scholarly journals Assessment of Genetic Diversity in Bamboo Accessions of India Using Molecular Markers

2015 ◽  
Vol 3 (2) ◽  
pp. 330-336
Author(s):  
Bharat Gami ◽  
Bakhtiyar Alam Syed ◽  
Beena Patel
Keyword(s):  
Genetic Diversity ◽  
Abiotic Stress ◽  
Genetic Distance ◽  
Stress Resistance ◽  
Inter Simple Sequence Repeat ◽  
Biofuel Production ◽  
Bambusa Balcooa ◽  
Bambusa Vulgaris ◽  
Minimum Genetic Distance ◽  
Wide Scale

Bamboo is an important grass with wide scale applications in paper industries, medicines, constructions industries. It is potential feedstock for advanced biofuel production due to its favourable characteristics, natural abundance, rapid growth, perennial nature and higher CO2 sequestration. The objective of this study is to understand genetic diversity between the bamboo accessions with respect to geographical origin to correlate molecular information with feedstock characterization and adaptation to abiotic stress. In this study, genomic DNA was extracted from twenty bamboo accessions collected from different regions of India and genetic variations were assessed by inter simple sequence repeat (ISSR) based molecular marker approach using 8 primers. Maximum genetic distance was observed between Bambusa wamin-Itanagar & B. ventricosa-Durg (0.48221) & minimum genetic distance between Bambusa balcooa-Modasa & Bambusa balcooa-Tripura (0.00787). Bambusa balcooa and Bambusa vulgaris were genetically similar as compared to other accessions. The genetic distance is independent of geographical distance for the bamboo accessions considered in this study. The findings of this study will help to understand the degree of differences between bamboo accessions under the same environmental conditions and to identify the representative accessions that can be used for abiotic stress resistance studies. The information can be explored for screening of closely related bamboo accessions for abiotic stress resistance screening trials.Int J Appl Sci Biotechnol, Vol 3(2): 330-336 DOI: http://dx.doi.org/10.3126/ijasbt.v3i2.12587 

scholarly journals Genetic diversity of Pongamia pinnata in Bali, Indonesia using Inter Simple Sequence Repeat markers

2019 ◽  
Vol 20 (8) ◽  
Author(s):  
Ni Luh Arpiwi ◽  
I Gusti Ayu Sugi Wahyuni ◽  
I Ketut Muksin
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Simple Sequence Repeat ◽  
Inter Simple Sequence Repeat ◽  
Pongamia Pinnata ◽  
Sequence Repeat ◽  
Binary Matrix ◽  
Simple Sequence Repeat Markers ◽  
Group I ◽  
Simple Sequence

Abstract. Arpiwi NL, Wahyuni IGAS, Muksin IK. 2019. Genetic diversity of Pongamia pinnata in Bali, Indonesia using Inter Simple Sequence Repeat markers. Biodiversitas 20: 2134-2142. Pongamia pinnata (L.) Pierre is a member of family Leguminosae that produces seed oil for biodiesel feedstock. The aim of the present study was to determine genetic diversity of pongamia trees that grow in Bali using Inter Simple Sequence Repeat (ISSR) markers. This study is important to support the breeding program for the improvement of the biodiesel producing species. Leaf samples were taken from 26 pongamia trees grown on northern and southern coastal areas of Bali. Genomic DNA was isolated from fresh leaves sample and was amplified by Polymerase Chain Reaction (PCR) using 9 ISSR primers. The banding patterns of DNA after PCR were scored and tabulated into a binary matrix. Genetic distance was generated by pairwise distance using composite maximum likelihood. A dendrogram was constructed using Unweighted Pair Group Method Arithmetic (UPGMA) method. The binary matrix was further analyzed for Nonmetric Multidimensional Scaling (NMDS) with Primer E V.6 software. DNA concentrations ranged from 98.59-100.55 ng/μL with sufficient quality for PCR. The number of alleles for 9 primers was 43, the number of the polymorphic band was 35, and the number of monomorphic bands was 8. Percentage of polymorphism ranged from 50 to 100%. Cluster analysis of 26 DNA of pongamia trees showed that the trees were grouped into two, namely group I and II. Group I consisted of two trees only, namely Uma Anyar 1 and Penarukan 1. Group II consisted of 24 pongamia trees which were divided into 3 subgroups, namely IIA, IIB, and IIC with close genetic distance. Analysis of NMDS supported cluster analysis that 23 out of 26 pongamia trees had close genetic distance, and possibly they come from a similar source. Genetic diversity of pongamia in Bali needs to be widen possibly by the introduction of new planting materials from across Indonesia or seed procurement from different sources.

scholarly journals Genetic Characterization of Swamp Eel of Bangladesh Through Dna Barcoding and Rapd Techniques

2021 ◽  
Vol 46 (2) ◽  
pp. 117-131
Author(s):  
Md Minhazul Abedin ◽  
Md Mostavi Enan Eshik ◽  
Nusrat Jahan Punom ◽  
Mst Khadiza Begum ◽  
Mohammad Shamsur Rahman
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Dna Barcoding ◽  
Rapd Analysis ◽  
Indian Subcontinent ◽  
Export Demand ◽  
Phylogenetic Tree Analysis ◽  
Fish Samples ◽  
Minimum Genetic Distance ◽  
Swamp Eel

The freshwater air-breathing swamp eel Monopterus spp. are native to the freshwater of Bangladesh and throughout the Indian subcontinent. To identify the different swamp eel species and to check the genetic diversity among them, a total of twelve swamp eel specimens were collected from four districts (Tangail, Bogura, Bagerhat and Sylhet) representing the four division of Bangladesh. The extracted DNA from twelve fish samples was amplified by the PCR technique for DNA barcoding and RAPD analysis. Among 12 specimens, 8 specimens showed a 95-100% similarity with M. cuchia species published in the NCBI GenBank database and BOLD system. The studied mct3 (collected from Tangail region), mcs1, mcs2 and mcs3 (collected from Sylhet region) specimens showed about 83% homology with Ophisternon sp. MFIV306-10 as per BLAST search; whereas BOLD private database showed 99% similarity with Ophisternon bengalense (Bengal eel). From the phylogenetic tree analysis, 8 samples were clustered with M. cuchia and 4 samples showed similarity with Ophisternon sp. MFIV306-10 and Ophisternon bengalense _ANGBF45828-19. In RAPD-PCR based analysis, it was found that the maximum genetic distance (1.6094) was observed between mcba2 and mcs3, while between mct1 and mct2, the minimum genetic distance was 0.000. A total of 192 bands, of which 35 were polymorphic with 17.88% polymorphisms among swamp eel species and the size of the amplified DNA fragments ranged from 250 to 1800 bp. The information on DNA barcoding and RAPD analysis help measure the genetic diversity among swamp eel species, ensure the reliability of the published taxonomic information, and initiate proper management programs to conserve these vulnerable species to meet future export demand. Asiat. Soc. Bangladesh, Sci. 46(2): 117-131, December 2020

scholarly journals Genetic diversity of Panax vietnamensis var. langbianensis populations in Lam Vien plateau - Vietnam detected by inter simple sequence repeat (ISSR) markers

2020 ◽  
Vol 17 (4) ◽  
pp. 651-661
Author(s):  
Le Ngoc Trieu ◽  
Nong Van Duy ◽  
Tran Van Tien
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Simple Sequence Repeat ◽  
Inter Simple Sequence Repeat ◽  
Issr Markers ◽  
Sequence Repeat ◽  
New Variety ◽  
Gene Differentiation ◽  
The Stability ◽  
Simple Sequence

Panax vietnamensis var. langbianensis is a new variety from Lam Vien plateau of Vietnam. In this study, inter simple sequence repeat (ISSR) markers were employed to investigate the genetic diversity and variability of 115 individuals belonging to two naturally distributed populations of this variety, which classified by habitat. Genetic diversity at the taxon level was high (HeT = 0.284 and PPBT = 97.2 %).   The result showed lightly higher genetic diversity in population in Lac Duong region (HeLD= 0.228 and PPBLD = 81.5 %) as compared to those located in Dam Rong region (HeDR= 0.213 and PPBDR = 79.4 %). The interpopulation gene differentiation was high (GST Total = 0.221) with the genetic distance among populations was DLD-DR = 0.191. Gene flow within populations was Nm = 0.8793. In Lac Duong population, the genetic diversity of older group (HeLD O = 0.233; PPBLD O = 77.1%) was higher than of younger group (HeLD Y = 0.214; PPBLD Y = 72.4 %) and the intergroup gene differentiation was GSTDL = 0.0205 with the genetic distance between these two group was DLD O-Y  = 0.0061 showed the risk of reduction in genetic diversity. In Dam Rong population, the genetic diversity of older group (HeDR O = 0.204; PPBDR O = 75.2 %) was equal to younger group (HeDR Y = 0.209; PPBDR Y = 72.7 %) and the intergroup gene differentiation was GSTDR = 0.0304 with the genetic distance between them was DDR O-Y = 0.01393 showed the stability in genetic diversity. Data for genetic diversity and variation from this study can be used to further investigate and protect this variety for conservation and development purposes and for sustainable exploiting and use of these valuable natural resources.

scholarly journals Determination of Genetic Diversity Based on RAPD molecular Marker and ParARF3 Gene Expressions in some Apricot Genotypes in Iraq

2021 ◽  
Vol 34 (2) ◽  
pp. 60-74
Author(s):  
Ali S. A. Al-Janabi ◽  
Arshad N. Alhasnawi
Keyword(s):  
Gene Expression ◽  
Genetic Diversity ◽  
Genetic Distance ◽  
Genetic Similarity ◽  
Marine Alga ◽  
Gene Expressions ◽  
Negative Results ◽  
Minimum Genetic Distance ◽  
Relative Gene

Employing DNA markers allowed determining genetic diversity and relationships amongst five apricot genotypes. In this study, two relative gene expressions pertaining to ParARF3 gene, which could be distinguished from the genotypes that were exposed to various concentrations of marine alga treatments. As per our results, screening of seven primers with the DNA of 5 apricot genotypes was done, and six primers were generated while the primer OPN–16 gave negative results. The total quantity of fragments generated by 6 primers was 80 at an average of 13.33 fragments ̸primer. The highest unique percentage band depicted in U-17 touched 23%, and the total number of polymorphic bands touched 17 fragments with the average reaching 2.83 fragments ̸primer. The number of monomorphic lied in the range of 5 to 10, with a total of 47 monomorphic. Primer M 32 yielded the highest number of monomorphic bands reaching 10. Between Zaghenia and Zinni, a maximum genetic distance value of 0.8 was reached with less similarity value of 20%. A minimum genetic distance value of 0.44721 was noted between Kaisy and Baia while the high similarity value touched 55.3%. According to the cluster tree analysis, the genotypes were generally split into two key groups: A and B. The Zinni group, which included one apricot genotype, showed genetic similarity of 20% with the other genotypes present in B group. The B group was split into two sub-clusters B1 and B2 and the genetic similarity reached 44%. The ParARF3 relative gene expression pertaining to Zinni genotypes was second as well as convergent with that of gene expression for Zaghenia genotype results. Baia and Kaisy genotypes lied in between the lowest and highest ParARF3 value gene expression exposed to Marine Alga. These outcomes showed that RAPD markers offer an effectual alternative for the plant species genetic characterisation.

Genetic diversity of the Andean tuber-bearing species, oca (Oxalis tuberosa Mol.), investigated by inter-simple sequence repeats

Genome ◽  
2006 ◽  
Vol 49 (1) ◽  
pp. 8-16 ◽  
Author(s):  
A Pissard ◽  
M Ghislain ◽  
P Bertin
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Vegetative Propagation ◽  
Inter Simple Sequence Repeat ◽  
Group Method ◽  
Factorial Correspondence Analysis ◽  
Oxalis Tuberosa ◽  
Reproduction Strategy ◽  
Simple Sequence

The Andean tuber-bearing species, Oxalis tuberosa Mol., is a vegetatively propagated crop cultivated in the uplands of the Andes. Its genetic diversity was investigated in the present study using the inter-simple sequence repeat (ISSR) technique. Thirty-two accessions originating from South America (Argentina, Bolivia, Chile, and Peru) and maintained in vitro were chosen to represent the ecogeographic diversity of its cultivation area. Twenty-two primers were tested and 9 were selected according to fingerprinting quality and reproducibility. Genetic diversity analysis was performed with 90 markers. Jaccard's genetic distance between accessions ranged from 0 to 0.49 with an average of 0.28 ± 0.08 (mean ± SD). Dendrogram (UPGMA (unweighted pair-group method with arithmetic averaging)) and factorial correspondence analysis (FCA) showed that the genetic structure was influenced by the collection site. The two most distant clusters contained all of the Peruvian accessions, one from Bolivia, none from Argentina or Chile. Analysis by country revealed that Peru presented the greatest genetic distances from the other countries and possessed the highest intra-country genetic distance (0.30 ± 0.08). This suggests that the Peruvian oca accessions form a distinct genetic group. The relatively low level of genetic diversity in the oca species may be related to its predominating reproduction strategy, i.e., vegetative propagation. The extent and structure of the genetic diversity of the species detailed here should help the establishment of conservation strategies.Key words: oca, Oxalis tuberosa, Andean tuber, genetic diversity, ISSR, vegetative propagation.

scholarly journals Estimation of Genetic Diversity among Canola Accessions using Simple Sequence Repeat Markers

2021 ◽  
Vol 8 (4) ◽  
pp. 86-94
Author(s):  
Jaleel Ahmad ◽  
Muhammad Baber ◽  
Wajid Nazeer ◽  
Sana Hamdullah ◽  
Aleena Ahmad Somroo
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Gene Diversity ◽  
Molecular Genetic ◽  
Genetic Distances ◽  
Genetic Studies ◽  
Molecular Genetic Basis ◽  
Ssr Primers ◽  
Minimum Genetic Distance ◽  
Simple Sequence

Genetic studies through molecular markers proved important to find out the genetic diversity of canola. In this study, 50 lines of canola were used to find the polymorphism using 15 SSR primers and investigated the genetic diversity, PIC values, frequency-based genetic distance, and allelic frequencies. Mean gene diversity, frequency-based genetic distance, and PIC values were 0.8777, 0.233 and 0.8666, respectively for the canola lines. A good range of genetic diversity was found among studied canola lines with value 85.91% polymorphism. Maximum and minimum genetic distances among 50 lines were 1 and 0.26, respectively. Accessions ACC-26068, ACC-24241, ACC-24244, ACC-24233, ACC-24423 and ACC-24224 have maximum genetic distance. Accessions ACC-24879 and ACC-24169 had minimum genetic distance i.e., 0.26. Dendrogram based on genetic distances showed four main clusters that were further dividing into several sub-clusters. The primers utilized in the present study, were valuable to identify different accessions of canola to find the variability present. This variability will be helpful to initiate the breeding program with their molecular genetic basis.

scholarly journals ISSR based analysis of genetic diversity in some endangered species of Allium subg. Melanocrommyum

Genetika ◽  
2018 ◽  
Vol 50 (1) ◽  
pp. 59-68
Author(s):  
Jalal Rezaei ◽  
Zare Mehrjerdi ◽  
Hassan Mastali
Keyword(s):  
Genetic Diversity ◽  
Endangered Species ◽  
Genetic Distance ◽  
Gene Diversity ◽  
Program Planning ◽  
Inter Simple Sequence Repeat ◽  
Issr Markers ◽  
Polymorphic Band ◽  
Upgma Cluster Analysis ◽  
Two Populations

Melanocrommyum, a subgenus of the Allium genus, is found in different regions of Iran and is in danger of extinction due to excessive exploitation. This study aimed to determine the genetic diversity in 170 individuals representing 17 wild populations belonging to six endangered species of Allium subg. Melanocrommyum using inter simple sequence repeat (ISSR) markers. The 10 selected ISSR primers produced 178 polymorphic fragments (100%). Polymorphic band number varied from 12 (primer 8) to 22 (primer 2). The average observed number of alleles, effective number of alleles, Shannon?s indices and Nei?s gene diversity were 1.48, 1.2, 0.2 and 0.1, respectively. According to Nei?s genetic distance, the lowest genetic distance (0.048) was observed among both two populations of A. elburzense (Emamzadeh Ebrahim and Kamelat), and two populations of A. subakaka (Jame Shoran and Ghalelan) while the highest distance (0.097) was observed among a population of A. kurdistanicum (Taze Abad Oryeh) with both A. pseudobodeanum (Shen Jari), and A. derderianum (Dareh Oson) populations. In UPGMA cluster analysis, the populations were grouped into four main clusters at a cutoff value of 0.07. The analysis of molecular variance showed that the maximum value of genetic variation was found within the populations (68%), where as a low genetic differentiation was observed among the populations (32%). Our results revealed that ISSR molecular markers are useful to display the diversity in Allium genus and can be used to improve the classification accuracy. This study provided valuable information for the conservation of these species and breeding program planning.

scholarly journals APPLICATIONS OF ISSR MARKERS IN STUDIES OF GENETIC DIVERSITY OF Pityrocarpa moniliformis

2020 ◽  
Vol 33 (4) ◽  
pp. 1017-1024
Author(s):  
FRANCIVAL CARDOSO FELIX ◽  
KYVIA PONTES TEIXEIRA DAS CHAGAS ◽  
CIBELE DOS SANTOS FERRARI ◽  
FÁBIO DE ALMEIDA VIEIRA ◽  
MAURO VASCONCELOS PACHECO
Keyword(s):  
Genetic Diversity ◽  
Molecular Markers ◽  
Genetic Distance ◽  
Inter Simple Sequence Repeat ◽  
Issr Markers ◽  
Shannon Index ◽  
Resolving Power ◽  
Development Programs ◽  
Diversity Studies ◽  
Issr Molecular Markers

ABSTRACT Pityrocarpa moniliformis (Benth.) Luckow & R. W. Jobson (Fabaceae) is a native brazilian species with high potential for economic development programs in semiarid regions, mainly related to the production of honey, animal food and firewood. Thus, the objective of this work was to select Inter-Simple Sequence Repeat (ISSR) molecular markers for genetic diversity studies, as well as to test the efficiency of this approach in quantifying the genetic diversity of a natural P. moniliformis population. For this, 28 ISSR molecular markers were tested, evaluating the total number of loci, polymorphism rate and the Polymorphism Information Content (PIC) for the selected primers, the “Marker Index”, and the “Resolving Power”. Genetic diversity parameters (Nei genetic distance and Shannon index) were evaluated for 30 individuals located in Macaíba, Rio Grande do Norte State, Brazil. Seven primers were selected, which provided 74 loci, with 82% being polymorphic, while the PIC value was 0.344. The Nei genetic distance was 0.244, and the Shannon index was 0.374. Therefore, ISSR molecular markers (UBC 827, 840, 844, 857, 859, 860 and 873) are considered efficient in studying the genetic diversity of populations for the selection of matrices and germplasm banks, and may contribute to the conservation and genetic improvement of P. moniliformis populations.

scholarly journals Report of high genetic diversity of filarial worm, Wuchereria bancrofti from endemic region of Eastern Maharashtra (India)

2017 ◽  
Vol 54 (4) ◽  
pp. 292-297 ◽  
Author(s):  
A. L. Mahakalkar ◽  
H. P. Sapkal ◽  
M. M. Baig
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Hot Spot ◽  
Wuchereria Bancrofti ◽  
Distance Matrix ◽  
Endemic Region ◽  
High Genetic Diversity ◽  
Filarial Worm ◽  
Rapd Pcr ◽  
Minimum Genetic Distance

Summary “Filariasis free India” is National Health Policy’s vision. Currently, India has undertaken Mass Drug Administration drive (MDA) to eliminate the filariasis infection. Taking this into account, the emergence of new Wuchereria bancrofti resistant strains against the current choice of drugs cannot be ruled out. In this study, we report the genetic diversity of Wuchereria bancrofti from four districts (Amravati, Nagpur, Chandrapur and Wardha) of Vidarbha, a region in the eastern part of Maharashtra state of India and considered a hot spot of filariasis infections. The RAPD profiles were generated for 21 populations using nine random RAPD primers. The RAPD-PCR based distance matrix shows maximum genetic distance of 0.425 between the parasites from Nagpur and Amravati region and minimum genetic distance of 0.210 between the parasites of Wardha and Nagpur. The tree inferred by Neighbour-Joining (NJ) method shows four distinct clusters. With the single exception of isolates from Amravati, all other clusters show the intermingling of isolates with other districts. Further, the representation of isolates from Chandrapur in three out of four clusters revealed to be a founder and indicates towards the entry of the filarial worm into the Maharashtra state through southern route.

scholarly journals Genetic diversity of grapevine (Vitis vinifera L.) cultivars in Al-Madinah Al-Munawara based on molecular markers and morphological traits

2020 ◽  
Vol 27 (1) ◽  
pp. 113-127
Author(s):  
Usama K Abdel Hameed ◽  
Khawla Abdelaziz ◽  
Nahla El Sherif
Keyword(s):  
Genetic Diversity ◽  
Molecular Markers ◽  
Genetic Distance ◽  
Fruit Trees ◽  
Inter Simple Sequence Repeat ◽  
Morphological Data ◽  
Start Codon ◽  
Vitis Vinifera L ◽  
Plant Taxon ◽  
Issr Primers

Grapevine is one of the major fruit trees in the Kingdom of Saudi Arabia. This study aims to discriminate and assess the genetic diversity in three grapevine cultivars in Al- Madinah through the combination of characterization using both classical ampelographic as well as ampelometric studies with molecular markers using Randomly Amplified Polymorphic DNA (RAPD), Inter Simple Sequence Repeat (ISSR) and Start Codon Targeted Polymorphism (SCoT). For the ampelographic analysis, twelve OIV descriptors were used, and for the ampelometric analysis, the fully expanded mature leaves area were automatedly measured. The genetic distance among the three grapevines cultivars, calculated using Jaccard's coefficient, ranged from 0.7577 (between AL Nakheel and Banati) to 0.4501 (between AL Nakheel and Ahmer). The molecular analysis was based on the use of thirty-one primers; ten RAPD primers, seven ISSR primers and fourteen SCoT primers. RAPD primers generated the highest polymorphism (67%), while the level of polymorphism with ISSR primers was 36% and with SCoT 44%. All of the three markers generated similar dendrograms, and the genetic distance generated with RAPD was higher compared with SCoT and ISSR. The three markers RAPD, ISSR and SCoT were combined and amalgamated with the morphological data, and combined dendrogram was generated and discussed. AL Nakheel and Ahmer cultivars were found to be more closely related to each other than Banati which was separated in a different cluster. Both methods were effectively efficient for complete identification of grapevine and for studying the genetic diversity between closely related cultivars. Bangladesh J. Plant Taxon. 27(1): 113-127, 2020 (June)

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