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

Evaluation of Genetic Diversity in Castor (Ricinus communis L.) using RAPD Markes

2011 ◽  
Vol 343-344 ◽  
pp. 981-987
Author(s):  
Feng Juan Li ◽  
Chang Lu Wang ◽  
Dong He ◽  
Ya Qiong Liu ◽  
Mian Hua Chen ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Tree ◽  
Genetic Distance ◽  
Oil Content ◽  
Rapd Markers ◽  
Rapd Analysis ◽  
Ricinus Communis ◽  
Major Group ◽  
Ricinus Communis L ◽  
Polymorphic Bands

RAPD markers are used to study the genetic diversity of the main planting on 37 castor varieties widely cultivated in china according to the oil content and other characteristic of different castor varieties. Genetic distance of 37 Chinese castor varieties is studied by RAPD markers analysis. RAPD analysis shows that a total of 122 bands are amplified from random primers of 20 S series, including 71 polymorphic bands with polymorphic rate of 58.20%. 37 castor beans are divided into four major groups in the phylogenetic tree. One castor germplasm is included in1, 2, 3 groups respectively, and two sub-groups are included in the 4 major group.

scholarly journals KERAGAMAN GENETIK IKAN TIGER FISH (Datnioides sp.) ASAL KALIMANTAN DAN SUMATERA

2018 ◽  
Vol 13 (3) ◽  
pp. 191
Author(s):  
Melta Rini Fahmi ◽  
Erma Primanita Hayuningtyas ◽  
Mochammad Zamroni ◽  
Bastiar Nur ◽  
Shofihar Sinansari
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Cytochrome Oxidase ◽  
Dna Barcoding ◽  
Cytochrome B ◽  
Molecular Identification ◽  
Coi Gene ◽  
Cyt B ◽  
Cytochrome Oxidase 1 ◽  
Rag2 Gene

Ikan tiger fish (Datnioides sp.) merupakan ikan hias air tawar yang memiliki nilai ekonomis penting. Distribusi populasi ikan ini meliputi Papua, Kalimantan, dan Sumatera, dengan tingkat eksploitasi yang cukup tinggi di dua lokasi terakhir. Penelitian ini dilakukan untuk mendapatkan informasi keragaman genetik ikan tiger fish yang mendiami perairan Kalimantan dan Sumatera. Sebanyak 24 sampel ikan uji dikoleksi dari Sungai Kapuas, Kalimantan Barat dan Sungai Musi, Sumatera Selatan. Penelitian dilakukan dalam dua tahap, tahap pertama yaitu identifikasi molekuler dengan menggunakan DNA barcoding gen cytochrome oxidase 1 (COI), tahap kedua adalah analisis keragaman genetik dengan menggunakan marka DNA mitokondria gen cytochrome b (Cyt b), dan DNA inti gen recombination activating gene (RAG2). Hasil identifikasi secara molekuler menunjukkan bahwa ikan hasil koleksi memiliki kesamaan genetik sebesar 100% dengan spesies D. undecimradiatus. Keragaman genetik ikan tiger fish antar populasi berkisar pada nilai 0,023 (standar deviasi 0,001) sedangkan keragaman intra populasi adalah sebesar 0,002 dan 0,003 masing-masing untuk populasi Kalimantan dan Sumatera. Jarak genetik sampel baik yang berasal dari Sumatera maupun Kalimantan dengan spesies D. undeciumradiatus masing-masing 0,003 dan 0,006; sedangkan dengan spesies D. microlepis yaitu 0,142. Analisis menggunakan gen RAG2 menunjukkan sampel yang diuji memiliki struktur populasi yang terpisah ditandai dengan terjadinya mutasi pada enam nukleotida dan tiga asam amino.The Tiger fish (Datnioides sp.) is a freshwater ornamental fish that has important economic value. The distribution of this fish included Papua, Kalimantan, and Sumatra, but intensive exploitation occurs in the last two population. This research was conducted to obtain the genetic diversity of tiger fish that inhabited in Kalimantan and Sumatra. A total of 24 fish were collected from Kapuas River, West Kalimantan and Musi River, at Sumatra. The study was conducted in two stages, the first stage is molecular identification of sample by using DNA barcoding cytochrome oxidase 1 (COI) gene, the second stage is analyses of genetic diversity of tiger fish within and between population by using the mitochondrial DNA cytochrome b (Cyt b) gene, and nucleus DNA recombination (RAG2) gene. The molecular identification has shown that the collected fish has a genetic similarity of 100% with D. undecimradiatus. The genetic diversity of tiger fish between populations is 0.023 (standard deviation of 0.001) whereas intra-population is 0.002 and 0.003 for Kalimantan and Sumatra, respectively. The genetic distance of samples with species D. undeciumradiatus were 0.003 and 0.006 for Kalimantan and Sumatera, respectively, whereas the genetic distance with D. microlepis was 0.142. The analysis of mutation on RAG2 gene shows there are six nucleotides and three amino acids have mutation.

scholarly journals The Genetic Diversity of Two Subpopulations of Shenxian Pigs as Revealed by Genome Resequencing

2021 ◽  
Author(s):  
Liu Diao ◽  
Cao Hongzhan ◽  
Lu Chunlian ◽  
Li Shang ◽  
Jia Mengyu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Evolutionary Process ◽  
Principal Component ◽  
Hebei Province ◽  
Genome Resequencing ◽  
Phylogenetic Tree Analysis ◽  
Tree Analysis ◽  
Phenotypic Characters ◽  
Whole Genome Resequencing

ABSTRACTShenxian pigs can be divided into two main strains from their shape and appearance: Huangguazui and Wuhuatou. There are significant differences in the phenotypic characters between the two subpopulations. The Shenxian pig, as the only local pig breed listed in China Pig Breeds in Hebei Province, has the excellent traits of Chinese local pigs. In order to explore the genetic diversity and genetic distance of the different subpopulations of Shenxian pig, as well as understand their evolutionary process, whole genome resequencing and genetic structure analyses were performed for the two sub-population types of Shenxian pigs.The results showed that a total of 14,509,223 SNP sites were detected in the Huangguazui type and 13,660,201 SNP sites were detected in the Wuhuatou type. This study’s principal component analysis results showed that the genetic differentiation of the Shenxian pig population was serious, and there was obvious stratification in the population. The phylogenetic tree analysis results indicated that there was a certain genetic distance between the Huangguazui and Wuhuatou types.

scholarly journals RAGAM GENOTIPE IKAN TENGADAK, Barbonymus schwanenfeldii (Bleeker 1854) PERSILANGAN POPULASI JAWA DAN KALIMANTAN BERDASARKAN RAPD

2016 ◽  
Vol 11 (2) ◽  
pp. 99
Author(s):  
Deni Radona ◽  
Dinar Tri Soelistyowati ◽  
Rudhy Gustiano ◽  
Odang Carman ◽  
Irin Iriana Kusmini ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Rapd Analysis ◽  
Whole Body ◽  
Hybrid Female ◽  
Hybrid Fish ◽  
Genetic Assessment ◽  
The Relationship ◽  
Aquaculture Development

Dalam rangka pengelolaan sumber genetik untuk pengembangan budidaya ikan tengadak maka perlu dilakukan evaluasi sumber genetik ikan tengadak asal Jawa dan Kalimantan, serta progeni hibridanya. Analisis genetik dilakukan secara molekuler dengan metode RAPD. Jumlah sampel yang digunakan untuk analisis RAPD sebanyak 10 ekor setiap populasi. Spesimen yang digunakan untuk analisis RAPD adalah sirip untuk induk dan whole body untuk hibrida. Hasil menunjukkan polimorfisme (32,43%) dan heterozigositas (0,13) tertinggi terdapat pada ikan tengadak hasil persilangan betina Jawa x jantan Kalimantan, sedangkan yang terendah diperoleh pada persilangan betina Kalimantan x jantan Jawa (polimorfisme: 21,62% dan heterozigositas: 0,10). Berdasarkan dendrogram hubungan kekerabatan interpopulasi ikan tengadak hasil persilangan (betina Kalimantan x jantan Jawa) dengan induknya (populasi Jawa dan Kalimantan) menggunakan tiga primer RAPD (OPA-08, OPA-09, dan OPC-02) menunjukkan jarak genetik berkisar 0,48. Ikan tengadak betina asal Jawa dan jantan asal Kalimantan potensial meningkatkan keragaman genetik.In order to maintain the genetic sources of tinfoil barb for aquaculture development, it is necessary to evaluate the genetic diversity crossbred results of tinfoil barb from Java and Kalimantan. The genetic assessment was conducted by genotype trails using RAPD methods. The samples used for the analysis of RAPD was as much as 10 individuals. Specimens used for RAPD analysis was a fin for broodstock and whole body for the hybrid fish. The result showed that the highest polymorphism and heterozygosity were found 32.43% and 0.13 in population crossbred of female Java x male Kalimantan. While the lowest polymorphism and heterozygosity were detected on population of f Kalimantan x m  Java (21.62% and 0.10, respectively). Based on the relationship between tinfoil barb hybrid (female Kalimantan x male Java) with a both broodstock population using three RAPD primers (OPA-08, OPA-09, and OPC-02) resulted in genetic distance of 0.48. Females tinfoil barb from Kalimantan and males from Java potential could increase genetic diversity. 

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.

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 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 Genetic Diversity of Croton (Codiaeum variegatum (L.) Rumph.ex A. Juss) and Its Offspring Based on RAPD Markers

2019 ◽  
Vol 4 (2) ◽  
pp. 52
Author(s):  
Mufit Daryatun Asniawati ◽  
Aziz Purwantoro
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Rapd Markers ◽  
Rapd Analysis ◽  
Female Parent ◽  
Dna Amplification ◽  
Male Parent ◽  
Native Plant ◽  
Codiaeum Variegatum ◽  
Polymorphic Bands

Croton (Puring) is a native  plant of Indonesia which has varied leaf shapes and colors. The diversity of croton increase through hybridization. The information on genetic diversity and relationship between parent and its offspring of crotons is very limited. This study aims to analyze the genetic diversity of cultivar Mawar (MW) and Walet (W) as parent compare to their offspring i.e, Black Marlet (BM), Kingkit 1 (KA), Kingkit 2 (KB), and Kamaratih (KM) using RAPD markers. This study used DNA extraction from the fresh leaf of six cultivars. The next steps were DNA quantification, primary optimization, DNA amplification with PCR, and electrophoresis. Statistical analysis was carried out using Genalex software. A total of 40 primers were screened, out of which 10 were selected for the analysis of genetic diversity. A total of 106 polymorphic bands were generated, ranging from 130 to 1850 bp. The results of RAPD analysis showed that Mawar as female parent had the highest polymorphic bands percentage of 69.01%, while Walet as male parent and its offspring ranged from 31.15 % to 43.94%. The genetic distance of the offspring with Walet ranged from 0.176 to 0.234 and genetic distance of the offspring with Mawar ranged from 0.314 to 0.372. It was indicated that all of offspring were closer to the male parent.

Assessment of molecular diversity of greengram [Vigna radiata (L.) Wilzek] through RAPD

2016 ◽  
Author(s):  
Gunnjeet Kaur ◽  
Arunabh Joshi ◽  
Devendra Jain ◽  
Ganesh Rajamani ◽  
Divya Vyas
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Polymorphism Information Content ◽  
Vigna Radiata ◽  
Molecular Diversity ◽  
Rapd Analysis ◽  
Similarity Coefficient ◽  
Green Gram ◽  
Randomly Amplified Polymorphic Dna ◽  
Legume Crop

A total twenty three genotypes of green gram (Vigna radiata) were subjected to Randomly amplified polymorphic DNA (RAPD) analysis for molecular characterization. A total of 25 randomly selected decamers were screened, out of which only 15 generated 126 amplification products from which 117 bands were found polymorphic, the average polymorphism being 93.48%. The total number of amplified bands varied between 2 (primer OPP-09) to 17 (primer OPA-1) with an average of 9.5 bands per primer. The overall size of PCR amplified products ranged between 200 bp to 2900 bp. The average Polymorphism Information Content(PIC) was 0.32 ranging from 0.17 to 0.46. Primer OPA-01 and OPP-06 detected two unique bands ranged between 250 bp to 2500 bp in two genotypes (PUSA-672 and HUM-12). Jaccard's similarity coefficient values ranged from 0.28-0.90 with an average of 0.59. Based on dendrogram generated through UPGMA method and PCA, most of the genotypes got divided into four main clusters. Genotype EC-398885 lay far apart and thus showed maximum genetic distance. The assessment of genetic diversity is a prerequisite and important step for the improvement of any legume crop. Thus, present results of the present study could be further extrapolated to other green gram accessions in Vigna germplasm.

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.

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