Applicability of inter-primer binding site iPBS- retrotransposon marker system for the assessment of genetic diversity and population structure of Peruvian rosewood (Aniba rosaeodora Ducke) germplasm

2022 ◽  
Author(s):  
Faheem Shehzad Baloch ◽  
Stalin Juan Vasquez Guizado ◽  
Muhammad Tanveer Altaf ◽  
Ilker Yüce ◽  
Yeter Çilesiz ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Binding Site ◽  
Primer Binding Site ◽  
Marker System

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.

scholarly journals Consequences of geographical habitats on population structure and genetic diversity in Campanula spp.

2010 ◽  
Vol 1 (1) ◽  
pp. 5 ◽  
Author(s):  
Matteo Caser ◽  
Valentina Scariot ◽  
Paul Arens
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Binding Site ◽  
Geographical Location ◽  
Nucleotide Binding ◽  
Nonparametric Test ◽  
Nucleotide Binding Site ◽  
Gene Profiling ◽  
R Gene ◽  
Nbs Profiling

Characterization of populations by means of DNA techniques provides a tool for precise identification and a quantitative estimate of genetic diversity, crucial in evaluation of genetic fragmentation within and among populations. NBS profiling are PCR-based approaches that sample genetic variation in resistance genes (R-gene), and R gene analogs (RGA). To date, myb patterns have not been used for evaluating genetic diversity in other species. NBS primers are homologous to the conserved sequences in the Nucleotide-Binding-Site of the NBS-LRR class of R-genes. A total of 12 populations from five Campanula species (C. barbata L., C. latifolia L., C. rapunculoides L., C. spicata L. and C. trachelium L.), autochthonous of the West Italian Alps, were genotyped via nucleotide-binding site (NBS) and myb gene profiling. The selected markers produced a total of 361 bands, showing high levels of polymorphism. Genetic diversity among and within species and population structure was evaluated by different statistical analyses performed using TREECON software, Mantel Nonparametric Test, NTSYS package, AMOVA and STRUCTURE. The correlation between genetic variability and geographical location suggests that the five Campanula species have been subjected to long-term evolutionary processes consistent with the natural fragmentation of continuous mountains areas.

Inter-primer binding site (iPBS) markers reveal the population genetic diversity and structure of tropical climbing Cissampelopsis (Asteraceae) in Thailand

2020 ◽  
Vol 21 (9) ◽  
Author(s):  
ONGKARN VANIJAJIVA ◽  
Pimwadee Pornpongrungrueng
Keyword(s):  
Genetic Diversity ◽  
Binding Site ◽  
Population Genetic ◽  
Regional Distribution ◽  
Primer Binding Site ◽  
Evergreen Forest ◽  
Gene Pools ◽  
Population Genetic Diversity ◽  
Genetic Diversity And Structure ◽  
Amova Analysis

Abstract. Vanijajiva O, Pornpongrungrueng P. 2020. Inter-primer binding site (iPBS) markers reveal the population genetic diversity and structure of tropical climbing Cissampelopsis (Asteraceae) in Thailand. Biodiversitas 21: 3919-3928. Cissampelopsis is a small climbing tropical Asian genus of Asteraceae-Senecioneae. In Thailand, the genus is represented by two species, C. corifolia and C. Volubilis, distributed through the mountain evergreen forest. Study on the genetic diversity and structure of populations of both Cissampelopsis species provide better understanding of the biology and pattern of species diversification in the genus. To identify the genetic diversity, we used the inter-primer binding site (iPBS) retrotransposon system, in 96 accessions of Cissampelopsis species collected from different regions in Thailand. A total of 120 iPBS bands were scored as presence⁄ absence characters. Results from UPGMA and PCoA analyses indicated that C. corifolia and C. volubilis are different species. Genetic diversity and genetic differentiation among and within populations of C. volubilis is higher than C. corifolia. Molecular Variance (AMOVA) analysis of both species indicated that the genetic variance value within populations is higher than among populations of each species. Bayesian model-based STRUCTURE analysis detected two gene pools for both Cissampelopsis and showed admixture within individuals. Differences among the two Cissampelopsis species, in total diversities and levels of population differentiation, indicated that the genetic structure of Cissampelopsis populations are congruent with long-lived perennial habit with regional distribution, even for congeneric species, may vary considerably. This study suggests the effectiveness of the iPBS marker system to estimate the population genetic diversity and structure of Cissampelopsis genotypes.

Genetic diversity and population structure of Populus yunnanensis revealed by SSR markers

2020 ◽  
Vol 52 (6) ◽  
Author(s):  
Anpei Zhou ◽  
Dan Zong ◽  
Peihua Gan ◽  
Yao Zhang ◽  
Dan Li ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Ssr Markers
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