Molecular markers to assess genetic diversity of Gentiana lutea L. from the Ukrainian Carpathians

2014 ◽  
Vol 13 (3) ◽  
pp. 266-273 ◽  
Author(s):  
Maryana Z. Mosula ◽  
Igor O. Andreev ◽  
Olena M. Bublyk ◽  
Vitaliy M. Mel'nyk ◽  
Iryna I. Konvalyuk ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Random Amplified Polymorphic Dna ◽  
Pcr Primers ◽  
Inter Simple Sequence Repeat ◽  
Resolving Power ◽  
Bootstrap Support ◽  
Gentiana Lutea ◽  
Discriminating Power ◽  
Index Value ◽  
Degree Of Differentiation

The aim of the study was to develop the system of polymerase chain reaction (PCR)-based markers for the assessment of genetic diversity and population genetic studies of Gentiana lutea L. as well as to determine the utility of two indices of marker informativeness. The informativeness was determined for 40 PCR primers of different types (random amplified polymorphic DNA, inter simple sequence repeat, inter-retrotransposon amplified polymorphism, resistance gene analog polymorphism and conserved DNA-derived polymorphism markers) by evaluating discriminating power (DL) and resolving power (Rp) in a sample of 30 plants from two populations. Analysis of correlation between the index value and the number of differentiated pairs of genotypes in the given sample revealed that DL is more efficient than Rp; therefore, we selected primers based on the DL value. In total, 12 primers with the largest values of DL were chosen. Analysis of genetic relationship among 86 plants from six populations showed that the number of bands produced by the three of selected primers was sufficient to give average bootstrap support across six key nodes in the dendrogram higher than 85%, while using six of the primers resulted in average bootstrap value exceeding 99%. Thus, a minimal set of three to six selected primers are sufficient for a quick assessment of genetic diversity of G. lutea populations, depending on the sample size and degree of differentiation between populations, while the rest of the primers with DL values above 0.8 may be used for ecogenetic surveys. Preliminary results obtained with selected primers indicate the moderate level of genetic variation within the species and significant differentiation among individual populations.

scholarly journals A comparative analysis of genetic diversity in Portuguese grape germplasm from ampelographic collections fit for quality wine production

2016 ◽  
Vol 14 (4) ◽  
pp. e0712 ◽  
Author(s):  
Isaura Castro ◽  
Olinda Pinto-Carnide ◽  
Jesús M. Ortiz ◽  
Vanessa Ferreira ◽  
Juan P. Martín
Keyword(s):  
Genetic Diversity ◽  
Random Amplified Polymorphic Dna ◽  
Morphological Characters ◽  
Inter Simple Sequence Repeat ◽  
Issr Markers ◽  
Molecular Techniques ◽  
Wine Production ◽  
Rapd And Issr ◽  
Simple Sequence

Grapevine cultivars diversity is vast and full of synonyms and homonyms. Up to few decades ago characterization of grapevine was based on morphological characters. In the last decades, molecular markers were developed and have been used as tools to study genetic diversity in a range of different plant species. Fifty-six Portuguese accessions representative of ‘Vinhos Verdes’ and ‘Douro’ Controlled Designations of Origin (DOC) were analysed through DNA fingerprints generated by Random Amplified Polymorphic DNA (RAPD) and Inter Simple Sequence Repeat (ISSR). The study aimed to compare the effectiveness of RAPD and ISSR molecular techniques in the detection of synonyms, homonyms and misnames. RAPD and ISSR analysis enabled the detection of 36 different band patterns, reducing in about 36% the initial material. Several accessions grown under different names, between and within collections, were confirmed as the same genotype, namely Gouveio/Verdelho, Sousão Douro/Vinhão and Arinto Oeste/Pedernã. Similarly, some homonyms/misnames were also identified, namely within Azal Tinto and Rabigato accessions. RAPD and ISSR markers revealed to be adequate molecular techniques for grapevine varieties fingerprinting with advantages over other molecular procedures, contributing for a good management of grapevine collections.

Genetic diversity analysis and metabolite profiling of pharmaceutical value Indigenous rice varieties of Tamil Nadu (Oryza sativa Linn.)

2021 ◽  
Vol 23 (10) ◽  
pp. 447-464
Author(s):  
Rajalakshmi Settu ◽  
◽  
Jayanthi Balakrishnan ◽  
Sarathi Kannan Dhavamani ◽  
Manoj Srinivas Ravi ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Oryza Sativa ◽  
Tamil Nadu ◽  
Random Amplified Polymorphic Dna ◽  
Rice Variety ◽  
Resolving Power ◽  
Bioactive Metabolites ◽  
Similarity Coefficients ◽  
Rice Varieties ◽  
Indigenous Rice Varieties

Evaluation of local indigenous medicinal rice (Oryza sativa Linn.) varieties using molecular and metabolic profiling plays dynamic role for unravelling the genetic variability and restorative bio actives. In the present study, 18 screened random decamer (RAPD) markers were used to analyze genetic diversity and relationship among 25 indigenous landraces and 1 commercial rice varieties (White ponni), and GC-MS profiling of phylogenetic clusters positioned 4 random indigenous rice varieties and 1 White ponni rice were documented for exploring bioactive metabolites. Random amplified polymorphic DNA (RAPD) analysis of twenty-six rice varieties of Tamil Nadu divulges significant genetic differentiation. The primers produced total of 92 bands with size ranges from 100-8500bp out of 74 were polymorphic bands indicating 80% polymorphism. The mean values of RAPD for polymorphism information content (PIC) of 0.268, effective multiple ratio (EMR) of 23.38, marker index (MI) of 7.39 and the resolving power (Rp) of 4.34. The primer OPA-02, OPD-08, OPF-13 produced maximum number of bands (8), OPAA-07 produced minimum number of band (2). The UPGMA dendrogram were constructed based on Jaccard’s similarity coefficients. The dendrogram resolved the indigenous rice varieties into 3 main clusters and 3 monoclades ranged from 0.467 to 0.860, commercial rice variety shows marginal ungrouped position of 1. In the 3-main clustering, based GC-MS profilling (methanol and acetone rice bran extracts) of Karuppu Kavuni, Karuthakar, Kottara samba, Kaivara samba and ungrouped position of White ponni revealed 88 distinctive bioactive metabolites. And profiling results substantiate that the traditional rice varieties hold promising therapeutic metabolites for sedentary lifestyle disorders.

Phylogenetic analysis and genetic diversity of Phytophthora palmivora causing black pod disease of cocoa in Malaysia.

2021 ◽  
Author(s):  
Wael Alsultan ◽  
Ganesan Vadamalai ◽  
Halimi Mohd Saud ◽  
Ahmad Khairulmazmi ◽  
Mui Yun Wong ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Random Amplified Polymorphic Dna ◽  
Phylogenetic Analyses ◽  
Inter Simple Sequence Repeat ◽  
Its Rdna ◽  
Phytophthora Palmivora ◽  
High Genetic Diversity ◽  
Study Results ◽  
Black Pod ◽  
Black Pod Disease

Black pod, caused by Phytophthora spp., occurs worldwide and is a major problem to cocoa farmers in Malaysia. Limited studies addressed causal agents of black pod disease of cocoa in Malaysia as well as their genetic diversity. Therefore, this study was initiated to isolate and identify Phytophthora from the main cocoa plantations infected by black pod in Malaysia using sequence analyses of the ITS rDNA, EF-1α, and COX I gene regions. A total of 36 Phytophthora isolates were obtained from infected cocoa plantations from five states of Malaysia in 2016 and 14 isolates in 2013. Six Phytophthora isolates obtained from durian crop in 2013 were also used in this study. Results of phylogenetic analyses of combined dataset of the ITS rDNA, COX I and EF-1α confirmed that all Phytophthora isolates belonged to P. palmivora. P. palmivora isolates obtained from cocoa and durian clustered into different subclades based on the three regions examined. The study also examined the genetic diversity within a population of 56 P. palmivora isolates using random amplified polymorphic DNA (RAPD) and Inter-simple sequence repeat (ISSR) markers. The results of both markers indicated relatively high diversity among P. palmivora isolates. The complete separation was based on host and year of isolation. The study suggests that one species of Phytophthora viz. P. palmivora, is responsible for black pod of cocoa in Malaysia. However, the relatively high genetic diversity and separation of isolates into different clades may suggest that P. palmivora has been introduced into Malaysia via different sources.

scholarly journals Inter simple sequence repeat markers to assess genetic diversity of the desert date (Balanites aegyptiaca Del.) for Sahelian ecosystem restoration

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Selouka Mint Abdelaziz ◽  
Leila Medraoui ◽  
Mohammed Alami ◽  
Ouafae Pakhrou ◽  
Meryem Makkaoui ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Natural Populations ◽  
Inter Simple Sequence Repeat ◽  
Resolving Power ◽  
Balanites Aegyptiaca ◽  
Marker Index ◽  
Information Index ◽  
Genetic Diversity And Structure ◽  
Two Populations ◽  
Amova Analysis

Abstract Drought and desertification are the major environmental constraints facing the Sahelian agro-ecosystems for decades. Assessing genetic diversity of native tree species is critical to assist ecosystems restoration efforts. Here we describe genetic diversity and structure of seven Balanites aegyptiaca L. natural populations distributed across the Sahelian-Saharan zone of Mauritania using 16 polymorphic ISSR primers. These generated 505 polymorphic bands. Polymorphism information content (PIC) varied from (0.13–0.29) with an average 0.23, marker index (MI) averaged 7.3 (range 3.3–10.3) and resolving power (RP) ranged from (4.53–14.6) with an average 9.9. The number of observed alleles (Na) ranged from (0.62–1.39), Effective number of alleles (Ne) varied from (1.26–1.37), Shannon’s information index (I) ranged from (0.25–0.36). AMOVA analysis showed that 80% of the genetic variation was fined within populations, which is supported by a low level of genetic differentiation between population (GST = 0.21) and an overall estimate of gene flow among populations (Nm = 1.9). The dendrogram based on Jaccard's similarity coefficient and the structure analysis divided the seven populations into two main clusters in which two populations from the Saharan zone were grouped. Our results provide baseline data for genetic conservation programs of this Sahelian neglected crop and with an important econ-ecological role.

Genetic Diversity of Stephanie kwangsiensis H. S. Lo and Salvia prionitis Hance after Transplanted and Micropropagated

2012 ◽  
Vol 518-523 ◽  
pp. 5460-5467
Author(s):  
Chuan Ming Fu ◽  
Yan Qin ◽  
Feng Luan Tang ◽  
Yun Ping Shi ◽  
Zhi Guo Zhao ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Tissue Culture ◽  
Gene Diversity ◽  
Random Amplified Polymorphic Dna ◽  
Inter Simple Sequence Repeat ◽  
Issr Markers ◽  
Chinese Herbs ◽  
High Genetic Diversity ◽  
Information Index ◽  
Rapd Pcr

Stephanie Kwangsiensis H. S. Lo and Salvia prionitis Hance were two rare and valuable Chinese herbs. Genetic diversity of the two plants were studied by using random amplified polymorphic DNA (RAPD) and inter simple sequence repeat (ISSR) markers after they were transplantation and tissue culture. Results indicated that Nei’s gene diversity (H), Shannon’s information index (I), the percentage of polymorphic loci (PPL) of source / transplantation / tissue culture materials of S. Kwangsiensis H. S. Lo were H=0.282 / 0.195/ 0.056, I=0.415 / 0.290 / 0.087, PPL=75.6% / 56.1% /19.5% based on RAPDs and H=0.295 / 0.292 / 0.111, I=0.445 / 0.435 / 0.166, PPL=85.3% / 85.3% / 32.8% based ISSRs. And the same parameters of source / transplantation / tissue culture materials of S. prionitis Hance were H=0.193 / 0.192 / 0.231, I=0.291 / 0.289 /0.347, PPL=57.8% / 57.2% / 68.6% based on RAPDs and H=0.217 / 0.217 / 0.155, I=0.327 / 0.326 /0.235, and PPL=64.2% / 64.2% / 49.1% based on ISSRs instead. For the transplanted materials, genetic diversity was slightly declining with the disappearance of adversity. And for the tissue culture materials, more genets sampled for tissue culture, less reduction of genetic diversity; and fewer genets sampled, more reduction of genetic diversity. In addition, high genetic diversity appearing in tissue culture materials of S. prionitis Hance partially generate from somatic mutations. And these mutations maybe related to RAPD-PCR regions and just had been checked out by RAPDs.

scholarly journals Garlic (Allium sativum L.): Overview on its Biology and Genetic Markers Available for the Analysis of Its Diversity in West Africa

2021 ◽  
pp. 1-10
Author(s):  
Timothée Kouassi Agbo So ◽  
Rabiou Abdou ◽  
Idi Saidou Sani ◽  
Abdoul Karim Toudou ◽  
Yacoubou Bakasso
Keyword(s):  
Genetic Diversity ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Allium Sativum ◽  
Fragment Length Polymorphism ◽  
Random Amplified Polymorphic Dna ◽  
Inter Simple Sequence Repeat ◽  
Ssrs Markers ◽  
Taxonomic Groups ◽  
Simple Sequence

Garlic belongs to the Allium genus, which includes more than 750 species divided into more than 60 taxonomic groups. It is cultivated in many countries throughout the world for the bulb and used as a spice and functional food. The plant vegetatively propagates. This review will focus on origins, biology, analysis of genetic diversity, pharmacological properties of garlic. It appears from this synthesis that the Allium sativum species is derived from Allium longicuspis and is native to Central Asia. Studies on the analysis of genetic diversity through morphological markers revealed a wide variation in the color, shape and number of cloves and the ability to flower. Biochemical markers such as Esterase (EST), Phosphoglucomutase (PGI), Malate Deshydrogenase (MDH), and Diaphorase (DIA as well as molecular markers such as Random Amplified Polymorphic DNA (RAPD), restriction fragment length polymorphism (RFLP), Amplified Fragment Length Polymorphism (AFLP), and Simple Sequence Repeats (SSRS) Inter-Simple Sequence Repeat (ISSR) were successfully used. RFLPs or RAPD are the most used for assessing genetic variability within asexually reproducing garlic species. Work using SSRs markers is limited in garlic relative to other crops.

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