exploitation, and conservation of germplasms.

scholarly journals Assessment of Genetic Diversity of Niger Plant (Guizotia abyssinica L.) in Moiben Sub County, Kenya, Using Inter Simple Sequence Repeat Markers

2021 ◽  
Vol 8 (1) ◽  
pp. 126-131
Author(s):  
Lynnete Moraa Oimbo
Keyword(s):  
Genetic Diversity ◽  
Simple Sequence Repeat ◽  
Gene Diversity ◽  
Distance Matrix ◽  
Inter Simple Sequence Repeat ◽  
Issr Markers ◽  
Guizotia Abyssinica ◽  
Sequence Repeat ◽  
Euclidean Distance Matrix ◽  
Simple Sequence

Niger plant (Guizotia abyssinica), exhibits phenotypic plasticity in different environments. There is need to assess its genetic diversity since guizotia species has a high number of species which may be confused amongst themselves. To achieve this, inter simple sequence repeat (ISSR) markers were used to estimate genetic diversity among 12 wild populations of Niger plant from Moiben sub-county. Total genomic DNA was extracted as per the cetyltrimethylammonium bromide (Ctab) method and subjected to ISSR analysis using 20 primers. None of the primers produced unique banding patterns. ISSR data were used to calculate a squared-euclidean distance matrix. All the twenty primers (100%) gave polymorphic bands thus they were all considered for further analysis. The allele frequency of all the primers was below 0.95 indicating that they were all polymorphic in character. Gene diversity was high ranging from 0.3550 to 0.7337 with a mean value of 0.6302. The ISSR based upgma clustering produced four clusters. Niger plant within Moiben sub-county was found to be genetically diverse though heterozygosity was not noticed. The study recommends further analysis of Niger plant so as to form a basis for further development of the plant.

scholarly journals Molecular Characterization and Population Genetic Structure of Fagopyrum Species Cultivated in Himalayan Regions

2021 ◽  
Vol 13 (21) ◽  
pp. 12165
Author(s):  
Fayaz Ahmad Dar ◽  
Inayatullah Tahir ◽  
Sameer H Qari ◽  
Aala A Abulfaraj ◽  
Maha Aljabri ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Molecular Characterization ◽  
Inter Simple Sequence Repeat ◽  
Variance Partitioning ◽  
Specific Level ◽  
The North ◽  
Close Phylogenetic Relationship ◽  
Information Indices ◽  
North Western ◽  
Simple Sequence

Fagopyrum spp. (buckwheat) is a dicotyledonous pseudocereal crop mainly cultivated in the north-western Himalayan regions for its highly nutritional, antioxidant and therapeutic values. In the present investigation, molecular characterization was performed by using ISSR (inter simple sequence repeat) markers on 42 accessions of four buckwheat species (Fagopyrum esculentum, F. sagittatum, F. tataricum and F. kashmirianum). The 12 pre-screened ISSR primers amplified 102 bands, and amongst them 85 bands exhibited polymorphism with an average polymorphism of 82.73%. The results revealed that Shannon’s information indices (I) and Nei’s genetic diversity (H) were low for F. tataricum (I = 0.1028 ± 0.2307; H = 0.0707 ± 0.1617) and high for F. esculentum (I = 0.1715 ± 0.2622; H = 0.1164 ± 0.1796). It was estimated that within the accessions of Fagopyrum species, the species diversity (HT) and mean diversity (HS) were 0.3200 and 0.1041, respectively. Molecular variance partitioning by AMOVA also indicated a significant genetic differentiation accounting for 73% among and 27% within the accessions of Fagopyrum species. Overall, accessions of F. esculentum had the greatest distance from the other accessions of buckwheat species, which includes F. sagittatum, F. tataricum and F. kashmirianum as revealed by FST distance and Nei’s unbiased genetic distance. The dendograms based on UPGMA and PCoA segregated 42 accessions of four buckwheat species into three major groups. This study clearly reveals a considerable amount of genetic diversity at the intra-specific level in F. esculentum, F. sagittatum and F. kashmirianum accessions. The factors responsible for it are diverse geographical conditions, pollinating behavior and cultivation practices adapted in these regions. The study also indicated a close phylogenetic relationship between F. tataricum and F. kashmirianum.

Genetic diversity of Symplocos paniculata of Hunan province revealed by inter-simple sequence repeat (ISSR)

2019 ◽  
Vol 51 (5) ◽  
Author(s):  
Huifang Cao ◽  
Qiang Lin ◽  
Peiwang Li ◽  
Jingzhen Chen ◽  
Changzhu Li ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Simple Sequence Repeat ◽  
Inter Simple Sequence Repeat ◽  
Hunan Province ◽  
Sequence Repeat ◽  
Simple Sequence
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