Comparative analysis of diversity based on morpho-metric and molecular markers in chickpea over different environments

2018 ◽  
Author(s):  
Indu Rialch ◽  
Rama Kalia ◽  
H. K. Chaudhary ◽  
B. Kumar ◽  
J. C. Bhandari ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Molecular Markers ◽  
Rapd Markers ◽  
Agronomic Traits ◽  
Rapd Analysis ◽  
Polymorphic Information Content ◽  
Random Amplified Polymorphic Dna ◽  
Similarity Coefficient ◽  
Breeding Programme ◽  
Metric Traits

Ten morpho-agronomic traits and 80 random amplified polymorphic DNA (RAPD) molecular markers were used to survey genetic diversity in 25 chickpea genotypes. Analysis of variance revealed significant variability among different genotypes for morpho-metric traits. The cluster analysis done using morpho-metric traits grouped 25 genotypes into seven and six clusters in Environment I (Env. I) and Environment II (Env. II), respectively. Three genotypes viz., ICCV-96904, HPG-17, ICCV-95503 and L-HR-1 belonging to diverse clusters were identified divergent and may use in heterosis breeding programme. Of 80 random RAPD markers, 25 were found polymorphic. Three major clusters were identified using 25 polymorphic RAPD markers. The genetic similarity coefficient among genotypes ranged from 0.57 to 0.91. The average polymorphic information content (PIC) for 25 RAPD markers ranges from 0.12 to 0.40. D2-statistic, RAPD analysis and study of genotypes performance revealed sufficient genetic diversity among chickpea genotypes which would be useful in future breeding programme.

scholarly journals Assessment of genetic diversity using DNA markers among Brassica rapa var. yellow sarson germplasm lines collected from Eastern Uttar Pradesh and Uttarakhand hills

2016 ◽  
Vol 8 (3) ◽  
pp. 1333-1340
Author(s):  
Harsha Harsha ◽  
Jitendra Kumar Meena ◽  
Ram Bhajan ◽  
Usha Pant ◽  
Mohammed Talha
Keyword(s):  
Genetic Diversity ◽  
Rapd Markers ◽  
Polymorphic Information Content ◽  
Random Amplified Polymorphic Dna ◽  
Similarity Coefficient ◽  
Principal Coordinate Analysis ◽  
Molecular Profile ◽  
Polymorphic Band ◽  
Germplasm Management ◽  
High Genetic Diversity

The genetic diversity and the relatedness among thirty-one germplasm lines of yellow sarson collected from eastern UP were evaluated using morphological characters and Random Amplified Polymorphic DNA (RAPD) markers. Molecular parameters, viz. A total number of bands, average polymorphic band, average percent polymorphism, average polymorphic information content (PIC), Jaccard’s similarity coefficient, Principal Coordinate Analysis (PCA) and dendrogram generated using RAPD markers. A total of 148 different polymorphic amplification products were obtained using 10 selected decamer primers. The Jaccard similarity coefficient ranged from 0.557-0.899. Maximum polymorphism detected was 100 %.The range of amplification was from 190bp to 9 kb. Some unique bands were also reported with different primers that can be used for the identification of particular accession. PYSC-11-11 and PYSC-11-36 genotypes showed a maximum number of unique loci of different size. 31 germplasm lines grouped into two major clusters I and II based on RAPD profiling. Morphological characterization was done on the basis of leaf, petal and beak characteristics. The similarity value among the germplasm lines ranged from 0.222 to 1.000 using morphological descriptors. The dendrogram generated grouped the germplasm accession into two major groups at 44% similarity value. The cluster analysis was comparable up to some extent with Principal Coordinate Analysis (PCA) of two and three-dimensional plots. The variability revealed by morphological and molecular profile were found to be non-comparable. This study indicated the presence of high genetic diversity among collected yellow sarson germplasm, which could be used for developing for breeding and germplasm management purposes.

Detection of genetic diversity in tea (Camellia sinensis) using RAPD markers

Genome ◽  
1995 ◽  
Vol 38 (2) ◽  
pp. 201-210 ◽  
Author(s):  
F. N. Wachira ◽  
R. Waugh ◽  
W. Powell ◽  
C. A. Hackett
Keyword(s):  
Genetic Diversity ◽  
Genetic Variability ◽  
Southeast Asia ◽  
Camellia Sinensis ◽  
Rapd Markers ◽  
Rapd Analysis ◽  
Random Amplified Polymorphic Dna ◽  
Systematic Assessment ◽  
Tree Crop ◽  
Taxonomic Relationships

Camellia sinensis is a beverage tree crop native to Southeast Asia and introductions have been made into several nonindigenous countries. No systematic assessment of genetic variability in tea has been done anywhere. In this study, random amplified polymorphic DNA (RAPD) analysis was used to estimate genetic diversity and taxonomic relationships in 38 clones belonging to the three tea varieties, assamica, sinensis, and assamica ssp. lasiocalyx. Extensive genetic variability was detected between species, which was partitioned into between and within population components. Seventy percent of the variation was detected within populations. Analyses based on band sharing separated the three populations in a manner consistent with both the present taxonomy of tea and with the known pedigrees of some clones. RAPD analysis also discriminated all of the 38 commercial clones, even those which cannot be distinguished on the basis of morphological and phenotypic traits.Key words: genetic diversity, RAPDs, Camellia sinensis.

scholarly journals Morphological, Chemical, and Genetic Characteristics of Korean Native Thyme Bak-Ri-Hyang (Thymus quinquecostatus Celak.)

Antibiotics ◽  
2020 ◽  
Vol 9 (6) ◽  
pp. 289
Author(s):  
Minju Kim ◽  
Jun-Cheol Moon ◽  
Songmun Kim ◽  
Kandhasamy Sowndhararajan
Keyword(s):  
Essential Oil ◽  
Rapd Markers ◽  
Rapd Analysis ◽  
Random Amplified Polymorphic Dna ◽  
Essential Oil Composition ◽  
Similarity Coefficient ◽  
Gas Chromatography Mass Spectrometry ◽  
Aromatic Plant ◽  
Oil Composition ◽  
Genetic Characteristics

Bak-ri-hyang (Thymus quinquecostatus Celak.) is an important medicinal and aromatic plant in Korea. T. quinquecostatus population and is always mixed with other thyme cultivars during cultivation and marketing. Hence, this study aimed to determine the genetic variability and the essential oil composition of three Korean native thyme, T. quinquecostatus cultivars collected from the Wolchul, Jiri, and Odae mountains, in comparison with six commercial thyme cultivars (T. vulgaris), to distinguish Bak-ri-hyang from other thyme cultivars. The composition of essential oils obtained from nine individuals was analyzed by gas chromatography–mass spectrometry (GC–MS). The random amplified polymorphic DNA (RAPD) analysis was accomplished using 16 different primers. The GC–MS analysis revealed that Wolchul, creeping, golden, and orange cultivars belong to the geraniol chemotype. Whereas the Odae, lemon, and silver cultivars belong to the thymol chemotype. Further, linalool was the most abundant component in carpet and Jiri cultivars. The RAPD analysis demonstrated that all thyme cultivars showed characteristic RAPD patterns that allowed their identification. In total, 133 bands were obtained using 16 primers, and 124 bands were polymorphic, corresponding to 93.2% polymorphism. Cluster analysis of RAPD markers established the presence of clear separation from nine thyme cultivars. The highest dissimilarity and similarity coefficient of the RAPD markers were 0.58 and 0.98, respectively. According to the RAPD patterns, the nine thyme cultivars could be divided into two major clusters. Among three Korean cultivars, the Wolchul and Odae cultivars were placed into the same cluster, but they did not show identical clustering with their essential oil compositions. The findings of the present study suggest that RAPD analysis can be a useful tool for marker-assisted identification of T. quinquecostatus from other Thymus species.

scholarly journals Assessment of Genetic Diversity in Cultivated Tomato (Solanum Lycopersicum L.) Genotypes Using Rapd Primers

2013 ◽  
Vol 21 (1) ◽  
pp. 83-89 ◽  
Author(s):  
Saida Sharifova ◽  
Sabina Mehdiyeva ◽  
Konstantinos Theodorikas ◽  
Konstantinos Roubos
Keyword(s):  
Genetic Diversity ◽  
Rapd Analysis ◽  
Diversity Index ◽  
Random Amplified Polymorphic Dna ◽  
Arithmetic Mean ◽  
Similarity Coefficient ◽  
Group Method ◽  
Solanum Lycopersicum L ◽  
Pair Group ◽  
Upgma Cluster Analysis

Abstract Random Amplified Polymorphic DNA (RAPD) analysis was carried out on 19 Azerbaijan tomato genotypes, both cultivars and local populations. A total of 26 amplified products were revealed by 6 primers. The genetic similarity among evaluated genotypes ranged from 0.188 to 1.000. The lowest similarity was observed between cultivars ‘Azerbaijan’ and ‘Shakar’ (0.188), while the highest between ‘Elnur’ and ‘Garatag’ (1.000). The Unweighted Pair Group Method with Arithmetic Mean (UPGMA) cluster analysis based on Jaccard’s similarity coefficient divided genotypes into four main groups. The first group was the largest and consisted of 12 genotypes, while the fourth group was the smallest consisted of 1 genotype only. The most polymorphic primer was OPB-18 that presented a genetic diversity index of 0.823, while the least informative was primer OPG-17 with an index of 0.349. The average genetic diversity calculated from RAPD data was 0.665.

scholarly journals Characterization of genetic diversity of cactus species (Opuntia spp.) in Morocco by morphological traits and molecular markers

2017 ◽  
Vol 5 (2) ◽  
pp. 149-159 ◽  
Author(s):  
Y. El Kharrassi ◽  
M.A. Mazri ◽  
M.H. Sedra ◽  
A. Mabrouk ◽  
B . Nasser ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Molecular Markers ◽  
Morphological Traits ◽  
Polymorphic Information Content ◽  
Random Amplified Polymorphic Dna ◽  
Rapd Marker ◽  
Group Method ◽  
Rapd Primer ◽  
Opuntia Spp ◽  
Issr Primers

The genetic diversity within and among 124 accessions of Opuntia spp. collected from different regions of Morocco was assessed using morphological descriptors and molecular markers. Based on 10 morphological traits, the accessions were separated into 3 main clusters; each cluster was containing accessions from different regions and species. Polymerase chain reaction (PCR) was then performed on 22 accessions from different regions and species, with 10 inter-simple sequence repeat (ISSR) primers and one random amplified polymorphic DNA (RAPD) primer. ISSR primers produced 66 bands overall, 64 (96.9 %) of which were polymorphic while 6 bands were generated by the RAPD marker, all polymorphic. The polymorphic information content (PIC) values ranged from 0.62 to 0.97, with an average of 0.82. The dendrogram of genetic differences generated using the unweighted pair-group method using arithmetic averages (UPGMA) method showed 7 different clusters at a similarity of 0.76, which was confirmed by the principal component analysis (PCA). The main conclusion of our work is the high genetic similarity between Opuntia ficus indica and Opuntia megacantha species in Morocco. Our results will be useful for plant breeding and genetic resource conservation programs.

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 Assessment of RAPD Markers to Analyse the Genetic Diversity among Sunflower (Helianthus annuus L.) Genotypes

2018 ◽  
Vol 6 (1) ◽  
pp. 107 ◽  
Author(s):  
Ali Raza ◽  
Haseeb Shaukat ◽  
Qasim Ali ◽  
Madiha Habib
Keyword(s):  
Genetic Diversity ◽  
Genetic Similarity ◽  
Rapd Markers ◽  
Polymorphic Information Content ◽  
Random Amplified Polymorphic Dna ◽  
Future Studies ◽  
Group 2 ◽  
Maximum Similarity ◽  
Sunflower Genome ◽  
Group 1

Genetic diversity estimation among different species is an important tool for genetic improvement to maximize the yield, desirable quality, wider adaptation, pest and insect resistance that ultimately boosting traditional plant breeding methods. The most efficient way of diversity estimation is application of molecular markers. In this study, twenty random amplified polymorphic DNA (RAPD) primers were utilized to estimate the genetic diversity between ten sunflower genotypes. Overall 227 bands were amplified by 20 primers with an average of 11.35 bands per primer. RAPD data showed 86.34% polymorophic bands and 13.65% of monomorophic bands. Genetic similarity was ranged from 50.22% to 87.22%. The lowest similarity (50.22%) was observed between FH-352 and FH-359 and the maximum similarity 87.22% was observed between A-23 and G-46. Polymorphic information content (PIC) values were varying from 0.05 to 0.12 with a mean of 0.09. Cluster analysis based on RAPD results displayed two major distinct groups 1 and 2. Group-2 contains FH-352 which was the most diverse genotype, while group-1 consists of few sub groups with all other genotypes. Ample diversity was found in all the genotypes. Present study reveals novel information about sunflower genome which can be used in future studies for sunflower improvement.

scholarly journals Genetic Differentiation of Portuguese Tea Plant using RAPD Markers

HortScience ◽  
2003 ◽  
Vol 38 (6) ◽  
pp. 1191-1197 ◽  
Author(s):  
S. Jorge ◽  
M.C. Pedroso ◽  
D.B. Neale ◽  
G. Brown
Keyword(s):  
Genetic Diversity ◽  
Rapd Markers ◽  
Rapd Analysis ◽  
Random Amplified Polymorphic Dna ◽  
Good Method ◽  
Tea Plant ◽  
Jaccard Coefficient ◽  
Plant Populations ◽  
Arbitrary Primers ◽  
Tea Plants

Random amplified polymorphic DNA (RAPD) analysis was used to estimate genetic similarities between Portuguese Camelliasinensis (L.) O. Kuntze (tea plant) accessions and those obtained from the germplasm collections from the Tea Research Foundation of Kenya and from the National Research Institute of Vegetables, Ornamental Plants, and Tea of Japan. The accessions studied are taxonomically classified as C. sinensis, var. sinensis, var. assamica, or ssp. lasiocalyx. A set of 118 ten-base arbitrary primers was tested, of which 25 produced informative, reproducible, and polymorphic banding patterns. These primers were used to amplify DNA from 71 tea plant accessions and produced a total of 282 bands, of which 195 were polymorphic. The phenotypic frequencies were calculated using Shannon's Index and employed in estimating genetic diversity within tea plant populations. Our study demonstrates that tea plant populations, including the Portuguese tea plants, show considerable genetic variability. From the UPGMA cluster analysis based on a matrix using the Jaccard coefficient, it was possible to distinguish the Portuguese tea plants from the remaining accessions. The RAPD markers discriminated the three C. sinensis varieties. Moreover, within each variety cluster, subclusters formed according to geographic distribution. The RAPD analysis also separated the commercially cultivated tea plants from the Taiwanese wild tea plants. The present results show that RAPD analysis constitutes a good method to estimate genetic diversity within C. sinensis, and to differentiate C. sinensis accessions according to taxonomic variety and geographical distribution.

scholarly journals Genetic Diversities within Camellia Species Confirmed by Random Amplified Polymorphic DNA (RAPD) Markers

HortScience ◽  
2005 ◽  
Vol 40 (4) ◽  
pp. 1105A-1105
Author(s):  
Lianghong Chen ◽  
Shizhou Wang ◽  
Mack Nelson
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Molecular Markers ◽  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Camellia Japonica ◽  
Average Percentage ◽  
Study Research ◽  
Camellia Reticulata ◽  
Camellia Species

In this study research was conducted to evaluate the feasibility of characterizing genetic variation within camellia species using random amplified polymorphic DNAs (RAPD) markers. Eight varieties of species Camellia japonica and four varieties of species Camellia reticulata, provided by the America Camellia Society, Fort Valley, Ga., were investigated. RAPD profiles generated by five selected 10-based random primers (out of 20 primers) exhibited distinct patterns of amplified bands for all 12 tested varieties. A total of 344 bands were produced among the eight varieties of species C. japonica, with an average of 8.6 bands, ranging from 220 to 2072 bp in size, scored per primer. Among the 344 amplified bands, 74.4% of the bands presented polymorphic. The four varieties of species C. reticulata produced a total of 180 markers, with an average percentage of 57.8% polymorphisms. The amplified bands were in the range of 236–1760 bp. An average of nine amplified bands was generated per primer. The large percentages of polymorphisms displayed among 12 varieties within the two different species indicate that the expected genetic diversity among varieties within camellia species existed. It was concluded that the RAPD molecular markers are capable of revealing appreciable levels of genetic variation within camellia species.

scholarly journals Genetic Diversity Analysis of Elops machnata (Forskal) Populations in South East and West Coasts of India Using RAPD Markers

2014 ◽  
Vol 6 (4) ◽  
pp. 399-406
Author(s):  
Vellaichamy RAMANADEVI ◽  
Muthusamy THANGARAJ
Keyword(s):  
Genetic Diversity ◽  
Coastal Waters ◽  
Rapd Markers ◽  
South India ◽  
Rapd Analysis ◽  
Random Amplified Polymorphic Dna ◽  
Geographic Distance ◽  
Eastern Africa ◽  
International Union ◽  
South Indian

The Random Amplified Polymorphic DNA (RAPD) technique was used to study the genetic diversity of four Elops machnata populations in South India. Elops machnata is considered as a least concern species (LC), categorized by the International Union for Conservation and Nature (IUCN). The population trends are currently stable in Indian Ocean, Eastern Africa, but are unknown throughout the rest of its expansive range, especially in Indian estuaries. Among the ten RAPD primers tested, eight primers got amplified and gave scorable bands. In total, 119 scorable bands were observed in all populations. The overall observed and effective number of alleles was found to be 2.000 ± 0.000 and 1.5307 ± 0.2503 respectively for the entire population. The overall polymorphic loci were 61.00% and the overall gene flow among the four populations was predicted to 0.1032. The genetic distance and geographic distance between the four populations showed a positive correlation. The highest genetic similarity (0.6824) was found between Parangipettai and Muthupettai population, which reflected the geographical relationship between them. Tow main clusters were obtained based on UPGMA dendrogram. This study proves that RAPD analysis has the ability to discriminate E. machnata populations in South Indian coastal waters.

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