scholarly journals Random Amplification of Polymorphic DNA Analysis for Genetic Characterization of Two Breeds of Dogs, German Shepherd and Japanese Spitz

2013 ◽  
Vol 13 (2) ◽  
pp. 73-78
Author(s):  
Jarina Joshsi ◽  
Lumanti Manandhar ◽  
Patima Shrestha ◽  
Rani Gupta ◽  
Rojlina Manadhar ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Rapd Markers ◽  
Dna Analysis ◽  
Genetic Characterization ◽  
Random Amplified Polymorphic Dna ◽  
Neighbor Joining ◽  
German Shepherd ◽  
Polymorphic Loci ◽  
Random Amplification

Random amplified polymorphic DNA (RAPD) markers were used to study genetic diversity in dog samples belonging to populations of German Shepherd and Japanese Spitz. A total of twelve samples were typed using eight RAPD primers. Out of eight primers, three primers gave result in six individuals of dogs. The phylogenetic tree constructed by the neighbor joining method based on Nei. Original measures revealed highest genetic identity found in German Shepherd as 0.9444 and highest genetic distance as 1.2809. The analysis predicts the number of polymorphic loci as 15 and the percentage of polymorphic loci as 83.3. Nepal Journal of Science and Technology Vol. 13, No. 2 (2012) 73-78 DOI: http://dx.doi.org/10.3126/njst.v13i2.7717

Genotypic Characterization of Rhizopus Spp. Tempeh and Usar: Traditional Inoculum of Tempeh in Indonesia

2020 ◽  
Vol 14 (3) ◽  
pp. 3
Author(s):  
Tati Barus ◽  
Jason Wiranata Sanjaya ◽  
Anastasia Tatik Hartanti ◽  
Adi Yulandi ◽  
Vivitri Dewi Prasasty ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Internal Transcribed Spacer ◽  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Its Sequence ◽  
Rhizopus Microsporus ◽  
Rhizopus Delemar

Abstract. Soybeans tempeh (tempeh) is processed by fermentation using Rhizopus spp. Tempeh is an important source of protein in Indonesia. The traditional inoculum in fermentation locally is known as Usar which is made from the leaves of Hibiscus tiliaceus. However, Rhizopus information from Usar is still limited. Therefore, this study aims to identify and investigate the genetic diversity of Rhizopus species from Usar and tempeh based on the Internal Transcribed Spacer (ITS) sequence and the Random Amplified Polymorphic DNA (RAPD) markers. Twenty-three Rhizopus strains were isolated from Usar and ten Rhizopus strains were isolated from tempeh. Based on ITS sequences, the isolates were similar to R Rhizopus microsporus (30 isolates) and Rhizopus delemar (3 isolates) with 98-99% similarity. The genetics of R. microsporus and R. delemar are varied and different from the genetics of R. microsporus from tempeh. The growth temperature of R. microsporus varies from 33 to 48°C and R. delemar can grow to a maximum at 33°C. The role of R. microsporus and R. delemar from Usar in determining the quality of tempeh is still limited. Therefore, it needs to be investigated further.

scholarly journals Genetic characterization of the Moxotó goat breed using RAPD markers

2005 ◽  
Vol 40 (3) ◽  
pp. 233-239 ◽  
Author(s):  
Rejane Rodrigues de Oliveira ◽  
Andréa Alves do Egito ◽  
Maria Norma Ribeiro ◽  
Samuel Rezende Paiva ◽  
Maria do Socorro Maués Albuquerque ◽  
...  
Keyword(s):  
Genetic Variability ◽  
Rapd Markers ◽  
Genetic Characterization ◽  
Random Amplified Polymorphic Dna ◽  
Genetic Distances ◽  
Goat Breed ◽  
Breeding Programs ◽  
Analysis Of Molecular Variance ◽  
Polymorphic Bands

The objective of this study was to verify the genetic diversity between and within seven populations of Moxotó goat (n = 264) from the States of Pernambuco, Paraíba and Rio Grande do Norte, using RAPD (Random Amplified Polymorphic DNA). Moxotó, as well as other naturalized breeds, suffers genetic losses due to the indiscriminate miscegenation with breeds raised in the Northeast Region of Brazil. The genetic characterization of these genetic resources is essential to conservation and breeding programs. DNA was extracted from lymphocytes using a non-organic protocol. The 16 primers used were selected from 120 decamer oligonucleotide primers and generated 56 polymorphic bands. The analysis of molecular variance (AMOVA) showed that the greater part of total genetic variability (71.55%) was due to differences between individuals within populations, while 21.21% was among populations. The analysis of variance among the pairs of populations demonstrated that the populations located in Floresta, PE x Angicos, RN presented a smaller value of intrapopulational differentiation (8.9%), indicating low genetic variability among them. Nei's genetic distances varied between 0.0546 and 0.1868 in the populations. The dendrogram generated showed that the Canindé breed, used as outgroup, clustered with the populations of Moxotó, indicating a possible common origin of the naturalized goat breeds.

scholarly journals Evaluation of Genetic Diversity among Persian Fig Cultivars by Morphological Traits and RAPD Markers

HortScience ◽  
2018 ◽  
Vol 53 (5) ◽  
pp. 613-619 ◽  
Author(s):  
Ghazal Baziar ◽  
Moslem Jafari ◽  
Mansoureh Sadat Sharifi Noori ◽  
Samira Samarfard
Keyword(s):  
Genetic Diversity ◽  
Rapd Markers ◽  
Polymorphic Information Content ◽  
Random Amplified Polymorphic Dna ◽  
Hierarchical Cluster ◽  
Fruit Trees ◽  
Group Method ◽  
Fars Province ◽  
Pair Group

Ficus carica L. is one of the most ancient fruit trees cultivated in Persia (Iran). The conservation and characterization of fig genetic resources is essential for sustainable fig production and food security. Given these considerations, this study characterizes the genetic variability of 21 edible F. carica cultivars in the Fars Province using random amplified polymorphic DNA (RAPD) markers. The collected cultivars were also characterized for their morphological features. A total of 16 RAPD primers produced 229 reproducible bands, of which, 170 loci (74.43%) were polymorphic with an average polymorphic information content (PIC) value of 0.899. Genetic analysis using an unweighted pair-group method with arithmetic averaging (UPGMA) revealed genetic structure and relationships among the local germplasms. The dendrogram resulting from UPGMA hierarchical cluster analysis separated the fig cultivars into five groups. These results demonstrate that analysis of molecular variance allows for the partitioning of genetic variation between fig groups and illustrates greater variation within fig groups and subgroups. RAPD-based classification often corresponded with the morphological similarities and differences of the collected fig cultivars. This study suggests that RAPD markers are suitable for analysis of diversity and cultivars’ fingerprinting. Accordingly, understanding of the genetic diversity and population structure of F. carica in Iran may provide insight into the conservation and management of this species.

scholarly journals Genetic diversity analysis in Brassica varieties through RAPD markers

1970 ◽  
Vol 34 (3) ◽  
pp. 493-503 ◽  
Author(s):  
KK Ghosh ◽  
ME Haque ◽  
S Parvin ◽  
F Akhter ◽  
MM Rahim
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Rapd Markers ◽  
Gene Diversity ◽  
Random Amplified Polymorphic Dna ◽  
Arithmetic Mean ◽  
Polymorphic Band ◽  
Group Method ◽  
Polymorphic Loci ◽  
Pair Group

This investigation was aimed at exploring the genetic diversity and relationship among nine Brassica varieties, namely BARI Sharisha-12, Agrani, Sampad, BINA Sharisha-4, BINA Sharisha-5, BARI Sharisha-13, Daulot, Rai-5, Alboglabra using Random Amplified Polymorphic DNA (RAPD) markers. In total, 59 reproducible DNA bands were generated by four arbitrary selected primers of which 58 (98.03%) bands were proved to be polymorphic. These bands ranged from 212 to 30686 bp in size. The highest proportion of polymorphic loci and gene diversity values were 37.29% and 0.1373, respectively, for BARI Sharisha-12 and the lowest proportion of polymorphic loci and gene diversity values were 8.47% and 0.0318, 8.47% and 0.0382 for BINA Sharisha-4 and Rai-5, respectively. A dendrogram was constructed using unweighted pair group method of arithmetic mean (UPGMA). The result of cluster analysis indicated that the 9 accessions were capable of being classified into 2 major groups. One group consists of BARI Sharisha-12, Agrani, Sampad, Daulot, Rai-5, Alboglabra. where Daulot and Rai-5 showed the lowest genetic distance of 0.049. And another group contains BINA Sharisha-4, BINA Sharisha-5, and BARI Sharisha-1 3, where BINA Sharisha-5 and BARI sharisha-13 showed genetic distance of 0.071. Key Words: RAPD, Brassica, genetic distance, polymorphic band. DOI: 10.3329/bjar.v34i3.3976 Bangladesh J. Agril. Res. 34(3) : 493-5032, September 2009

scholarly journals GENETIC DIVERSITY OF SABAH RICE CULTIVARS USING RANDOM AMPLIFIED POLYMORPHIC DNA (RAPD) MARKERS

2020 ◽  
pp. 35
Author(s):  
Alvina Simon ◽  
Vijay Kumar Subbiah ◽  
Chee Fong Tyng ◽  
Noor Hydayaty Md Yusuf
Keyword(s):  
Genetic Diversity ◽  
Rapd Markers ◽  
Genetic Relationships ◽  
Random Amplified Polymorphic Dna ◽  
Random Amplification ◽  
Commercial Cultivars ◽  
Rice Samples ◽  
Staple Crop ◽  
Upland Condition ◽  
Insight Into

Rice is the most important staple crop in Malaysia and is cultivated all over the country, including the state of Sabah. The uniqueness of rice cultivation in Sabah lies in the type of rice itself, deriving mainly from local or non-commercial cultivars but with distinctive characteristics including long grains, aromatic properties, and drought tolerance. However, despite having these important agricultural traits, information on the genetic diversity of Sabah rice remains limited. Hence, the purpose of this study was to determine the genetic polymorphisms of Sabah rice using random amplification of polymorphic DNA (RAPD) markers. A total of 101 alleles were profiled, from which 94% were identified as polymorphic. Phylogenetic analysis grouped the rice samples into three clusters, with two clusters classifying the ability of rice to grow under different planting conditions, suitable for growth irrigate and upland condition. The first cluster was dominated by cultivars that could survive in wet (irrigated) areas, while the other featured those that were found in dry (upland) areas. Furthermore, two alleles, OPA-05-B2 and OPA-01-B11, were found to be unique to cultivars within the upland cluster and were thus proposed to be involved in dry environmental adaptation. The results of the present study provide an insight into the genetic relationships and diversity of Sabah rice.

scholarly journals Molecular Characterization of Kiwifruit (Actinidia) Cultivars and Selections Using SSR Markers

2004 ◽  
Vol 129 (3) ◽  
pp. 374-382 ◽  
Author(s):  
Yiqi Zhen ◽  
Zuozhou Li ◽  
Hongwen Huang ◽  
Ying Wang
Keyword(s):  
Genetic Diversity ◽  
Molecular Characterization ◽  
Ssr Markers ◽  
Rapd Markers ◽  
Reliable Method ◽  
Cultivar Identification ◽  
Direct Count ◽  
Polymorphic Loci ◽  
Single Genotype

Forty-eight kiwifruit cultivars and selections, representing more than 90% of total world kiwifruit production, were investigated using nine SSR markers to establish genetic identities, and evaluate genetic diversity and relatedness. These nine SSRs were polymorphic and a total of 213 alleles were detected, resulting in a mean number of 23.7 alleles per locus, ranging from nine to 38 alleles. One hundred and thirty-three alleles were found to be common to both A. chinensis and A. deliciosa, while 33 and 36 were specific to A. chinensis and A. deliciosa, respectively. In addition, 34 alleles were specific to one single genotype and provided a set of valuable alleles for cultivar identification. A single SSR locus UDK 96-414 could differentiate all 48 genotypes except two presumable clones. Mean number of alleles per locus (A), percentage of polymorphic loci (P), and direct count heterozygosity (Ho) assessed for each genotype over all loci revealed considerable differences among these 48 genotypes. On average, A = 2.6, P = 89.4% and Ho = 0.546 were found in A. chinensis cultivars, while A = 3.5, P = 97.0% and Ho = 0.671 in A. deliciosa cultivars. Consensus fingerprint profiling using SSR markers is a useful and reliable method for establishing genetic identities of kiwifruit cultivars and selections. It also improves evaluation effectiveness of genetic diversity and relatedness compared to RAPD markers.

scholarly journals GENETIC CHARACTERIZATION OF GALOBA DURIAN (AMONUM SPP.) IN AMBON ISLAND BASED ON RANDOM AMPLIFIED POLYMORPHIC DNA (RAPD)

2018 ◽  
Vol 3 (1) ◽  
pp. 27-33
Author(s):  
Fuadiska Salamena ◽  
Cecilia Anna Seumahu
Keyword(s):  
Genetic Diversity ◽  
Molecular Markers ◽  
Genetic Characterization ◽  
Kidney Diseases ◽  
Random Amplified Polymorphic Dna ◽  
Quantitative Result ◽  
Dna Amplification ◽  
Polymorphic Band ◽  
Qualitative And Quantitative

Galoba durian is one of the endemic floras from Maluku. Galoba durian is a species belonging to the Amomum genera Zingiberaceae family. It is also used as a medicinal plant for waist and kidney diseases. Based on the color of the fruit, galoba durian is divided into two nmely red galoba durian and green galoba durian. Distribution of this plant in Ambon can found in a few places such as highland and coastal area. Different locations influence phenotypic of plants, but may not show different genetic characteristic. Genetic diversity can detected by molecular markers. Genetic characterization from galoba durian using RAPD markers has not been done before. This study aimed to analyze genetic diversity from galoba durian using molecular markers RAPD. Samples of plants are used red galoba durian from Hatu and green galoba durian from Hatalae. The result of the first study, characterization of the morphology of the galoba durian, showed that both galoba have almost similar characteristics. Further DNA was tested by qualitative and quantitative. Result shows good qualitative and quantitative of DNA genomic. The second study was amplification by PCR-RAPD. DNA amplifications were performed using 3 primers out of 9 screened random primers. The primers selection was based on hight polymorphism. DNA amplification has 36 bands which were 100% polymorphic. The size of each bands from visualization of agarose was determined by linear regression. Number of band amplified was range from 120 to 1612 bp. Polymorphic band of RAPD showed the highest  genetic diversity. It can be concluded that the two plants of galoba durian are different species

scholarly journals Genetic characterization of cotton landraces found in the Paraíba and Rio Grande do Norte states

2015 ◽  
Vol 15 (1) ◽  
pp. 26-32 ◽  
Author(s):  
Ivandilson Pessoa Pinto de Menezes ◽  
Lúcia Vieira Hoffmann ◽  
Paulo Augusto Vianna Barroso
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Unbiased Estimator ◽  
Genetic Characterization ◽  
Rio Grande ◽  
Microsatellite Primers ◽  
Polymorphic Loci ◽  
Valuable Source

The objective of this study was to estimate genetic diversity of cotton mocó planted in Paraíba and Rio Grande do Norte using microsatellite markers, since mocó landraces are a valuable source of genetic diversity. A set of 38 accessions - 21 plants from Rio Grande do Norte and 17 from Paraiba - was analyzed using 24 pairs of cotton microsatellite primers, which amplified 20 polymorphic loci. The average inbreeding was 0.432, and was slightly higher in individuals from Paraíba than from Rio Grande do Norte. Genetic diversity (Nei´s unbiased estimator) between individuals from each state's populations had similar values (HT = 0.327 and 0.302 in Paraíba and Rio Grande do Norte, respectively), indicating that comparable variability has been maintained. Moreover, the proportion of diversity between populations was extremely low (DST = 0.007), but expressive between mesoregions (DST = 0.069). These data led us to conclude that the genetic similarities between populations are high.

scholarly journals RAPD profiling in detecting genetic variation in Stellaria L. (Caryophyllaceae)

Genetika ◽  
2021 ◽  
Vol 53 (1) ◽  
pp. 349-362
Author(s):  
Xiaobang Peng ◽  
Majid Khayyatnezhad ◽  
Leila Ghezeljehmeidan
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Rapd Markers ◽  
Genetic Difference ◽  
Random Amplified Polymorphic Dna ◽  
Molecular Data ◽  
Shannon Index ◽  
Neighbor Joining ◽  
Medicinal Value ◽  
Main Center

Stellaria species are common herbs, preferred humid mountainously slopes, but some grew in desert. Main center of diversification for Stellaria is Eurasia, with a center of distribution in the mountains of central Asia. Some species are also cosmopolitan. It is represented by 9 species in Iran. The genus has high medicinal value. To determine the genetic diversity and understand the species? limits within the Iranian Stellaria, we produced molecular data using 139 randomly collected plants representing 8 species from five provinces of Iran. A total of 122 reproducible bands were generated by 10 of 25 random amplified polymorphic DNA (RAPD) primers, with an average of 12.2 bands/primer and 33% polymorphism. Largest number of effective alleles (Ne), genetic diversity (H), and Shannon Index (I) were shown by S. media. Our data depicted highest similarity between S. media and S. pallida and lowest between S. media and S. graminea. S. pallida showed relatively low level of genetic variation. Finally, the Neighbor Joining (NJ) trees based on RAPD markers data divided the populations into two different clusters, indicating their genetic difference which is discussed in details.

scholarly journals Assessment of the genetic diversity among oily spot (Xanthomonas axonopodis pv. punicae) pathogen of pomegranate by randomly amplified polymorphic DNA analysis

2015 ◽  
Vol 7 (2) ◽  
pp. 1006-1011
Author(s):  
Wayde Jitendra Eknath ◽  
Akshay S. Dange ◽  
Trishala A. Pagar ◽  
Deepak Rameshwar Sapkal ◽  
Monika Bansal
Keyword(s):  
Genetic Diversity ◽  
Rapd Markers ◽  
Dna Analysis ◽  
Punica Granatum ◽  
Economic Loss ◽  
Xanthomonas Axonopodis ◽  
Major Region ◽  
Relationship Of ◽  
Punica Granatum L

Pomegranate (Punica granatum L.) is an important fruit crop of India and other subtropical countries. Bacterial blight caused by Xanthomonas axonopodis pv. Punicae is becoming a major threat in Maharashtra as well as other states of India. It causes yield losses up to the extent of 80 – 90 %. This study aims to the collection of 7 strains (X. axonopodis) and utilized for assessment of genetic diversity by using RAPD markers. Whereas 7 strains of X. axonopodis were differentiated and distinguished into seven major region representing Malegaon, Nampur, Satana, Khakurdi, Ramnagar, Rahuri and Nashik region. However the genetic similarity within 7strains of X. axonopodis was ranged between 72.72-100 %. Similarly the genetic relationship of strains X. axonopodis was also established and showed 72.72 %, 72.72 %, 72.72 % 92.30%, 94.11% and 100 % similarity with region of Malegaon, Nampur, Satana, Khakurdi, Ramnagar, Rahuri and Nashik region. Average polymorphism in strains of X. axanopodis based on RAPD analysis was 84.095 %. The combine data analysis by using UPGMA method also revealed the two distinct groups representing seven strains of X. axonopodis and in first group M1 and second group R4 and subgroup RH6, N2, NS7, S3, K5, these genotypes were present respectively. Considering predominance and economic loss caused by X. axonopodis pv. punicae in pomegranate, it is an essential to undertake preliminary work on characterization of this pathogen at the molecular level.

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