scholarly journals Exploring the Genetic Diversity and Population Structure of Turkish Laurel Germplasm by the iPBS-Retrotransposon Marker System

Agronomy ◽  
2019 ◽  
Vol 9 (10) ◽  
pp. 647 ◽  
Author(s):  
Ünal Karık ◽  
Muhammad Azhar Nadeem ◽  
Ephrem Habyarimana ◽  
Sezai Ercişli ◽  
Mehtap Yildiz ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Gene Diversity ◽  
Diversity Indices ◽  
Primer Binding Site ◽  
Neighbor Joining ◽  
Marker System ◽  
Information Index ◽  
Geographical Regions ◽  
The World

Laurel is a medicinally important plant and is known to the world for its essential oil. Turkey is the main market in the laurel leaf trade by sharing about 90% of the world trade. Here we made an effort to elucidate genetic diversity and population structure of 94 Turkish laurel genotypes collected from 26 provinces and four geographical regions using inter-primer binding site (iPBS) retrotransposon markers. A total of 13 most polymorphic primers were selected which yielded 195 total bands, of which 84.10% were found polymorphic. Mean polymorphism information content (PIC) was (0.361) and diversity indices including mean effective number of alleles (1.36), mean Shannon’s information index (0.35) and overall gene diversity (0.22) revealed the existence of sufficient amount of genetic diversity in the studied plant material. Most diversity was found in genotypes collected from the Mediterranean region. Analysis of molecular variance (AMOVA) revealed that most of the variation (85%) in Turkish laurel germplasm is due to differences within populations. Model-based structure, principal coordinate analysis (PCoA) and neighbor-joining algorithms were found in agreement and clustered the studied germplasm according to their collection provinces and regions. This is a very first study exploring the genetic diversity and population structure of laurel germplasm using iPBS-retrotransposon marker system. We believe that information provided in this work will be helpful for the scientific community to take more interest in this forgotten but the medicinally important plant.

Exploring the genetic diversity and population structure of Turkish common bean germplasm by the iPBS-retrotransposons markers

2018 ◽  
Author(s):  
Muhammet Fatih Aydin ◽  
Faheem Shehzad Baloch
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Common Bean ◽  
Gene Diversity ◽  
Developed Countries ◽  
Least Developed Countries ◽  
Information Index ◽  
Geographical Regions ◽  
Group A ◽  
Growth Habits

Present study was aimed to investigate the genetic diversity and population structure of Turkish common bean germplasm. A total of 96 bean genotypes were characterized with iPBS-retrotansposons that yielded a mean polymorphism information contents of 0.8. Mean gene diversity and Shannon information index were 0.14 and 0.25, respectively. Neighbor joining analysis divided the bean genotypes into two main group (A and B) according to their geographical regions, growth habits and seed size. Bingol-l7, Sivas-14 and Hakkari-11 genotypes were found very distinct and can be used as candidate parents for the bean breeding. The higher efficiency and reproducibility of iPBS-retrotransposons was witnessed in common bean as compared to earlier studies using the same marker system. Results of this study will boost up the investigators for genotyping the larger germplasm of common bean with minimum laboratory infrastructure in developing and least developed countries.

scholarly journals Genetic diversity and population structure of endangered rosewood from the Peruvian Amazon using ISSR markers

2020 ◽  
Vol 50 (3) ◽  
pp. 204-212
Author(s):  
Stalin Juan Vasquez GUIZADO ◽  
Muhammad Azhar NADEEM ◽  
Fawad ALI ◽  
Muzaffer BARUT ◽  
Ephrem HABYARIMANA ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Gene Diversity ◽  
Population Level ◽  
Diversity Indices ◽  
Issr Markers ◽  
Neighbor Joining ◽  
Peruvian Amazon ◽  
Over Exploitation ◽  
Issr Primers

ABSTRACT Rosewood, Aniba rosaeodora is an endangered species in Amazon forests and its natural stands have been heavily depleted due to over-exploitation for the cosmetic industry. This study aimed to investigate the genetic diversity and population structure of 90 rosewood accessions from eight localities in the Peruvian Amazon through 11 Inter Simple Sequence Repeats (ISSR) primers. The ISSR primers produced a sum of 378 bands, of which 375 (99.2%) were polymorphic, with an average polymorphism information content (PIC) value of 0.774. The mean effective number of alleles (Ne), Shannon informative index (I), gene diversity (He) and total gene diversity (Ht) were 1.485, 0.294, 0.453 and 0.252, respectively. Analysis of molecular variance (AMOVA) showed the presence of maximum variability within populations (88%). The Structure algorithm, neighbor joining and principal coordinate analysis (PCoA) grouped the 90 rosewood accessions into three main populations (A, B and C). Diversity indices at the inter-population level revealed a greater genetic diversity in population A, due to higher gene flow. The neighbor-joining analysis grouped populations A and B, while population C was found to be divergent at the inter population level. We concluded that population A reflects higher genetic diversity and should be prioritized for future management and conservation plans.

Genetic diversity and population structure of pencil yam (Vigna lanceolata) (Phaseoleae, Fabaceae), a wild herbaceous legume endemic to Australia, revealed by microsatellite markers

Botany ◽  
2015 ◽  
Vol 93 (3) ◽  
pp. 183-191 ◽  
Author(s):  
Phakchana Nubankoh ◽  
Sarocha Pimtong ◽  
Prakit Somta ◽  
Sujinna Dachapak ◽  
Peerasak Srinives
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Gene Diversity ◽  
Taxonomic Revision ◽  
Neighbor Joining ◽  
Complex Species ◽  
Vigna Species ◽  
Vigna Umbellata ◽  
Its Gene ◽  
Simple Sequence

Pencil yam (Vigna lanceolata Benth.) (Phaseoleae, Fabaceae) is a herbaceous legume endemic to Australia. A previous morphological study suggested that pencil yam is a complex species of two or more related taxa with seven distinct morphological types (morphotypes) and, thus, taxonomic revision is necessary. In this study, we assessed genetic diversity and determined the genetic structure of a pencil yam collection of 62 accessions from seven morphotypes using 18 microsatellite (simple sequence repeat) markers with the aim to provide information for taxonomic study. In total, 138 alleles were detected with a mean of 7.67 alleles per locus. Polymorphism information content per marker varied between 0.06 and 0.90 with a mean of 0.61, while the overall gene diversity was 0.62. Bayesian clustering, principal coordinate, and neighbor-joining analyses consistently revealed that these accessions are grouped into two subpopulations with difference in number of alleles, allelic richness, and gene diversity. The population structure was not related to either morphotype or geographical origin. Gene diversity of V. lanceolata was higher than that of wild Vigna radiata (L.) Wilczek and wild Vigna umbellata (Thunb.) Ohwi & Ohashi, comparable with that of wild Vigna mungo (L.) Hepper, Vigna exilis Tateishi & Maxted, and Vigna grandiflora (Prain) Tateishi & Maxted, and lower than that of wild Vigna angularis (Willd.) Ohwi & Ohashi. These results indicated that the taxonomy of V. lanceolata should be revised and that its gene diversity was moderate compared with the other wild Vigna species.

scholarly journals Genetic Diversity and Population Structure of Endangered Catfish Rita rita (Hamilton, 1822) Revealed by Heterologous DNA Microsatellite Markers

2021 ◽  
Vol 34 (2) ◽  
Author(s):  
MUHAMMAD FORHAD ALI ◽  
◽  
MD. RAFIQUL ISLAM SARDER ◽  
MOHAMMAD MATIUR RAHMAN ◽  
MD. FAZLUL AWAL MOLLAH ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Gene Diversity ◽  
Polymorphic Information Content ◽  
Genetic Difference ◽  
Information Index ◽  
Hardy Weinberg Equilibrium ◽  
High Gene ◽  
High Level ◽  
Dna Microsatellite

Genetic information is essential for conservation and future aquaculture development of the endangered catfish Rita rita (Hamilton, 1822). Two hundred catfish, R. rita, 50 from four rivers, the Old Brahmaputra, Jamuna, Meghna and Kangsa were collected and analysed to evaluate the genetic diversity and population structure using five microsatellite primers (Cba06-KUL, Cba08-KUL, Cba09-KUL, Phy03-KUL and Phy07-KUL). Four of the five amplified loci were found polymorphic (P95) in all the populations and 46 alleles were recorded with 9 to 14 alleles per locus. Differences were observed in the total number of alleles ranging from 41 to 44, effective number of alleles from 29.96 to 37.46, observed heterozygosity from 0.57 to 0.76, Shannon’s information index from 2.09 to 2.30 and polymorphic information content from 0.84 to 0.88 among the four populations. Results exposed the highest levels of genetic diversity in the Meghna population while the lowest in the Kangsa population of R. rita. All the populations were significantly deviated (P < 0.001) from the Hardy-Weinberg equilibrium for all the loci. Nei’s genetic distance between populations ranged 0.007 to 0.017 with low overall genetic difference FST = 0.011 and high gene flow Nm = 24.333, indicating that R. rita populations were not subdivided. This study revealed a high level of gene diversity with deficiency in genetic heterogeneity in all the populations of R. rita, emphasising natural management, conservation and rehabilitation measures of this species.

scholarly journals Gene-Targeted markers to assess genetic diversity and population structure within Tunisian Phoenix dactylifera L. cultivars

2020 ◽  
Vol 69 (1) ◽  
pp. 29-35
Author(s):  
Rhouma-Chatti Soumaya ◽  
Choulak Sarra ◽  
Moussa Maha ◽  
Chatti Khaled ◽  
Chatti Noureddine
Keyword(s):  
Genetic Diversity ◽  
Date Palm ◽  
Gene Diversity ◽  
Phoenix Dactylifera ◽  
Start Codon ◽  
Marker System ◽  
Average Value ◽  
Information Index ◽  
Scot Marker ◽  
Phoenix Dactylifera L

AbstractGenetic variability in date palm genotypes collected from different regions of southern Tunisia was analyzed using a Start Codon Targeted (SCoT) marker system. Thirty-one accessions collected from three locations were investigated. One hundred and nine amplicons were produced among which 84 % were polymorphic. The PIC value and the Rp values testified of the efficiency of used primers. The percentage of polymorphic loci (Pp) varied from 44.57 to 83.70 %, Nei‘s gene diversity (H) from 0.175 to 0.273 with a mean of 0.228, and Shannon‘s information index (I) values ranging from 0.257 to 0.409 with an average value of 0.338 were illustrated. The Tunisian date palm populations exhibited high genetic differentiation (GST = 0.319) and gene flow (Nm = 1.063). The AMOVA analysis presented 70 % of the variation within the population and 30 % of the variation between them. Phylogenetic analysis and the Bayesian clustering approach also revealed high genetic variation among genetic variants with a net divergence of the wild insular population of Kerkennah from other cultivars. The present investigation suggests the effectiveness of the SCoT marker system to estimate the genetic diversity of Phoenix dactylifera genotypes.

scholarly journals Diversity and phylogeny of saffron (Crocus sativus L.) accessions based on iPBS markers

Genetika ◽  
2018 ◽  
Vol 50 (1) ◽  
pp. 33-44 ◽  
Author(s):  
Mahdi Bayat ◽  
Reza Amirnia ◽  
Hakan Özkan ◽  
Aysun Gedik ◽  
Duygu Ates ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Trees ◽  
Gene Diversity ◽  
Low Cost ◽  
Crocus Sativus ◽  
Phylogenetic Structure ◽  
Information Index ◽  
Geographical Regions ◽  
High Efficient ◽  
Crocus Sativus L

This study sought to measure genetic diversity and phylogenetic structure among 196 individuals of saffron from 20 geographically separate accessions from Iran, Spain and Turkey using retrotransposon derived iPBS markers. Twenty-eight primers amplified a total of 179 polymorphic alleles with an average of 6.4 bands per primer. The average of parameters shannon's information index, genetic distance and gene diversity was 0.483, 0.286 and 0.841 respectively. Polymorphic information index ranged from 0.407 to 0.953 with an average of 0.824. Primers 2298, 2229 and 2393 with 0.953, 0.943 and 0.943 PIC respectively, identified as the most informative primers in this study. The results of phylogenetic trees showed that twenty saffron accessions were placed into four major clusters that matched with their geographical locations completely. These results are supported by principal coordinate analysis. Overall, we can confirm that iPBS markers as low cost and high efficient molecular markers are a powerful DNA fingerprinting for assessing genetic diversity and phylogenetic analysis among saffron accessions originating from different geographical regions.

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.

scholarly journals Genetic diversity and population structure of rice stripe virus in China

2009 ◽  
Vol 90 (4) ◽  
pp. 1025-1034 ◽  
Author(s):  
Tai-Yun Wei ◽  
Jin-Guang Yang ◽  
Fu-Long Liao ◽  
Fang-Luan Gao ◽  
Lian-Ming Lu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Yunnan Province ◽  
Southwest China ◽  
Eastern China ◽  
Rice Stripe Virus ◽  
Genetic Distances ◽  
Geographical Regions ◽  
Strong Negative Selection ◽  
Recent Outbreak

Rice stripe virus (RSV) is one of the most economically important pathogens of rice and is repeatedly epidemic in China, Japan and Korea. The most recent outbreak of RSV in eastern China in 2000 caused significant losses and raised serious concerns. In this paper, we provide a genotyping profile of RSV field isolates and describe the population structure of RSV in China, based on the nucleotide sequences of isolates collected from different geographical regions during 1997–2004. RSV isolates could be divided into two or three subtypes, depending on which gene was analysed. The genetic distances between subtypes range from 0.050 to 0.067. The population from eastern China is composed only of subtype I/IB isolates. In contrast, the population from Yunnan province (southwest China) is composed mainly of subtype II isolates, but also contains a small proportion of subtype I/IB isolates and subtype IA isolates. However, subpopulations collected from different districts in eastern China or Yunnan province are not genetically differentiated and show frequent gene flow. RSV genes were found to be under strong negative selection. Our data suggest that the most recent outbreak of RSV in eastern China was not due to the invasion of new RSV subtype(s). The evolutionary processes contributing to the observed genetic diversity and population structure are discussed.

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