Molecular Characterization of Tropical Strawberry Genotypes

Genetic variability of tropical strawberry genotypes was determined through Ramdom Amplified Polymorphic DNA (RAPD) primers. Out of 14 RAPD primers six showed reproducible and polymorphic bands. The results revealed that the maximum polymorphic bands were produced by the primer OPB 12. Ten genotypes were differentiated into two clusters on the basis of Unweighted Pair Group Method With Arithmetic Averages (UPGMA). Genotypic variation based on molecular characterization indicated that genotypes belonging to two different clusters depend on their genetic component. So, selection of parents from different clusters will provide the maximum heterosis in yield.Plant Tissue Cult. & Biotech. 27(1): 33-39, 2017 (June)

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Molecular Characterization of 12 Mango Germplasm Using RAPD markers

Plant Tissue Culture and Biotechnology ◽

10.3329/ptcb.v20i1.5972 ◽

2010 ◽

Vol 20 (1) ◽

pp. 91-99

Author(s):

R. C. Jena ◽

K. C. Samal ◽

P. K. Chand ◽

B. K. Das

Keyword(s):

Molecular Characterization ◽

Rapd Markers ◽

Mangifera Indica ◽

Pcr Amplification ◽

Similarity Coefficient ◽

Group Method ◽

Base Pairs ◽

Relationship Analysis ◽

Pair Group

Randomly amplified polymorphic DNA (RAPD) markers were used for the genetic variation and relationship analysis among 12 Mango (Mangifera indica L.) germplasm. Five oligonucleotide primers were employed to amplify DNA from 12 cultivars. PCR amplification with five primers generated 45 reproducible, clear and distinct bands, out of which 41 bands are considered polymorphic and the remaining four fragments (8.88%) monomorphic. The size of amplified product ranged from 200 (RPI-5) to 3000 base pairs (RPI-1) with an average of nine bands per primer. The average polymorphism in all the 12 cultivars using the five primers was found to be 91.91%. Among all the primers RPI-2 and RPI-4 have shown 100% polymorphism while RPI-5 was found to be least polymorphism (81.81%). One specific band, namely was found with RPI-5, in a particular variety, Chiratpuri. The UPGMA (Unweighted Pair Group Method of Arithmetic Mean) dendrogram based on Jaccard’s similarity coefficient segregated the 12 mango germplasm into two clusters. Langra, Chiratpuri, Pravasankar, Alphanso, Sindhu and Kesar formed one cluster and rest six mango germplasm grouped together into another cluster. Sindhu and Alphanso cultivar pair was very close to each other with highest similarity coefficient (0.78), which was comparatively higher than all other cultivar pairs. On the other hand, Pravasankar and Neelam cultivar pair was more distinct to each other with the lowest intervarietal similarity coefficient 0.38. This study showed clearly that cultivars from Orissa unveiled maximum diversity and indicated the potential of RAPD markers for the identification of management of mango germplasm for breeding purposes. Key words: Molecular characterization, Mango germplasm, Dversity D.O.I. 10.3329/ptcb.v20i1.5972 Plant Tissue Cult. & Biotech. 20(1): 91-99, 2010 (June)

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MOLECULAR CHARACTERIZATION OF QUALITY PROTEIN MAIZE AND DOWNY MILDEW RESISTANCE LINES BASED ON SIMPLE SEQUENCE REPEATS (SSRs) MARKER

Zuriat ◽

10.24198/zuriat.v16i1.6779 ◽

2015 ◽

Vol 16 (1) ◽

Cited By ~ 1

Author(s):

D. Ruswandi ◽

N. Wicaksana ◽

M. B. Pabendon ◽

M. Azrai ◽

M. Rachmadi ◽

...

Keyword(s):

Molecular Characterization ◽

Genetic Relationship ◽

Genetic Relatedness ◽

Genotypic Variation ◽

Group Method ◽

Maize Breeding ◽

Pair Group ◽

Group A ◽

Ssrs Markers ◽

Relationship Of

The information on germplasm diversity and genetic relatedness among elite breeding materials is an important element in maize breeding. Molecular characterization and genetic relationship of 11 QPM-DMR lines were analysed using thirty three SSRs markers. Genetic relationship was determined using Jaccard’s similarity coefficient, and dendogram was then constructed based on the unweighted pair-group method with arithmetical averages (UPGMA). Result showed that (i) all SSRs loci were informative for describing the genotypic variation as showed by their PIC, which ranged from 0.19 for umc1304 to 0.93 for phi112; (ii) the eleven maize inbred lines were clustered into one major group A and small groups B and C that corresponds well with the breeding programs adopted at different institutes of release, and (iii) thus, SSRs marker system is a valuable marker for varietals identification and for genetic diversity study of elite breeding materials.

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MOLECULAR CHARACTERIZATION OF ENDANGERED MEDICINAL PLANT SPECIES HEDYCHIUM CORONARIUM FROM EASTERN INDIA

International Journal of Pharmacy and Pharmaceutical Sciences ◽

10.22159/ijpps.2017v9i1.13815 ◽

2016 ◽

Vol 9 (1) ◽

pp. 173 ◽

Cited By ~ 2

Author(s):

Reena Parida ◽

Sujata Mohanty ◽

Sanghamitra Nayak

Keyword(s):

Molecular Characterization ◽

Random Amplified Polymorphic Dna ◽

Group Method ◽

Pair Group ◽

Hedychium Coronarium ◽

Biotechnological Approach ◽

Endangered Medicinal Plant ◽

Inter Simple Sequence Repeats ◽

Clustering Pattern

Objective: Molecular characterization of Hedychium coronarium from 4 different populations of Odisha using 9 inter simple sequence repeats and 15 random amplified polymorphic DNA markers to indicate the closeness of species and hybrids quickly and efficiently.Methods: A dendrogram was constructed through sequential agglomerative hierarchial and nested (SAHN) clustering and un-weighted pair group method with arithmetic mean (UPGMA) analysis using Jaccard’s similarity coefficient of combined markers using this particular species.Results: Two major clusters were found, i.e., cluster-I (Malkangiri-1, Phulabani-1, Phulabani-3, Malkangiri-2, Khurda-1, Khurda-2, Khurda-3, Angul-3, Angul-1, Angul-2 and Phulabani-2) and cluster-II (Malkangiri-3). The clustering pattern also revealed moreover the extent of genetic similarity between germplasms collected from four different regions population. Conclusion: The potential of this technique would be further realised to the fullest extent for the identification and tagging of the important novel gene in different taxa, unexplored yet, thus facilitating the improvement of desired taxa of Zingiberaceae. The findings would be of immense enough significance for complementing the strategies of conservation and characterization of these important taxa of Zingiberaceae following modern biotechnological approach.

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Morphological and Molecular Characterization of Rhizoctonia solani Isolates from Two Different Rice Varieties

Jurnal Perlindungan Tanaman Indonesia ◽

10.22146/jpti.25469 ◽

2018 ◽

Vol 21 (2) ◽

pp. 72 ◽

Cited By ~ 1

Author(s):

Aisyah Surya Bintang ◽

Arif Wibowo ◽

Achmadi Priyatmojo ◽

Siti Subandiyah

Keyword(s):

Maximum Likelihood ◽

Rhizoctonia Solani ◽

Molecular Characterization ◽

Morphological Characters ◽

Group Method ◽

Rice Varieties ◽

Pair Group ◽

Maximum Likelihood Tree ◽

Morphological And Molecular Characterization

Six isolates of Rhizoctonia solani, i.e. two isolates collected from infected rice plants and four isolates from laboratory collection were studied by using morphological characters and molecular analysis. Un-weighted pair group method with arithmetic mean dendogram constructed based on cluster analysis showed that these isolates were grouped into three clusters at the 0.77 similarity coefficient. Cluster I consisted of BA, BNJ, and NBR isolates with 100% similarity and indicated that those were from AG 1 IA sub group, cluster II consisted of BND, and cluster III consisted of SL1 and SL2. Mycelium was very light brown or whitish with few and moderate sclerotia except SL1 and SL2. Molecular characterization showed that BA, BNJ, and NBR were amplified at 140 bp using Rs1F/Rs2R specific primer for R. solani AG1 IA. All isolates were amplified between 350−400 bp using Rhsp1 primer, meanwhile SL1 and SL2 were not amplified using AG2sp and AG22sp2 primers. Based on Maximum Likelihood tree analysis showed that SL1 and SL2 had high similarity based on ITS sequence data.IntisariEnam isolat Rhizoctonia solani yang berasal dari tanaman padi bergejala dan koleksi laboratorium diuji secara morfologi dan molekuler. Analisis UPGMA dengan koefisien persamaan 0,77 menunjukkan bahwa enam isolat tersebut terbagi atas tiga klaster. Klaster I terdiri atas isolat BA, BNJ, dan NBR dengan kesamaan 100% dan menunjukkan bahwa isolat tersebut berasal dari subgrup AG 1 IA , klaster II yakni isolat BND, dan klaster III terdiri atas isolat SL1 dan SL2. Miselium berwarna putih hingga cokelat muda dengan jumlah sklerotia sedang, kecuali isolat SL1 dan SL2. Uji keragaman secara molekuler menunjukkan bahwa isolat BA, BNJ, dan NBR teramplifikasi pada kisaran 140 bp dengan menggunakan primer Rs1F/Rs2R yang merupakan primer spesifik dari R. solani AG1 IA. Seluruh isolat teramplifikasi pada kisaran 350−400 bp dengan menggunakan primer Rhsp1, sedangkan isolat SL1 dan SL2 keduanya tidak teramplifikasi oleh primer AG2sp dan AG22sp2. Analisis Maximum Likelihood tree berdasar data sekuen ITS menunjukkan bahwa isolat SL1 dan SL2 memiliki tingkat kesamaan yang tinggi.

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Phenotypic and Genotypic Characterization of Non-Starter Lactic Acid Bacteria in Mature Cheddar Cheese

Applied and Environmental Microbiology ◽

10.1128/aem.65.8.3418-3426.1999 ◽

1999 ◽

Vol 65 (8) ◽

pp. 3418-3426 ◽

Cited By ~ 118

Author(s):

N. A. Fitzsimons ◽

T. M. Cogan ◽

S. Condon ◽

T. Beresford

Keyword(s):

Lactic Acid ◽

Lactic Acid Bacteria ◽

Rapd Analysis ◽

Cheddar Cheese ◽

Group Method ◽

Pair Group ◽

Unidentified Species ◽

Reference Strains ◽

Selection Of

ABSTRACT Non-starter lactic acid bacteria were isolated from 14 premium-quality and 3 sensorially defective mature Irish Cheddar cheeses, obtained from six manufacturers. From countable plates ofLactobacillus-selective agar, 20 single isolated colonies were randomly picked per cheese. All 331 viable isolates were biochemically characterized as mesophilic (i.e., group II)Lactobacillus spp. Phenotypically, the isolates comprised 96.4% L. paracasei, 2.1% L. plantarum, 0.3%L. curvatus, 0.3% L. brevis, and 0.9% unidentified species. Randomly amplified polymorphic DNA (RAPD) analysis was used to rapidly identify the dominant strain groups in nine cheeses from three of the factories, and through clustering by the unweighted pair group method with arithmetic averages, an average of seven strains were found per cheese. In general, strains isolated from cheese produced at the same factory clustered together. The majority of isolates associated with premium-quality cheese grouped together and apart from clusters of strains from defective-quality cheese. No correlation was found between the isomer of lactate produced and RAPD profiles, although isolates which did not ferment ribose clustered together. The phenotypic and genotypic methods employed were validated with a selection of 31 type and reference strains of mesophilicLactobacillus spp. commonly found in Cheddar cheese. RAPD analysis was found to be a useful and rapid method for identifying isolates to the species level. The low homology exhibited between RAPD banding profiles for cheese isolates and collection strains demonstrated the heterogeneity of the L. paracasei complex.

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Characterization of genotypes and genetic relationships of cili (Rosa roxburghii) and its relatives using RAPD markers

Chinese Journal of Agricultural Biotechnology ◽

10.1079/cjb200425 ◽

2004 ◽

Vol 1 (2) ◽

pp. 79-84

Author(s):

Wen Xiao-Peng ◽

Deng Xiu-Xin

Keyword(s):

Rapd Markers ◽

Genetic Relationships ◽

Arithmetic Mean ◽

Group Method ◽

Arbitrary Primers ◽

Pair Group ◽

Rosa Roxburghii ◽

Widespread Interest ◽

Unweighted Pair Group Method

AbstractCili (Rosa roxburghii Tratt), characterized by containing the highest vitamin C content among fruits and showing attractive senescence-retarding and cancer-preventing effects, has gained widespread interest. RAPD markers were applied to identify the seven genotypes of cili and to evaluate the genetic relationships within cili, as well as among its relatives. Sixteen arbitrary primers screened from 154 were adopted to analyse polymorphism in RAPD profiles for the 15 samples. A total of 137 RAPD bands ranging in size from 480 bp to 3.3 kb were obtained, among which 95 were polymorphic, covering 69.3% of the total bands obtained; and an average of 8.6 bands/primer was scored. The genotypes of cili and seedless cili could be identified efficiently by 14 genotype-specific bands, which were obtained from the polymorphic primers OPB-11, OPAF-16 and OPW-02. Additionally, using the unweighted pair group method with arithmetic mean, a dendrogram showing genetic relationships among the 15 samples was constructed based on cluster analysis of genetic distance. The possible origin of seedless cili and multiple-corolla cili is also discussed.

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Genetic variability of Corynespora cassiicola isolates from Amazonas, Brazil

Arquivos do Instituto Biológico ◽

10.1590/1808-1657000992017 ◽

2018 ◽

Vol 85 (0) ◽

Author(s):

Jânia Lília da Silva Bentes ◽

Francy Mary Galúcio Sousa ◽

Maria Teresa Gomes Lopes ◽

Mágno Sávio Ferreira Valente ◽

Fabíola Viana Almeida ◽

...

Keyword(s):

Genetic Variation ◽

Molecular Markers ◽

Genetic Variability ◽

The Other ◽

Group Method ◽

Corynespora Cassiicola ◽

Emerging Pathogen ◽

Pair Group ◽

Genetic Groups ◽

Unweighted Pair Group Method

ABSTRACT: Corynespora cassiicola is a cosmopolitan ascomycete widely known as phytopathogen in several crops, and more recently as an emerging pathogen in humans. In this study the genetic variability of 60 isolates of Corynespora cassiicola from different hosts and cities of Amazonas was evaluated, using AFLP molecular markers. Seven genetic groups were identified according to a dendrogram obtained by the Unweighted Pair Group Method using Arithmetical Averages, indicating significant variability among the isolates. Three isolates of different hosts (28, obtained from papaya; 55, obtained from cucumber; and 58, from tomato) remained as single individuals in distinct groups, suggesting marked genetic variation in comparison to the other isolates and possible specificity by the host.

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PENETAPAN KERAGAMAN GENETIK NILAM (Pogostemon sp.) HASIL FUSI PROTOPLAS DENGAN TEKNIK RAPD

Jurnal Penelitian Tanaman Industri ◽

10.21082/jlittri.v8n2.2002.39-44 ◽

2020 ◽

Vol 8 (2) ◽

pp. 39

Author(s):

YANG NURYANI ◽

OTIH ROSTIANA ◽

CHEPPY SYUKUR

Keyword(s):

Genetic Variability ◽

Somatic Hybrids ◽

Group Method ◽

Plant Materials ◽

Arithmetic Average ◽

Random Primers ◽

Modified Method ◽

Pair Group ◽

Materials Used ◽

Unweighted Pair Group Method

Keragaman genetik dan kckerabatan tanaman nilam hasil fusi protoplas antara Nilam Jawa (Girilaya) dan Nilam Aceh (Sidikalang dan TT 75) dianalisis dengan menggunakan penanda RAPD. Bahan tanaman yang digunakan dalam penelitian ini adalah 9 genotipa yang tcrdiri dari 3 tetua dan 6 tanaman hibrida somatik (9 II 33, 9 II 21, 2 IV 8, 9 IV14, 9 II 7 dan 9 II 10). Primer yang digunakan dalam analisis tcrdiri atas 5 primer acak yaitu OPD 03, OPD 20, OPH 09, OPH 19 dan Abi 117.17. DNA dickstraksi dengan metode OROZCO-CASTJLLO et al. (1994) yang sudah dimodifikasi. Konsentrasi DNA ditetapkan dengan metode sambrook el al. (1989) dengan pcrbandingan kuantifikasi spektrofotometrik. Koefisien kemiripan dan kckerabatan antar genotipa dianalisis dengan menggunakan program NTsys ver. 1.80 dan UPGMA untuk menentukan sidik gerombol dan dendogram. Hasil analisis menunjukkan bahwa koefisien kemiipan dari amplifikasi DNA dengan 5 primer acak dari ke- 9 genotipa berkisar antara 0.48-1.0. Berdasarkan niatrik jarak genetik, kescmbilan genotipa tanaman yang diuji membentuk 2 kelompok besar yaitu kelompok I, tetua Girilaya (Nilam Jawa) dan kelompok II tcrdiri dari tetua Sidikalang dan TT 75 (Nilam Aceh) serta hibrida somatik. Kelompok II, tcrbagi menjadi dua sub kelompok yaitu sub kelompok I (9 II 33 dan 9 II 7) dan sub kelompok II yang tcrdii dari sub-sub kelompok II-I (9 II 21, S, TT 75) dan sub-sub kelompok II-II (2 IV 8, 9 IV 14, 9 II 10).Kata kunci: Pogostemon sp., fusi protoplas, keragaman genetik, RAPD ABSTRACTS Assessment of genetic variability of patchoulli (Pogostemon sp.,) derived from protoplast fussion using RAPD Somatic hybrids of Pogostemon heyneaneus (cv. Girilaya) X P. cablin (cv. Sidikalang and TT 75) were tested for their genetic variability and relationship. The somatic hybrids tested were 9 II 33, 9 II 21, 2 IV 8, 9 IV14, 9 II 7 and 9 II 10. DNA of the plant materials used were extracted by using the modified method of orozcocastulo et al. (1994) and quantified spectrophotometrically according to SAMBROOK el al. (1989). Five random primers, OPD 03. OPD 20, OPH 09. OPH 19 and Abi 117.17, were applied to amplify the extracted DNA. The genetic relationship among the somatic hybrids were estimated by using the index of similarity to perform genctical matrix and dendogram. Index of similarity among genotypes were calculated by using NTsys ver. 1.80 program. Then, cluster analyses to perform dendogram were achieved based on similarity estimates by using the Unweighted Pair-Group Method Arithmetic Average (UPGMA). Results showed that index of similarities of the amplified DNA from 5 random primers ranged from 0.48 to 1.0. The somatic hybrids and their parental plants subjected to RAPD analyses were classified into 2 major groups, first, the parental group of Java patchouli and second, others parental plants, Aceh patchouli (Sidikalang and TT 75), and the somatic hybrids. The second group was then classified into 2 minor groups. First group consisted of somatic hybrids nos. 9 II 33 and 9 II 7, while the second were classified into 2 groups which consisted nos. 9 II 21, S, TT 75 and nos. 2 IV 8, 9 IV 14 and 9 II 10.Key words : Pogostemon sp., protoplast fusion, genetic variability, RAPD

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Molecular Diversity and Genetic Relatedness of Candida albicans Isolates from Birds in Hungary

Mycopathologia ◽

10.1007/s11046-021-00527-3 ◽

2021 ◽

Vol 186 (2) ◽

pp. 237-244

Author(s):

M. Domán ◽

L. Makrai ◽

Gy. Lengyel ◽

R. Kovács ◽

L. Majoros ◽

...

Keyword(s):

Candida Albicans ◽

Molecular Diversity ◽

Genetic Relatedness ◽

Group Method ◽

Pair Group ◽

Degree Of Separation ◽

Avian Origin ◽

Species Specific ◽

Sequence Types ◽

Unweighted Pair Group Method

AbstractThe molecular epidemiology of Candida albicans infections in animals has been rarely studied. In this study, multilocus sequence typing was used to characterise the genetic diversity and population structure of 24 avian origin C. albicans isolates collected from different birds with candidiasis and compared to human isolates. Fourteen diploid sequence types (DSTs) including six new DSTs were determined. Cluster analysis revealed that isolates grouped into 8 clades. Bird isolates mainly belonged to minor clades and Clade 15 with DST 172 was the most common (11 isolates; 45.8%). The remaining isolates were clustered into Clade 7 (5 isolates; 20.8%), Clade 10 (4 isolates; 16.6%), Clade 8 (2 isolates; 8.3%), Clade 4 (1 isolate; 4.2%) and Clade 16 (1 isolate; 4.2%). Unweighted pair group method with arithmetic averages (UPGMA) and eBURST analyses showed that the genetic construction of avian origin C. albicans population is fairly diverse. Although species-specific lineages were not found, some degree of separation in the evolution of bird and human strains could be observed.

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