scholarly journals Molecular diversity and phylogeny of Triticum-Aegilops species possessing D genome revealed by SSR and ISSR markers

2015 ◽  
Vol 71 (1) ◽  
pp. 81-95 ◽  
Author(s):  
Hoda Moradkhani ◽  
Ali Ashraf Mehrabi ◽  
Alireza Etminan ◽  
Alireza Pour-Aboughadareh
Keyword(s):  
Genetic Diversity ◽  
Gene Diversity ◽  
Genetic Relationships ◽  
Issr Markers ◽  
Issr Marker ◽  
D Genome ◽  
Ploidy Levels ◽  
Marker Data ◽  
Geographical Regions ◽  
High Level

AbstractThe aim of this study is investigation the applicability of SSR and ISSR markers in evaluating the genetic relationships in twenty accessions ofAegilopsandTriticumspecies with D genome in different ploidy levels. Totally, 119 bands and 46 alleles were detected using ten primers for ISSR and SSR markers, respectively. Polymorphism Information Content values for all primers ranged from 0.345 to 0.375 with an average of 0.367 for SSR, and varied from 0.29 to 0.44 with the average 0.37 for ISSR marker. Analysis of molecular variance (AMOVA) revealed that 81% (ISSR) and 84% (SSR) of variability was partitioned among individuals within populations. Comparing the genetic diversity ofAegilopsandTriticumaccessions, based on genetic parameters, shows that genetic variation ofAe. crassaandAe. tauschiispecies are higher than other species, especially in terms of Nei’s gene diversity. Cluster analysis, based on both markers, separated total accessions in three groups. However, classification based on SSR marker data was not conformed to classification according to ISSR marker data. Principal co-ordinate analysis (PCoA) for SSR and ISSR data showed that, the first two components clarified 53.48% and 49.91% of the total variation, respectively. This analysis (PCoA), also, indicated consistent patterns of genetic relationships for ISSR data sets, however, the grouping of accessions was not completely accorded to their own geographical origins. Consequently, a high level of genetic diversity was revealed from the accessions sampled from different eco-geographical regions of Iran.

Comparative assessment of SCoT and ISSR markers for analysis of genetic diversity and population structure in some Aegilops tauschii Coss. accessions

2021 ◽  
pp. 1-9
Author(s):  
Atefeh Nouri ◽  
Maryam Golabadi ◽  
Alireza Etminan ◽  
Abdolmajid Rezaei ◽  
Ali Ashraf Mehrabi
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Aegilops Tauschii ◽  
Inter Simple Sequence Repeat ◽  
Issr Markers ◽  
Start Codon ◽  
D Genome ◽  
Breeding Programmes ◽  
High Level ◽  
Effective Multiplex Ratio

Abstract Aegilops tauschii, the diploid progenitor of the wheat D-genome, is a valuable genetic resource for wheat breeders. In this study, we compared the efficiency of inter-simple sequence repeat (ISSR) (as an arbitrary technique) and start codon targeted (SCoT) (as a gene-targeting technique) markers in determining the genetic diversity and population structure of 90 accessions of Ae. tauschii. SCoT markers indicated the highest values for polymorphism information content, marker index and effective multiplex ratio compared to ISSR markers. The total genetic diversity (Ht) and genetic diversity within populations (Hs) parameters were comparably modest for the two marker systems. The results of the analysis of molecular variance showed that the genetic variation within populations was significantly higher than among them (ISSR: 92 versus 8%; SCoT: 88 versus 12%). Furthermore, SCoT markers discovered a high level of genetic differentiation among populations than ISSRs (0.19 versus 0.05), while the amount of gene flow detected by ISSR was higher than SCoT (2.13 versus 8.62). Cluster analysis and population structure of SCoT and ISSR data divided all investigated accessions into two and four main clusters, respectively. Our results revealed that SCoT and ISSR fingerprinting could be used to further molecular analysis in Ae. tauschii and other wild species. The high-genetic variability found in this study also indicates the valuable genetic potential present in the investigated Ae. tauschii germplasm, which could be utilized for future genetic analysis and linkage mapping in breeding programmes.

scholarly journals ISSR markers for genetic relationships in Caricaceae and sex differentiation in papaya

2011 ◽  
Vol 11 (4) ◽  
pp. 352-357 ◽  
Author(s):  
Fabiane Rabelo da Costa ◽  
Telma Nair Santana Pereira ◽  
Ana Paula Candido Gabriel ◽  
Messias Gonzaga Pereira
Keyword(s):  
Genetic Diversity ◽  
Plant Species ◽  
Genetic Relationships ◽  
Sex Differentiation ◽  
Issr Markers ◽  
Issr Marker ◽  
Phylogenetic Studies ◽  
Issr Pcr

ISSR markers are polymorphic and their results easily reproducible. They are therefore intensely used in phylogenetic studies and sex differentiation of some economically interesting plant species. The objectives of this study were to analyze the genetic diversity in Caricaceae using ISSR markers, to identify a specific ISSR band that could distinguish female from hermaphrodite papaya genotypes and to verify whether this marker could be used for early sex differentiation. The ISSR-PCR was performed with nine primers and they could distinguish all species. It was observed that Jacaratia spinosa was closer to Vasconcellea than to Carica. The species C. papaya was only distantly related to both genera. A 500 bp ISSR marker was found in 25 % of the papaya genotypes studied. Specifically in these cases this marker could be used for early sex differentiation in papaya.

scholarly journals Eficiența unor marcheri moleculari în discriminarea populațiilor de lupoaie originare din China

2021 ◽  
Author(s):  
Maria Duca ◽  
◽  
Ana Mutu ◽  
Ina Bivol ◽  
Steliana Clapco ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Gene Diversity ◽  
Issr Markers ◽  
Resolving Power ◽  
Information Index ◽  
Combined Use ◽  
Different Types ◽  
High Level ◽  
Different Levels

In this study, the effectiveness of different types of molecular markers in assessing genetic diversity of populations of O. cumana from China was determined. ISSR and SSR markers detected different levels of genetic variability among and within broomrape populations. SSR markers analysis showed high level of genetic variation within the populations as revealed by high average values of Nei's gene diversity (H=0,75) and Shannon's information index (I=1,44), while genotyping with ISSR markers showed greater ability to discriminate genotypes according to Resolving power (Rp=7,24). Thus, the combined use of ISSR and SSR markers allowed the detection of higher polymorphism than either set of marker alone.

scholarly journals Research Genetic diversity of Ottelia acuminata (Hydrocharitaceae) from the Eastern Himalayas, revealed by ISSR markers

1970 ◽  
Vol 7 ◽  
pp. 56-63 ◽  
Author(s):  
Chunlin Long ◽  
Zhutan Jiang ◽  
Zhiling Dao
Keyword(s):  
Genetic Diversity ◽  
Gene Diversity ◽  
Natural Populations ◽  
Inter Simple Sequence Repeat ◽  
Issr Markers ◽  
Ex Situ ◽  
Eastern Himalayas ◽  
Average Value ◽  
Geographical Distances ◽  
High Level

Ottelia acuminata (Gagnep.) Dandy (Hydrocharitaceae), an endangered aquatic species, was investigated in the Eastern Himalayas, especially in Yunnan Province of Southwest China. The genetic diversity among seven populations was examined using inter-simple sequence repeat (ISSR) amplification markers. The field survey showed that 43.5% natural populations of O. acuminata have become extinct during the last 30 years. Among 13 remaining wild populations, eight (61.5%) are on the edge of extinction and only five (38.5%) were unaffected. For the study on seven populations based on ten primers, 147 clear and reproducible DNA fragments were generated, of which 144 (97.96%) were polymorphic. Within populations, however, the polymorphic bands (PPB) generated by ISSRs was 53 and occupied 36.05% in population B, and similarly within population J (51 and 34.69%, respectively). The results showed that genetic variation is much higher among populations of O. acuminata than within populations. Analyses of Nei’s gene diversity, genetic distance and Shannon’s index also agreed with these results. The average value of Nei’s gene diversity (h) equaled 0.3710. The coefficient of genetic differentiation (Gst) equaled 0.5487, which means that 54.87% of the total molecular variance existed among populations. Such a high level of divergence present among populations may be caused by the complex topography and separated habitats which effectively restrict gene flow. Moreover, there is a lack of significant association between genetic and geographical distances (r = 0.28889, P > 0.05) in the populations of O. acuminata. Therefore, we proposed an appropriate strategy for conserving the genetic resources of O. acuminata in the Eastern Himalayas; namely, rescuing and conserving the core populations in situ, while selecting and preserving more populations with fewer individuals from each population ex situ. Key-words: Ottelia acuminata, genetic diversity, conservation, Eastern Himalayas, Yunnan Plateau, China DOI: 10.3126/botor.v7i0.4374Botanica Orientalis – Journal of Plant Science (2010) 7: 56-63

scholarly journals Evaluation of Molecular and Morphological Diversity of Capparis Spinosa

2021 ◽  
Author(s):  
Noshin Mahmodi ◽  
Gholam-Reza Sharifi-Sirchi ◽  
Kianoosh Cheghamirza
Keyword(s):  
Genetic Diversity ◽  
Cluster Analysis ◽  
Genetic Relationships ◽  
Perfect Match ◽  
Morphological Diversity ◽  
Issr Markers ◽  
Zagros Mountains ◽  
Geographical Regions ◽  
Capparis Spinosa ◽  
Polymorphic Bands

Abstract The objective of this study was the evaluation of molecular and morphological diversity among 80 caper (Capparis spinosa L.) genotypes from the 12 regions of the central Zagros Mountains located in the west of Iran. The results showed a high level of morphological genetic variation among the caper samples. According to the morphological cluster analysis, 80 genotypes were clustered into five main groups. The 15 factors justified 78.7 % of the total variation based on factor analysis. ISSR primers produced a total of 108 polymorphic bands (85.04%) from 127 bands and the PIC for primers ranged from 0.01 to 0.52. SCoT primers produced a total of 165 polymorphic bands (86.84%) from 190 bands and the PIC for primers ranged from 0.06 to 0.55. Ordination and cluster analysis by ISSR markers showed that the genetic relationships among all accessions could be separated into three major groups and by SCoT markers separated into six groups. The results did not show a perfect match between the molecular diversity groupings and geographical regions, because many natural factors and human activities shape the amount and pattern of genetic diversity in a plant population. SCoT markers were more informative than ISSR markers for the assessment of genetic diversity of caper germplasm. The combined (ISSR+SCoT) markers haven't shown more information of genetic diversity than single analysis of ISSR and SCoT. The results indicated the existence of dispersion and different levels of morphological variation and molecular genetic diversity in the genotypes collected from west of Iran.

scholarly journals Genetic Relationships and Diversity Analysis in Turkish Laurel (Laurus Nobilis L.) Germplasm Using ISSR and SCoT Markers

2021 ◽  
Author(s):  
Abdurrahim YILMAZ ◽  
Vahdettin Ciftci
Keyword(s):  
Genetic Diversity ◽  
Gene Diversity ◽  
Genetic Relationships ◽  
Genetic Distances ◽  
Laurus Nobilis ◽  
Information Index ◽  
Geographical Regions ◽  
Polymorphism Rate ◽  
Amova Analysis ◽  
Breeding Techniques

Abstract Laurel (Laurus nobilis L.) has been used in the Mediterranean basin since ancient ages. Nowadays, Turkey, Mexico, Portugal, Italy, Spain, France, Algeria, and Morocco use aromatic leaves for commercial purposes, and Turkey is the largest exporter in the world. In this study, molecular characterization and genetic relationships of 94 Turkish laurel genotypes were determined by ISSR and SCoT markers. The experiment was conducted with 16 ISSR and 10 SCoT markers. While 348 of 373 bands were polymorphic with a 94.04% polymorphism rate, Nei's genetic distances ranged between 0.17 and 0.70 with 0.39 mean in ISSR. In SCoT, 175 of 227 bands were polymorphic with 76.07% polymorphism rate, and Nei's distances varied between 0.12 and 0.51. Sufficient genetic diversity determined with diversity parameters consisting the average Shannon's information index (ISSR:0.46, SCoT:0.35), the overall gene diversity (ISSR:0.19, SCoT:0.18), and the effective number of alleles (ISSR:1.52, SCoT:1.38). AMOVA (Analysis of molecular variance) revealed most of the variation was within genotypes (%96). Neighbor-joining algorithms, principal coordinate analysis (PCoA), and model-based structure resulted in harmony and clustered according to the geographical regions and provinces they collected. Genotypes were divided into two groups in ISSR and SCoT with UPGMA clustering resulting in a similar polymorphism distribution. The correlation coefficient (r) determined by marker systems' Nei's genetic distance matrices was 0.88. The results of the study put forward resources for advanced breeding techniques, and contribute to the preservation of genetic diversity, and management of genetic resources for the breeders.

scholarly journals Genetic Diversity Of Plukenetia Volubilis L. Assessed By ISSR Markers

2015 ◽  
Vol 46 (4) ◽  
pp. 145-153 ◽  
Author(s):  
M. Ocelák ◽  
P. Hlásná Čepková ◽  
I. Viehmannová ◽  
Z. Dvořáková ◽  
D.C. Huansi ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Diversity Index ◽  
Gene Diversity ◽  
Genetic Relationships ◽  
Diversity Indices ◽  
Issr Markers ◽  
Information Index ◽  
Geographical Distances ◽  
Plukenetia Volubilis ◽  
Polymorphic Bands

Abstract The diversity and genetic relationships in 173 sacha inchi samples were analyzed using ISSR markers. Thirty ISSR primers were used, only 8 showed variability in tested samples. ISSR fragments ranged from 200 to 2500 bp. The mean number of bands per primer was 12 and the average number of polymorphic bands per primer was 11. The lowest percentages of polymorphic bands (27%), gene diversity (0.103), and Shannon’s information index (0.15) were exhibited by the Santa Lucia population, which was also geographically most distant. This fact may be attributed to a very small size of this group. In contrast, the Dos de Mayo population exhibited the highest percentage of polymorphic bands (78%), and the Santa Cruz population the highest Nei’s gene diversity index (0.238) and Shannon’s information index (0.357). The obtained level of genetic variability was 36% among tested populations and 64% within populations. Although the diversity indices were low, a cluster analysis revealed 8 clusters containing mainly samples belonging to individual populations. Principal coordinate analysis clearly distinguished Chumbaquihui, Pucallpa, Dos de Mayo, and Aguas de Oro populations, the others were intermixed. The obtained results indicated the level of genetic diversity present in this location of Peru, although it is influenced by anthropological aspects and independent on the geographical distances.

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.

scholarly journals Molecular analysis of genetic diversity in population of Silybum marianum (L.) Gaertn in Egypt

2019 ◽  
Vol 17 (1) ◽  
Author(s):  
Marwa Hamouda
Keyword(s):  
Genetic Diversity ◽  
Electrophoretic Pattern ◽  
Issr Markers ◽  
Silybum Marianum ◽  
Inter Simple Sequence Repeats ◽  
Sds Page ◽  
Dna Pattern ◽  
Pharmaceutical Properties ◽  
High Level ◽  
Rapd And Issr

Abstract Background Silybum marianum L. Gaertn is a medicinal plant of unique pharmaceutical properties in the treatment of liver disorders and diabetic nephropathy. Biochemical (SDS-PAGE) and molecular markers such as randomly amplified polymorphic DNA (RAPD) and inter-simple sequence repeats (ISSR) technologies were used in this work to detect genetic diversity of 14 collections of Silybum marianum population in Egypt. Results The electrophoretic pattern of seed protein gave different molecular weight bands, ranging from 24 to 111 KDa with the presence of unique bands. RAPD results revealed a high level of polymorphism (73.2%) using 12 RAPD primers, but only eight of them gave reproducible polymorphic DNA pattern. Sixteen primers were used in the ISSR method; only ten of them yielded clearly identifiable bands. The percentage of polymorphism is about 80% of the studied samples. Conclusion The obtained data confirmed that SDS-protein, RAPD, and ISSR markers are important tools for genetic analysis for Silybum marianum and recommended to give accurate results.

Genetic Diversity of Wild Oat (Avena fatua)Populations from China and the United States

Weed Science ◽  
2007 ◽  
Vol 55 (2) ◽  
pp. 95-101 ◽  
Author(s):  
Runzhi Li ◽  
Shiwen Wang ◽  
Liusheng Duan ◽  
Zhaohu Li ◽  
Michael J. Christoffers ◽  
...  
Keyword(s):  
United States ◽  
Genetic Diversity ◽  
Gene Diversity ◽  
Genetic Relationships ◽  
The United States ◽  
Mantel Test ◽  
Wild Oat ◽  
Chinese Populations ◽  
Nei's Distance ◽  
The Impact

Weed genetic diversity is important for understanding the ability of weeds to adapt to different environments and the impact of herbicide selection on weed populations. Genetic diversity within and among six wild oat populations in China varying in herbicide selection pressure and one population in North Dakota were surveyed using 64 polymorphic alleles resulting from 25 microsatellite loci. Mean Nei's gene diversity (h) for six wild oat populations from China was between 0.17 and 0.21, and total diversity (HT) was 0.23. A greater proportion of this diversity, however, was within (Hs= 0.19) rather than among (Gst= 0.15) populations. For the wild oat population from the United States,h= 0.24 andHT= 0.24 were comparable to the values for the six populations from China. Cluster analysis divided the seven populations into two groups, where one group was the United States population and the other group included the six Chinese populations. The genetic relationships among six populations from China were weakly correlated with their geographic distribution (r= 0.22) using the Mantel test. Minimal difference in gene diversity and small genetic distance (Nei's distance 0.07 or less) among six populations from China are consistent with wide dispersal of wild oat in the 1980s. Our results indicate that the wild oat populations in China are genetically diverse at a level similar to North America, and the genetic diversity of wild oat in the broad spatial scale is not substantially changed by environment, agronomic practices, or herbicide usage.

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